Homo sapiens complex locus WDHD1, encoding WD repeat and HMG-box DNA binding protein 1.
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SUMMARY back to top
RefSeq summary
[WDHD1] The protein encoded by this gene contains multiple N-terminal WD40 domains and a C-terminal high mobility group (HMG) box. WD40 domains are found in a variety of eukaryotic proteins and may function as adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly. HMG boxes are found in many eukaryotic proteins involved in chromatin assembly, transcription and replication. Alternative splicing results in two transcript variants encoding different isoforms. [provided by RefSeq].

RefSeq annotates 2 representative transcripts (NM included in AceView variants .a and .b), but Homo sapiens cDNA sequences in GenBank, dbEST, Trace and SRA, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 9 spliced variants.

AceView synopsis, each blue text links to tables and details
Note that this locus is complex: it appears to produce several proteins with no sequence overlap.
Expression: According to AceView, this gene is expressed at high level, 1.7 times the average gene in this release. The sequence of this gene is defined by 191 GenBank accessions from 178 cDNA clones, some from testis (seen 14 times), leiomyosarcoma (10), embryonic stem cells (8), embryonic stem cells, cell lines H1, H7, andh9 (8), uterus (8), brain (7), placenta (7) and 62 other tissues. We annotate structural defects or features in 2 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 31 distinct introns (30 gt-ag, 1 gc-ag). Transcription produces 10 different mRNAs, 9 alternatively spliced variants and 1 unspliced form. There are 3 probable alternative promotors, 2 non overlapping alternative last exons and 9 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, presence or absence of 4 cassette exons, overlapping exons with different boundaries, splicing versus retention of one intron.
Function: There are 9 articles specifically referring to this gene in PubMed. Proteins are expected to have molecular function (DNA binding) and to localize in various compartments (cytoplasm, nucleolus, nucleus, nucleoplasm). No phenotype has yet been reported to our knowledge: this gene's in vivo function is yet unknown.
Protein coding potential: 9 spliced mRNAs putatively encode good proteins, altogether 9 different isoforms (4 complete, 1 COOH complete, 4 partial), some containing WD domain, G-beta repeat [Pfam], a coiled coil stretch [Psort2]. The remaining mRNA variant (unspliced; partial) appears not to encode a good protein. Finally proteins from this gene may be modulated by acetylation; phosphorylation, as detailed at PhosphoSite.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 14, links to other databases and other names
Map: This gene WDHD1 maps on chromosome 14, at 14q22.2 according to Entrez Gene. In AceView, it covers 88.23 kb, from 55493815 to 55405581 (NCBI 37, August 2010), on the reverse strand.
Links to: manual annotations from PhosphoSite, the SNP view, gene overviews from Entrez Gene 11169, GeneCards, expression data from ECgene, UniGene, molecular and other annotations from UCSC, or our GOLD analysis.
The previous AceView annotation is here.
Other names: The gene is also known as WDHD1, CTF4, AND-1 or CHTF4, LOC11169. It has been described as WD repeat and HMG-box DNA-binding protein 1, Acidic nucleoplasmic DNA-binding protein 1, CTF4, chromosome transmission fidelity factor 4 homolog.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Wdhd1 (e= 10-112).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene 5L442 (e=10-48), which may contain interesting functional annotation.
The closest A.thaliana gene, according to BlastP, is the AceView gene AT3G42660 (e=4 10-71), which may contain interesting functional annotation
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
WDHD1 Gene expression in 15 primates, 16 tissues, from the NHPRTR project in sFPKM BAB SkeletalMuscle WholeBlood CHP Kidney Liver Lung Spleen CMC CMM Cerebellum HUM Brain Colon Heart LymphNode Ovary Testis JMI BoneMarrow MLM OWL PTM RMC RMI Pituitary SQM Thymus MST SMY RTL 0.17 2.35 0.68 0.18 0.72 0.15 1.78 1.45 2.05 2.35 4.39 1.91 1.91 1.26 1.91 0.29 1.91 1.26 0.59 2.35 8.19 2.70 13.3 14.3 4.71 4.39 2.70 0.89 8.78 5.04 1.35 3.82 28.5 3.33 4.10 2.35 1.10 1.26 0.59 9.41 2.19 2.52 4.71 0.68 0.39 0.78 3.82 4.71 0.83 1.91 2.35 0.34 1.02 0.72 0.42 0.08 4.71 6.21 12.4 0.96 1.35 0.63 7.64 0.83 0.78 14.3 2.35 2.52 2.05 1.02 0.68 0.83 0.34 6.65 5.79 5.79 7.13 16.4 2.52 1.66 0.68 0.68 16.4 4.71 2.70 6.21 11.6 0.96 1.78 2.90 2.35 6.65 0.68 1.18 0.42 1.66 7.64 0.68 5.40 10.8 0.55 2.52 1.02 1.02 0.68 3.57 1.66 4.71 4.39 11.6 3.57 2.35 1.66 3.82 3.82 1.78 1.10 12.4 4.10 4.71 5.40 7.64 1.78 5.04 1.78 3.33 1.91 0.96 4.71 5.79 10.1 1.35 0.83 3.82 2.90 3.82 28.5 1.35 4.10 3.10 3.57 1.10 1.10 0.72 1.45 0.42 3.82 12.4 9.41 28.5 4.39 2.05 3.33 6.65 7.64 2.19 5.04 Expression quantiles None Weak 1 2 3 4 5 6 7 8 10 20 This gene All genes log2 distributions RNA-seq gene expression profile across 16 selected tissues from the Non-Human Primates Reference Transcriptome Resource (link to NHPRTR project).
