Homo sapiens gene LOC100132062, encoding hypothetical LOC100132062.
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SUMMARY back to top
There is no NCBI RefSeq NM or XM model for this gene, but Homo sapiens cDNA sequences in GenBank, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 5 alternative spliced variants.
AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is well expressed, 1.4 times the average gene in this release. The sequence of this gene is defined by 156 GenBank accessions from 138 cDNA clones, some from testis (seen 26 times), thymus (14), cerebellum (10), uterus (8), placenta (5), amygdala (3), brain (3) and 29 other tissues. We annotate structural defects or features in 16 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 13 distinct introns (10 gt-ag, 3 gc-ag). Transcription produces 6 different mRNAs, 5 alternatively spliced variants and 1 unspliced form. There are 4 probable alternative promotors (see the diagram). The mRNAs appear to differ by truncation of the 5' end, presence or absence of 6 cassette exons, overlapping exons with different boundaries, splicing versus retention of 2 introns.
Efficacy of translation may be reduced by the presence of a shorter translated product (uORF) initiating at an AUG upstream of the main open reading frame (in variant dAug10) Proteins are expected to localize in membrane. No phenotype has yet been reported to our knowledge: this gene's in vivo function is yet unknown.
Protein coding potential: 3 spliced and the unspliced mRNAs putatively encode good proteins, altogether 3 different isoforms (2 complete, 1 COOH complete), apparently mammals specific. The remaining 2 mRNA variants (2 spliced; 2 partial) appear not to encode good proteins.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 5, links to other databases and other names
Map: This gene LOC100132062 maps on chromosome 5, at 5q35.3 according to Entrez Gene. In AceView, it covers 11.84 kb, from 180743354 to 180755196 (NCBI 37, August 2010), on the direct strand.
Links to: the SNP view, SNP view, gene overviews from Entrez Gene 388312, 100132062, GeneCards, expression data from ECgene, UniGene Hs.499578, Hs.591525, molecular and other annotations from UCSC. The previous AceView annotation is here.
Other names: The gene is also known as LOC100132062, FLJ60455, FLJ61476, LOC388312, plapeybo, swupeybo, GTF2I.7 or sharmo, risiri.
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
LOC100132062 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 0.32 0.18 0.68 2.52 2.35 2.05 2.90 3.10 7.64 5.40 1.26 5.40 11.6 5.79 0.17 0.09 0.10 0.10 0.10 0.10 0.07 0.10 0.14 0.10 0.09 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 LOC100132062 5' 3' encoded on plus strand of chromosome 5 from 180,743,354 to 180,755,197 2162 1 a 4011 6616 5770 2162 68 f 3 358 b 89 50 358 e c-u 2162 750 d 1 2kb 0 29 bp exon 29 bp exon 93 bp [gt-ag] intron 4 GenBank accessions 2158 RNA-seq supporting reads 369 UHR pooled cells 129 Brain 1658 Neuroblastoma 2 Other 89 bp exon 3407 bp [gc-ag] intron 1 GenBank accession 1611 bp exon 1 accession from placenta 1611 bp exon 134 bp exon 221 bp [gt-ag] intron 1 GenBank accession 4010 RNA-seq supporting reads 138 UHR pooled cells 101 Brain 946 Blood 2815 Neuroblastoma 10 Other 57 bp exon 