- Primates: Apes (HUM: Human (Illumina BodyMap 2), CHP: Chimpanzee), Old World monkeys (PTM: Pig-Tailed Macaque, JMI Japanese Macaque, RMI Rhesus Macaque Indian, RMC Rhesus Macaque Chinese, CMM Cynomolgus Macaque Mauritian, CMC Cynomolgus Macaque Chinese, BAB Olive Baboon, SMY Sooty Mangabey); New World monkeys (MST common Marmoset, SQM Squirrel Monkey, OWL Owl Monkey); and Lemurs (MLM Mouse Lemur, RTL Ring-Tailed Lemur).
- The level for significantly expressed genes is color coded in 8 equal sized bins (light to dark green). Light gray is for weak not-accurately measured expression (2 to 8 reads above intergenic background); dark gray for no expression or no sequence conservation (0 read in gene). The plot to the right shows the distribution of measured expression values in all tissues for all genes (blue) and for this gene (green), in Magic index = log2(1000 sFPKM).
You may also examine the strand-specific genome coverage plots on the experimental AceView/Magic hub at UCSC, by tissue or by species. Tracks may be slow to load; please reload if some tracks come up yellow-greenish, and thanks to UCSC for the great work!.
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          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the HTML5/SVG version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Gene WDHD1 5' 3' encoded on minus strand of chromosome 14 from 55,493,815 to 55,405,581 13070 11233 12478 13922 12592 10333 10359 13950 15019 10430 14558 14827 16598 19626 13362 14993 15040 21389 22672 24099 23091 21280 23515 29456 a [NM] 1032 11233 12478 13922 12592 10333 10359 13950 15019 10430 14558 14827 16598 19626 13362 14993 15040 21389 22672 24099 23091 21280 23515 29456 b [NM] 20 12478 13922 12592 10333 10359 h 158 16598 19626 13362 14993 15040 21389 22672 24099 23091 21280 23515 29456 c j-u 21389 22672 1647 23091 21280 23515 29456 d 13070 11233 12478 13922 12592 f 13362 14993 15040 21389 e 29456 g 25 75 i 5kb 0 70 bp exon 224 bp [gt-ag] intron 50 GenBank accessions 6889 RNA-seq supporting reads 2272 UHR pooled cells 176 Brain 309 Blood 4122 Neuroblastoma 10 Other (also 798 Primates bodymap) 93 bp exon 93 bp exon 13114 bp [gt-ag] intron 58 GenBank accessions 13012 RNA-seq supporting reads 4246 UHR pooled cells 250 Brain 462 Blood 8031 Neuroblastoma 23 Other (also 2770 Primates bodymap) 112 bp exon 3024 bp [gt-ag] intron 68 GenBank accessions 11165 RNA-seq supporting reads 3720 UHR pooled cells 243 Brain 431 Blood 6760 Neuroblastoma 11 Other (also 2262 Primates bodymap) 152 bp exon 1589 bp [gt-ag] intron 68 GenBank accessions 12410 RNA-seq supporting reads 4173 UHR pooled cells 338 Brain 495 Blood 7389 Neuroblastoma 15 Other (also 2258 Primates bodymap) 112 bp exon 241 bp [gt-ag] intron 65 GenBank accessions 13857 RNA-seq supporting reads 4708 UHR pooled cells 347 Brain 475 Blood 8319 Neuroblastoma 8 Other (also 2225 Primates bodymap) 51 bp exon 940 bp [gt-ag] intron 49 GenBank accessions 12543 RNA-seq supporting reads 4207 UHR pooled cells 305 Brain 640 Blood 7381 Neuroblastoma 10 Other (also 1895 Primates bodymap) 96 bp exon 5094 bp [gt-ag] intron 33 GenBank accessions 10300 RNA-seq supporting reads 3736 UHR pooled cells 267 Brain 404 Blood 5884 Neuroblastoma 9 Other (also 1653 Primates bodymap) 93 bp exon 1100 bp [gt-ag] intron 23 GenBank accessions 10336 RNA-seq supporting reads 3516 UHR pooled cells 246 Brain 517 Blood 6040 Neuroblastoma 17 Other (also 1436 Primates bodymap) 107 bp exon 241 bp [gt-ag] intron 12 GenBank accessions 13938 RNA-seq supporting reads 4710 UHR pooled cells 360 Brain 795 Blood 8063 Neuroblastoma 10 Other (also 1744 Primates bodymap) 142 bp exon 4689 bp [gt-ag] intron 13 GenBank accessions 15006 RNA-seq supporting reads 5512 UHR pooled cells 350 Brain 776 Blood 8355 Neuroblastoma 13 Other (also 2609 Primates bodymap) 211 bp exon 4202 bp [gt-ag] intron 14 GenBank accessions 10416 RNA-seq supporting reads 3559 UHR pooled cells 257 Brain 581 Blood 6002 Neuroblastoma 17 Other (also 1701 Primates bodymap) 188 bp exon 2000 bp [gt-ag] intron 16 GenBank accessions 14542 RNA-seq supporting reads 5036 UHR pooled cells 348 Brain 589 Blood 8555 Neuroblastoma 14 Other (also 1700 Primates bodymap) 185 bp exon 1640 bp [gt-ag] intron 15 GenBank accessions 14812 RNA-seq supporting reads 5563 UHR pooled cells 324 Brain 734 Blood 8169 Neuroblastoma 22 Other (also 1944 Primates bodymap) 242 bp exon 2285 bp [gt-ag] intron 15 GenBank accessions 16583 RNA-seq supporting reads 6140 UHR pooled cells 362 Brain 602 Blood 9454 Neuroblastoma 25 Other (also 2135 Primates bodymap) 138 bp exon 3026 bp [gc-ag] intron 16 GenBank accessions 19610 RNA-seq supporting reads 7518 UHR pooled cells 469 Brain 477 Blood 11117 Neuroblastoma 29 Other (also 1818 Primates bodymap) 157 bp exon 14145 bp [gt-ag] intron 17 GenBank accessions 13345 RNA-seq supporting reads 4817 UHR pooled cells 366 Brain 405 Blood 7735 Neuroblastoma 22 Other (also 1612 Primates bodymap) 115 bp exon 673 bp [gt-ag] intron 17 GenBank accessions 14976 RNA-seq supporting reads 5453 UHR pooled cells 436 Brain 634 Blood 8421 Neuroblastoma 32 Other (also 1899 Primates bodymap) 132 bp exon 3302 bp [gt-ag] intron 25 GenBank accessions 15015 RNA-seq supporting reads 5417 UHR pooled cells 400 Brain 412 Blood 8762 Neuroblastoma 24 Other (also 1448 Primates bodymap) 221 bp exon 98 bp [gt-ag] intron 26 GenBank accessions 21363 RNA-seq supporting reads 8156 UHR pooled cells 551 Brain 533 Blood 12100 Neuroblastoma 23 Other (also 1963 Primates bodymap) 116 bp exon 186 bp [gt-ag] intron 26 GenBank accessions 22646 RNA-seq supporting reads 8878 UHR pooled cells 537 Brain 431 Blood 12774 Neuroblastoma 26 Other (also 1703 Primates bodymap) 54 bp exon 4862 bp [gt-ag] intron 22 GenBank accessions 24077 RNA-seq supporting reads 9754 UHR pooled cells 599 Brain 438 Blood 13256 Neuroblastoma 30 Other (also 1921 Primates bodymap) 44 bp exon 387 bp [gt-ag] intron 22 GenBank accessions 23069 RNA-seq supporting reads 8993 UHR pooled cells 559 Brain 618 Blood 12866 Neuroblastoma 33 Other (also 2139 Primates bodymap) 171 bp exon 1339 bp [gt-ag] intron 22 GenBank accessions 21258 RNA-seq supporting reads 7911 UHR pooled cells 558 Brain 538 Blood 12226 Neuroblastoma 25 Other (also 1868 Primates bodymap) 134 bp exon 11090 bp [gt-ag] intron 22 GenBank accessions 23493 RNA-seq supporting reads 8957 UHR pooled cells 625 Brain 513 Blood 13371 Neuroblastoma 27 Other (also 1584 Primates bodymap) 139 bp exon 2641 bp [gt-ag] intron 28 GenBank accessions 29428 RNA-seq supporting reads 10718 UHR pooled cells 788 Brain 325 Blood 17558 Neuroblastoma 39 Other (also 1609 Primates bodymap) 2752 bp exon 54 accessions, NM_007086.3 some from testis (seen 10 times) embryonic stem cells (6) embryonic stem cells cell lines H1, H7, andh9 (4) brain (3), melanotic melanoma (3) capped 5' end, 21 accessions Validated 3' end, 1 accession Validated 3' end, 1 accession Validated 3' end, 1 accession 2752 bp exon 70 bp exon 13431 bp [gt-ag] intron 9 GenBank accessions 1023 RNA-seq supporting reads 384 UHR pooled cells 81 Brain 24 Blood 531 Neuroblastoma 3 Other (also 22 Primates bodymap) 112 bp exon 3024 bp [gt-ag] intron 68 GenBank accessions 11165 RNA-seq supporting reads 3720 UHR pooled cells 243 Brain 431 Blood 6760 Neuroblastoma 11 Other (also 2262 Primates bodymap) 152 bp exon 1589 bp [gt-ag] intron 68 GenBank accessions 12410 RNA-seq supporting reads 4173 UHR pooled cells 338 Brain 495 Blood 7389 Neuroblastoma 15 Other (also 2258 Primates bodymap) 112 bp exon 112 bp exon 241 bp [gt-ag] intron 65 GenBank accessions 13857 RNA-seq supporting reads 4708 UHR pooled cells 347 Brain 475 Blood 8319 Neuroblastoma 8 Other (also 2225 Primates bodymap) 51 bp exon 940 bp [gt-ag] intron 49 GenBank accessions 12543 RNA-seq supporting reads 4207 UHR pooled cells 305 Brain 640 Blood 7381 Neuroblastoma 10 Other (also 1895 Primates