566 bp [gt-ag] intron 1 GenBank accession 6615 RNA-seq supporting reads 540 UHR pooled cells 270 Brain 1040 Blood 4756 Neuroblastoma 9 Other (also 2 Primates bodymap) 65 bp exon 3099 bp [gt-ag] intron 1 GenBank accession 5769 RNA-seq supporting reads 519 UHR pooled cells 168 Brain 29 Blood 5047 Neuroblastoma 6 Other 58 bp exon 58 bp exon 93 bp [gt-ag] intron 4 GenBank accessions 2158 RNA-seq supporting reads 369 UHR pooled cells 129 Brain 1658 Neuroblastoma 2 Other 233 bp exon 844 bp [gt-ag] intron 1 GenBank accession 67 RNA-seq supporting reads 2 UHR pooled cells 22 Blood 43 Neuroblastoma 24 bp exon 1 accession from testis capped 5' end, 1 accession 24 bp exon 169 bp exon 227 bp [gt-ag] intron 1 GenBank accession 2 RNA-seq supporting reads 1 Brain 1 Neuroblastoma 58 bp exon 58 bp exon 93 bp [gt-ag] intron 3 GenBank accessions 355 RNA-seq supporting reads 33 UHR pooled cells 17 Brain 22 Blood 281 Neuroblastoma 2 Other 4143 bp exon 91 accessions, some from testis (seen 18 times) thymus (14), uterus (8) cerebellum (7), placenta (4) 4143 bp exon 776 bp exon 1099 bp [gt-ag] intron 2 GenBank accessions 87 RNA-seq supporting reads 1 Brain 26 Blood 60 Neuroblastoma 191 bp exon 2059 bp [gt-ag] fuzzy intron 1 GenBank accession 49 RNA-seq supporting reads 4 UHR pooled cells 1 Brain 10 Blood 34 Neuroblastoma 58 bp exon 58 bp exon 93 bp [gt-ag] intron 3 GenBank accessions 355 RNA-seq supporting reads 33 UHR pooled cells 17 Brain 22 Blood 281 Neuroblastoma 2 Other 3 accessions, some from testis (seen 2 times) tongue, tumor tissue (once) capped 5' end, 3 accessions 183 bp exon 531 bp exon 1121 bp possibly an intron 1121 bp exon 1121 bp exon 39 accessions, some from stomach (seen 5 times) pancreas (4), uterus (4) lung (3), purified pancreatic islet (3) capped 5' end, 1 accession Validated 3' end, 4 accessions Validated 3' end, 3 accessions 1121 bp exon 491 bp exon 491 bp exon 75 bp uORF 491 bp exon 227 bp [gt-ag] intron 1 GenBank accession 143 RNA-seq supporting reads 19 UHR pooled cells 7 Brain 3 Blood 114 Neuroblastoma 58 bp exon 58 bp exon 58 bp exon 93 bp [gt-ag] intron 4 GenBank accessions 2158 RNA-seq supporting reads 369 UHR pooled cells 129 Brain 1658 Neuroblastoma 2 Other 26 bp exon 26 bp exon 3407 bp [gc-ag] intron 1 GenBank accession 749 RNA-seq supporting reads 200 UHR pooled cells 76 Brain 473 Neuroblastoma 643 bp exon 643 bp exon 257 bp [gc-ag] intron 1 GenBank accession 32 RNA-seq supporting reads 5 UHR pooled cells 4 Brain 5 Blood 18 Neuroblastoma 532 bp exon 532 bp exon 4 accessions, some from cerebellum (seen 2 times) amygdala (once), testis (once) capped 5' end, 3 accessions 532 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 uORF Upstream sequence Transcription
unit
pre-mRNA		 Downstream sequence
aAug10 1729 bp 389 aa 26 bp 533 bp 2kb possibly including promoter 5229 bp 1kb
bAug10 4370 bp 389 aa 224 bp 2976 bp 2kb possibly including promoter 4690 bp 1kb
cAug10-unspliced 1677 bp 344 aa 841 bp 368 bp 2kb including Promoter 1678 bp 1kb
dAug10 1750 bp 248 aa 546 bp 457 bp 72 bp 2kb including Promoter 5734 bp 1kb
eAug10 1208 bp 62 aa 1022 bp 2kb including Promoter 4459 bp 1kb
fAug10 571 bp 86 aa 311 bp 2kb including Promoter 5394 bp 1kb

Gene neighbors and Navigator on chromosome 5q35.3 back to top