bodymap) 96 bp exon 5094 bp [gt-ag] intron 33 GenBank accessions 10300 RNA-seq supporting reads 3736 UHR pooled cells 267 Brain 404 Blood 5884 Neuroblastoma 9 Other (also 1653 Primates bodymap) 93 bp exon 1100 bp [gt-ag] intron 23 GenBank accessions 10336 RNA-seq supporting reads 3516 UHR pooled cells 246 Brain 517 Blood 6040 Neuroblastoma 17 Other (also 1436 Primates bodymap) 107 bp exon 241 bp [gt-ag] intron 12 GenBank accessions 13938 RNA-seq supporting reads 4710 UHR pooled cells 360 Brain 795 Blood 8063 Neuroblastoma 10 Other (also 1744 Primates bodymap) 142 bp exon 4689 bp [gt-ag] intron 13 GenBank accessions 15006 RNA-seq supporting reads 5512 UHR pooled cells 350 Brain 776 Blood 8355 Neuroblastoma 13 Other (also 2609 Primates bodymap) 211 bp exon 4202 bp [gt-ag] intron 14 GenBank accessions 10416 RNA-seq supporting reads 3559 UHR pooled cells 257 Brain 581 Blood 6002 Neuroblastoma 17 Other (also 1701 Primates bodymap) 188 bp exon 2000 bp [gt-ag] intron 16 GenBank accessions 14542 RNA-seq supporting reads 5036 UHR pooled cells 348 Brain 589 Blood 8555 Neuroblastoma 14 Other (also 1700 Primates bodymap) 185 bp exon 1640 bp [gt-ag] intron 15 GenBank accessions 14812 RNA-seq supporting reads 5563 UHR pooled cells 324 Brain 734 Blood 8169 Neuroblastoma 22 Other (also 1944 Primates bodymap) 242 bp exon 2285 bp [gt-ag] intron 15 GenBank accessions 16583 RNA-seq supporting reads 6140 UHR pooled cells 362 Brain 602 Blood 9454 Neuroblastoma 25 Other (also 2135 Primates bodymap) 138 bp exon 3026 bp [gc-ag] intron 16 GenBank accessions 19610 RNA-seq supporting reads 7518 UHR pooled cells 469 Brain 477 Blood 11117 Neuroblastoma 29 Other (also 1818 Primates bodymap) 157 bp exon 14145 bp [gt-ag] intron 17 GenBank accessions 13345 RNA-seq supporting reads 4817 UHR pooled cells 366 Brain 405 Blood 7735 Neuroblastoma 22 Other (also 1612 Primates bodymap) 115 bp exon 673 bp [gt-ag] intron 17 GenBank accessions 14976 RNA-seq supporting reads 5453 UHR pooled cells 436 Brain 634 Blood 8421 Neuroblastoma 32 Other (also 1899 Primates bodymap) 132 bp exon 3302 bp [gt-ag] intron 25 GenBank accessions 15015 RNA-seq supporting reads 5417 UHR pooled cells 400 Brain 412 Blood 8762 Neuroblastoma 24 Other (also 1448 Primates bodymap) 221 bp exon 98 bp [gt-ag] intron 26 GenBank accessions 21363 RNA-seq supporting reads 8156 UHR pooled cells 551 Brain 533 Blood 12100 Neuroblastoma 23 Other (also 1963 Primates bodymap) 116 bp exon 186 bp [gt-ag] intron 26 GenBank accessions 22646 RNA-seq supporting reads 8878 UHR pooled cells 537 Brain 431 Blood 12774 Neuroblastoma 26 Other (also 1703 Primates bodymap) 54 bp exon 4862 bp [gt-ag] intron 22 GenBank accessions 24077 RNA-seq supporting reads 9754 UHR pooled cells 599 Brain 438 Blood 13256 Neuroblastoma 30 Other (also 1921 Primates bodymap) 44 bp exon 387 bp [gt-ag] intron 22 GenBank accessions 23069 RNA-seq supporting reads 8993 UHR pooled cells 559 Brain 618 Blood 12866 Neuroblastoma 33 Other (also 2139 Primates bodymap) 171 bp exon 1339 bp [gt-ag] intron 22 GenBank accessions 21258 RNA-seq supporting reads 7911 UHR pooled cells 558 Brain 538 Blood 12226 Neuroblastoma 25 Other (also 1868 Primates bodymap) 134 bp exon 11090 bp [gt-ag] intron 22 GenBank accessions 23493 RNA-seq supporting reads 8957 UHR pooled cells 625 Brain 513 Blood 13371 Neuroblastoma 27 Other (also 1584 Primates bodymap) 139 bp exon 2641 bp [gt-ag] intron 28 GenBank accessions 29428 RNA-seq supporting reads 10718 UHR pooled cells 788 Brain 325 Blood 17558 Neuroblastoma 39 Other (also 1609 Primates bodymap) 2825 bp exon 115 accessions, NM_001008396.2 some from leiomyosarcoma (seen 5 times) lymph (5), placenta (5) pooled germ cell tumors (5) uterus (5) capped 5' end, 10 accessions Validated 3' end, 8 accessions Validated 3' end, 1 accession Validated 3' end, 7 accessions Validated 3' end, 3 accessions 2825 bp exon 36 bp exon 16567 bp [gt-ag] intron 1 GenBank accession 19 RNA-seq supporting reads 9 UHR pooled cells 9 Neuroblastoma 1 Other (also 1 Primates bodymap) 152 bp exon 1589 bp [gt-ag] intron 68 GenBank accessions 12410 RNA-seq supporting reads 4173 UHR pooled cells 338 Brain 495 Blood 7389 Neuroblastoma 15 Other (also 2258 Primates bodymap) 112 bp exon 112 bp exon 241 bp [gt-ag] intron 65 GenBank accessions 13857 RNA-seq supporting reads 4708 UHR pooled cells 347 Brain 475 Blood 8319 Neuroblastoma 8 Other (also 2225 Primates bodymap) 51 bp exon 940 bp [gt-ag] intron 49 GenBank accessions 12543 RNA-seq supporting reads 4207 UHR pooled cells 305 Brain 640 Blood 7381 Neuroblastoma 10 Other (also 1895 Primates bodymap) 96 bp exon 5094 bp [gt-ag] intron 33 GenBank accessions 10300 RNA-seq supporting reads 3736 UHR pooled cells 267 Brain 404 Blood 5884 Neuroblastoma 9 Other (also 1653 Primates bodymap) 93 bp exon 1100 bp [gt-ag] intron 23 GenBank accessions 10336 RNA-seq supporting reads 3516 UHR pooled cells 246 Brain 517 Blood 6040 Neuroblastoma 17 Other (also 1436 Primates bodymap) 49 bp exon 1 accession from thymus capped 5' end, 1 accession 49 bp exon 169 bp exon 169 bp exon 3825 bp [gt-ag] intron 2 GenBank accessions 156 RNA-seq supporting reads 28 UHR pooled cells 2 Brain 35 Blood 91 Neuroblastoma (also 45 Primates bodymap) 242 bp exon 2285 bp [gt-ag] intron 15 GenBank accessions 16583 RNA-seq supporting reads 6140 UHR pooled cells 362 Brain 602 Blood 9454 Neuroblastoma 25 Other (also 2135 Primates bodymap) 138 bp exon 3026 bp [gc-ag] intron 16 GenBank accessions 19610 RNA-seq supporting reads 7518 UHR pooled cells 469 Brain 477 Blood 11117 Neuroblastoma 29 Other (also 1818 Primates bodymap) 157 bp exon 14145 bp [gt-ag] intron 17 GenBank accessions 13345 RNA-seq supporting reads 4817 UHR pooled cells 366 Brain 405 Blood 7735 Neuroblastoma 22 Other (also 1612 Primates bodymap) 115 bp exon 673 bp [gt-ag] intron 17 GenBank accessions 14976 RNA-seq supporting reads 5453 UHR pooled cells 436 Brain 634 Blood 8421 Neuroblastoma 32 Other (also 1899 Primates bodymap) 132 bp exon 3302 bp [gt-ag] intron 25 GenBank accessions 15015 RNA-seq supporting reads 5417 UHR pooled cells 400 Brain 412 Blood 8762 Neuroblastoma 24 Other (also 1448 Primates bodymap) 221 bp exon 98 bp [gt-ag] intron 26 GenBank accessions 21363 RNA-seq supporting reads 8156 UHR pooled cells 551 Brain 533 Blood 12100 Neuroblastoma 23 Other (also 1963 Primates bodymap) 116 bp exon 186 bp [gt-ag] intron 26 GenBank accessions 22646 RNA-seq supporting reads 8878 UHR pooled cells 537 Brain 431 Blood 12774 Neuroblastoma 26 Other (also 1703 Primates bodymap) 54 bp exon 4862 bp [gt-ag] intron 22 GenBank accessions 24077 RNA-seq supporting reads 9754 UHR pooled cells 599 Brain 438 Blood 13256 Neuroblastoma 30 Other (also 1921 Primates bodymap) 44 bp exon 387 bp [gt-ag] intron 22 GenBank accessions 23069 RNA-seq supporting reads 8993 UHR pooled cells 559 Brain 618 Blood 12866 Neuroblastoma 33 Other (also 2139 Primates bodymap) 171 bp exon 1339 bp [gt-ag] intron 22 GenBank accessions 21258 RNA-seq supporting reads 7911 UHR pooled cells 558 Brain 538 Blood 12226 Neuroblastoma 25 Other (also 1868 Primates bodymap) 134 bp exon 11090 bp [gt-ag] intron 22 GenBank accessions 23493 RNA-seq supporting reads 8957 UHR pooled cells 625 Brain 513 Blood 13371 Neuroblastoma 27 Other (also 1584 Primates bodymap) 139 bp exon 2641 bp [gt-ag] intron 28 GenBank accessions 29428 RNA-seq supporting reads 10718 UHR pooled cells 788 Brain 325 Blood 17558 Neuroblastoma 39 Other (also 1609 Primates bodymap) 515 bp exon 2 accessions capped 5' end, 1 accession Validated 3' end, 1 accession 515 bp exon 381 bp exon 381 bp exon 1 accession from embryonic stem cells cell lines H1, H7, andh9 381 bp exon 214 bp exon 214 bp exon 98 bp [gt-ag] intron 26 GenBank accessions 21363 RNA-seq supporting reads 8156 UHR pooled cells 551 Brain 533 Blood 12100 Neuroblastoma 23 Other (also 1963 Primates bodymap) 116 bp exon 