BTNL8andBTNL3 C R P BTNL9 C R P G C OR2V2 C P R C R TRIM41 C I R P R C LOC100132062 R OR4F3 C P R RPL23AP45 C R P ZFP62 G C I R P TRIM7 R D C I R P GNB2L1andSNORD95andSNORD96A C R TRIM52 R 100kb 0 LOC729678, 95 accessions 8 variants BTNL8andBTNL3, 92 accessions 15 variants BTNL9, 143 accessions 15 variants LOC729707, 1 accession tenime, 2 accessions, 2 variants OR2V2, 1 accession karfley, 10 accessions 3 variants lostyby, 61 accessions 5 variants TRIM41, 240 accessions 10 variants jeyfley, 113 accessions 12 variants vawsnubu, 6 accessions LOC100132062, 152 accessions 6 variants OR4F3, 7 accessions verkoybu, 9 accessions 3 variants torsloyby, 1 accession leysterby, 1 accession weywuby, 1 accession keesmaby, 1 accession cherflu, 3 accessions keysmaby, 1 accession koysmaby, 1 accession bloyvubo, 1 accession nerura, 1 accession porsnubu, 1 accession duspubu, 1 accession dorspubu, 1 accession fashoby, 1 accession fyspubu, 1 accession vusloyby, 4 accessions vosloyby, 1 accession varsloyby, 11 accessions fushoby, 1 accession seysnubu, 1 accession steestoybu, 1 accession versloyby, 1 accession gawshoby, 1 accession voysloyby, 5 accessions tonime, 2 accessions wosloyby, 3 accessions vosnubu, 2 accessions worsloyby, 1 accession nosterby, 1 accession chovybo, 1 accession swystoybu, 1 accession zosloyby, 2 accessions zarsloyby, 1 accession sanime, 2 accessions zawsloyby, 1 accession wasnubu, 1 accession lershar, 1 accession geeshoby, 1 accession chorwuby, 1 accession neesterby, 7 accessions nahayu, 1 accession nersterby, 1 accession wawsnubu, 1 accession neysterby, 1 accession zoysloyby, 6 accessions waplaby, 8 accessions noshoby, 1 accession pysterby, 3 accessions leystyby, 1 accession worsnubu, 2 accessions RPL23AP45, 2 accessions posterby, 7 accessions nawshoby, 1 accession zasnubu, 1 accession lersterby, 2 accessions toysloyby, 2 accessions hetare, 183 accessions sersweebu, 12 accessions kersmaby, 3 accessions huhayu, 1 accession nuhoyu, 1 accession korsmaby, 1 accession lasmaby, 1 accession byspubu, 1 accession fospubu, 1 accession vasloyby, 1 accession vysloyby, 1 accession cheyflu, 3 accessions stostoybu, 5 accessions hehayu, 2 accessions stawstoybu, 1 accession hohayu, 1 accession kofley, 2 accessions royayu, 2 accessions, 2 variants vorsloyby, 2 accessions tawsnubu, 1 accession wasloyby, 1 accession vusnubu, 2 accessions varsnubu, 1 accession flyvubo, 2 accessions weysloyby, 5 accessions woysloyby, 1 accession veesnubu, 1 accession zysloyby, 1 accession versnubu, 1 accession shuma, 2 accessions steeky, 5 accessions jawshoby, 3 accessions zeesloyby, 1 accession swarstoybu, 1 accession wosnubu, 1 accession sinime, 4 accessions nihayu, 1 accession wersnubu, 1 accession smeesporbu, 8 accessions larshoby, 2 accessions swerstoybu, 8 accessions pusterby, 2 accessions ZFP62, 153 accessions 9 variants LOC100128762, 1 accession TRIM7, 80 accessions, 9 variants setere, 5 accessions GNB2L1andSNORD95andSNORD96A 970 accessions, 44 variants TRIM52, 128 accessions 6 variants momome, 6 accessions, 2 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c-u, .d, .e, .f Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes

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'.

If you know more about this gene, or found errors, please share your knowledge. Thank you !