186 bp [gt-ag] intron 26 GenBank accessions 22646 RNA-seq supporting reads 8878 UHR pooled cells 537 Brain 431 Blood 12774 Neuroblastoma 26 Other (also 1703 Primates bodymap) 54 bp exon 4868 bp [gt-ag] intron 3 GenBank accessions 1644 RNA-seq supporting reads 660 UHR pooled cells 37 Brain 30 Blood 916 Neuroblastoma 1 Other (also 140 Primates bodymap) 38 bp exon 387 bp [gt-ag] intron 22 GenBank accessions 23069 RNA-seq supporting reads 8993 UHR pooled cells 559 Brain 618 Blood 12866 Neuroblastoma 33 Other (also 2139 Primates bodymap) 171 bp exon 1339 bp [gt-ag] intron 22 GenBank accessions 21258 RNA-seq supporting reads 7911 UHR pooled cells 558 Brain 538 Blood 12226 Neuroblastoma 25 Other (also 1868 Primates bodymap) 134 bp exon 11090 bp [gt-ag] intron 22 GenBank accessions 23493 RNA-seq supporting reads 8957 UHR pooled cells 625 Brain 513 Blood 13371 Neuroblastoma 27 Other (also 1584 Primates bodymap) 139 bp exon 2641 bp [gt-ag] intron 28 GenBank accessions 29428 RNA-seq supporting reads 10718 UHR pooled cells 788 Brain 325 Blood 17558 Neuroblastoma 39 Other (also 1609 Primates bodymap) 166 bp exon 2 accessions, some from eye (seen once) lymph node (once), retinoblastoma (once) stomach (once) 166 bp exon 340 bp exon 340 bp exon 13114 bp [gt-ag] intron 58 GenBank accessions 13012 RNA-seq supporting reads 4246 UHR pooled cells 250 Brain 462 Blood 8031 Neuroblastoma 23 Other (also 2770 Primates bodymap) 112 bp exon 3024 bp [gt-ag] intron 68 GenBank accessions 11165 RNA-seq supporting reads 3720 UHR pooled cells 243 Brain 431 Blood 6760 Neuroblastoma 11 Other (also 2262 Primates bodymap) 152 bp exon 1589 bp [gt-ag] intron 68 GenBank accessions 12410 RNA-seq supporting reads 4173 UHR pooled cells 338 Brain 495 Blood 7389 Neuroblastoma 15 Other (also 2258 Primates bodymap) 112 bp exon 241 bp [gt-ag] intron 65 GenBank accessions 13857 RNA-seq supporting reads 4708 UHR pooled cells 347 Brain 475 Blood 8319 Neuroblastoma 8 Other (also 2225 Primates bodymap) 51 bp exon 940 bp [gt-ag] intron 49 GenBank accessions 12543 RNA-seq supporting reads 4207 UHR pooled cells 305 Brain 640 Blood 7381 Neuroblastoma 10 Other (also 1895 Primates bodymap) 19 bp exon 3 accessions, some from human embryonic stem cells (seen once) leiomyosarcoma (once) uterus (once) capped 5' end, 1 accession 19 bp exon 157 bp exon 157 bp exon 14145 bp [gt-ag] intron 17 GenBank accessions 13345 RNA-seq supporting reads 4817 UHR pooled cells 366 Brain 405 Blood 7735 Neuroblastoma 22 Other (also 1612 Primates bodymap) 115 bp exon 673 bp [gt-ag] intron 17 GenBank accessions 14976 RNA-seq supporting reads 5453 UHR pooled cells 436 Brain 634 Blood 8421 Neuroblastoma 32 Other (also 1899 Primates bodymap) 132 bp exon 3302 bp [gt-ag] intron 25 GenBank accessions 15015 RNA-seq supporting reads 5417 UHR pooled cells 400 Brain 412 Blood 8762 Neuroblastoma 24 Other (also 1448 Primates bodymap) 221 bp exon 98 bp [gt-ag] intron 26 GenBank accessions 21363 RNA-seq supporting reads 8156 UHR pooled cells 551 Brain 533 Blood 12100 Neuroblastoma 23 Other (also 1963 Primates bodymap) 134 bp exon 1 accession from embryonal carcinoma cell line from testis 134 bp exon 282 bp exon 282 bp exon 2641 bp [gt-ag] intron 28 GenBank accessions 29428 RNA-seq supporting reads 10718 UHR pooled cells 788 Brain 325 Blood 17558 Neuroblastoma 39 Other (also 1609 Primates bodymap) 2752 bp exon 2 accessions, some from leiomyosarcoma (seen 2 times) soft tissue (2) Validated 3' end, 1 accession 2752 bp exon 37 bp exon 37 bp exon 5725 bp [gt-ag] intron 1 GenBank accession 24 RNA-seq supporting reads 2 UHR pooled cells 1 Brain 1 Blood 20 Neuroblastoma 65 bp exon 7324 bp [gt-ag] intron 1 GenBank accession 74 RNA-seq supporting reads 5 UHR pooled cells 3 Brain 1 Blood 65 Neuroblastoma (also 2 Primates bodymap) 77 bp exon 1 accession from embryonic stem cells cell lines H1, H7, andh9 77 bp exon Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript.
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Sequences: click on the numbers to get the DNA back to top
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR Upstream sequence Transcription
unit
pre-mRNA		 Downstream sequence
aAug10 6027 bp 1129 aa 86 bp 2551 bp 2kb including Promoter 88159 bp 1kb
bAug10 6007 bp 1101 aa 362 bp 2624 bp 2kb including Promoter 88232 bp 1kb
cAug10 2347 bp 647 aa 89 bp 314 bp 2kb including Promoter 50206 bp 1kb
dAug10 1032 bp 343 aa 2kb 21641 bp 1kb
eAug10 759 bp 252 aa 2kb 18977 bp 1kb
fAug10 786 bp 174 aa 263 bp 2kb including Promoter 19694 bp 1kb
gAug10 3034 bp 132 aa 84 bp 2551 bp 2kb possibly including promoter 5675 bp 1kb
hAug10 589 bp 124 aa 216 bp 2kb including Promoter 26120 bp 1kb
iAug10 179 bp 36 aa 66 bp 2kb 13228 bp 1kb
jAug10-unspliced 381 bp 43 aa 248 bp 2kb 381 bp 1kb

Gene neighbors and Navigator on chromosome 14q22.2 back to top
CGRRF1 C R P SAMD4A C I R P SOCS4 C R P MAPK1IP1L C I R P LGALS3 D C I R P R UBE2L1andUBE2L7P D C P FBXO34 C I R P C R C R D C I R P GCH1 C R P WDHD1 C D C I R P DLGAP5 P COX5AP1 R C R P ATG14 C I R P TBPL2 100kb 0 CGRRF1, 193 accessions 15 variants SAMD4A, 289 accessions 16 variants SOCS4, 182 accessions 5 variants MAPK1IP1L, 536 accessions 9 variants LGALS3, 454 accessions 13 variants florslor, 3 accessions 3 variants UBE2L1andUBE2L7P, 28 accessions FBXO34, 267 accessions 8 variants varvoy, 10 accessions moyvoy, 1 accession slobyby, 2 accessions fawzer, 1 accession slarbyby, 4 accessions sneycherbu, 3 accessions slawbyby, 1 accession sleebyby, 1 accession glawsoybo, 6 accessions soneeby, 1 accession zeyneeby, 2 accessions smubyby, 1 accession glawneeby, 1 accession smobyby, 1 accession smeebyby, 1 accession smorbyby, 1 accession smoybyby, 3 accessions snabyby, 1 accession snubyby, 6 accessions feyzer, 2 accessions snuswee, 4 accessions snobyby, 1 accession snarbyby, 1 accession spycherbu, 3 accessions snawbyby, 1 accession sneebyby, 3 accessions snerbyby, 1 accession steepu, 19 accessions snorbyby, 2 accessions spybyby, 4 accessions spucherbu, 1 accession forzer, 1 accession pawvoy, 1 accession sparcherbu, 1 accession spawcherbu, 1 accession speecherbu, 1 accession spobyby, 1 accession sterpu, 3 accessions spawbyby, 1 accession speebyby, 1 accession sperbyby, 2 accessions speybyby, 1 accession sporbyby, 1 accession spoybyby, 1 accession skeeskoy, 2 accessions stabyby, 2 accessions starbyby, 1 accession stawbyby, 1 accession steebyby, 3 accessions smeeneeby, 1 accession sterbyby, 1 accession bador, 2 accessions stoybyby, 1 accession mohiri, 18 accessions swabyby, 2 accessions spoycherbu, 2 accessions swubyby, 3 accessions swobyby, 1 accession darnerby, 1 accession swapu, 1 accession swerbyby, 1 accession vawslor, 2 accessions swypu, 7 accessions sworbyby, 1 accession stuchobu, 3 accessions stacherbu, 1 accession deynerby, 2 accessions swarpu, 21 accessions stucherbu, 2 accessions bobuby, 1 accession seyami, 3 accessions, 2 variants bawbuby, 1 accession berbuby, 1 accession jornerby, 1 accession leenerby, 1 accession borbuby, 1 accession budor, 1 accession swycherbu, 1 accession swucherbu, 1 accession swocherbu, 1 accession gleesoybo, 1 accession swercherbu, 1 accession cheyslor, 18 accessions rernerby, 1 accession bawdor, 7 accessions sworcherbu, 7 accessions servoy, 1 accession doybuby, 1 accession fabuby, 1 accession swoycherbu, 1 accession fybuby, 1 accession flyslor, 4 accessions fobuby, 1 accession flerslor, 1 accession ferbuby, 1 accession tyvoy, 1 accession forbuby, 1 accession bawcheybu, 1 accession beecheybu, 1 accession foybuby, 1 accession gabuby, 3 accessions wynerby, 1 accession gybuby, 1 accession wunerby, 3 accessions gobuby, 1 accession garbuby, 1 accession gawbuby, 4 accessions geybuby, 1 accession goybuby, 3 accessions jybuby, 7 accessions teyvoy, 4 accessions kluslor, 2 accessions weenerby, 2 accessions sheynerby, 2 accessions shornerby, 1 accession dacheybu, 4 accessions jawbuby, 2 accessions gerzer, 3 accessions jerbuby, 2 accessions glorsoybo, 1 accession docheybu, 1 accession jorbuby, 1 accession deecheybu, 3 accessions planerby, 1 accession plunerby, 1 accession karbuby, 1 accession facheybu, 2 accessions jyzer, 16 accessions plornerby, 5 accessions kerbuby, 2 accessions koybuby, 2 accessions labuby, 2 accessions lububy, 1 accession lobuby, 1 accession skoynerby, 1 accession larbuby, 1 accession lawbuby, 1 accession farcheybu, 1 accession slabyby, 1 accession farzer, 1 accession slybyby, 1 accession snercherbu, 1 accession swodey, 4 accessions rerneeby, 1 accession stawpu, 1 accession smabyby, 3 accessions cheyneeby, 1 accession smarbyby, 3 accessions smawbyby, 2 accessions spacherbu, 1 accession smeybyby, 2 accessions snybyby, 2 accessions noyvoy, 1 accession sneybyby, 1 accession snoybyby, 1 accession spabyby, 2 accessions spubyby, 1 accession spercherbu, 1 accession sparbyby, 2 accessions foyzer, 5 accessions skoneeby, 3 accessions pervoy, 1 accession sluneeby, 1 accession stubyby, 1 accession sayami, 2 accessions storbyby, 1 accession sporcherbu, 1 accession swarbyby, 6 accessions swawbyby, 1 accession beenerby, 1 accession sweebyby, 1 accession siyami, 2 accessions, 2 variants sweybyby, 3 accessions swoybyby, 1 accession goynerby, 2 accessions suyami, 1 accession stocherbu, 2 accessions barbuby, 1 accession starcherbu, 1 accession jeenerby, 1 accession beebuby, 1 accession guzer, 6 accessions stawcherbu, 1 accession soyami, 2 accessions, 2 variants steecherbu, 1 accession kunerby, 1 accession storcherbu, 2 accessions kuturu, 1 accession nynerby, 1 accession neenerby, 1 accession dabuby, 3 accessions nornerby, 1 accession dybuby, 1 accession dububy, 1 accession punerby, 1 accession ravoy, 1 accession darbuby, 1 accession sweycherbu, 1 accession rornerby, 2 accessions farbuby, 1 accession bucheybu, 3 accessions glersoybo, 1 accession bupo, 1 accession vernerby, 1 accession tawvoy, 1 accession tervoy, 8 accessions gerbuby, 1 accession gorbuby, 1 accession jabuby, 1 accession jobuby, 1 accession sharnerby, 1 accession borcheybu, 3 accessions gleysoybo, 3 accessions jarbuby, 1 accession glarnerby, 1 accession jeebuby, 1 accession joybuby, 2 accessions dawcheybu, 1 accession kybuby, 1 accession deycheybu, 1 accession geyzer, 4 accessions, 2 variants dorcheybu, 1 accession gleynerby, 1 accession gloynerby, 2 accessions kobuby, 1 accession wyvoy, 1 accession bordor, 5 accessions kawbuby, 1 accession keebuby, 1 accession keybuby, 3 accessions lybuby, 1 accession juzer, 1 accession jozer, 1 accession fucheybu, 1 accession smernerby, 1 accession jawzer, 3 accessions GMFB, 424 accessions, 11 variants narumi, 7 accessions, 4 variants varslor, 5 accessions soheru, 7 accessions, 2 variants GCH1, 180 accessions, 11 variants WDHD1, 184 accessions 10 variants sweypu, 1 accession DLGAP5, 328 accessions 9 variants COX5AP1, 5 accessions barpo, 7 accessions, 3 variants ATG14, 129 accessions 5 variants TBPL2, 12 accessions ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               9 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h, .i, .j-u Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes C

To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function, regulation, related genes ' tab at the top of the page. The 'Gene Summary' page includes all we learnt about the gene, functional annotations of neighboring genes, maps, links to other sites and the bibliography. The 'Function, regulation, related genes ' page includes Diseases (D), Pathways, GO annotations, conserved domains (C), interactions (I) reference into function, and pointers to all genes with the same functional annotation.
To compare alternative variants, their summarized annotations, predicted proteins, introns and exons, or to access any sequence, click the 'Alternative mRNAs features' tab. To see a specific mRNA variant diagram, sequence and annotation, click the variant name in the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.

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