Homo sapiens gene HNF4A, encoding hepatocyte nuclear factor 4, alpha.
TABLE OF CONTENTS / OPEN CLOSE ALL PARAGRAPHS
SUMMARY back to top
RefSeq summary
[HNF4A] The protein encoded by this gene is a nuclear transcription factor which binds DNA as a homodimer. The encoded protein controls the expression of several genes, including hepatocyte nuclear factor 1 alpha, a transcription factor which regulates the expression of several hepatic genes. This gene may play a role in development of the liver, kidney, and intestines. Mutations in this gene have been associated with monogenic autosomal dominant non-insulin-dependent diabetes mellitus type I. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq].

RefSeq annotates 6 representative transcripts (NM included in AceView variants .a, .b, .d, .e, .f and .g), 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 8 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is well expressed, 0.5 times the average gene in this release. The sequence of this gene is defined by 66 GenBank accessions from 64 cDNA clones, some from liver (seen 8 times), kidney (7), colon (6), liver and spleen (6), colon est (3), pooled germ cell tumors (3), 2 pooled tumors (clear cell type) (2) and 14 other tissues. We annotate structural defects or features in 5 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 15 distinct introns (14 gt-ag, 1 other). Transcription produces 9 different mRNAs, 8 alternatively spliced variants and 1 unspliced form. There are 2 probable alternative promotors, 3 non overlapping alternative last exons and 2 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 2 cassette exons, overlapping exons with different boundaries. 89 bp of this gene are antisense to spliced gene jorpa, raising the possibility of regulated alternate expression.
Function: There are 247 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (OMIM: Diabetes mellitus, noninsulin-dependent; maturity-onset diabetes of the young; maturity-onset diabetes of the young, type 1; Other sources: Adenocarcinoma; Diabetes Mellitus, Type 1; Diabetes mellitus, type 2; Diabetic Nephropathies; Genetic Predisposition to Disease; Kidney Neoplasms; MODY, type I; Stomach Neoplasms), proposed to participate in pathway (Maturity onset diabetes of the young) and a process (regulation of transcription, DNA-dependent). Proteins are expected to have molecular functions (metal ion binding, steroid hormone receptor activity, zinc ion binding) and to localize in nucleus. Putative protein interactors have been described (AR, C5ORF56ANDRAD50, COPS5ANDLRRC67, CREBBP, CTNNB1, ELAC1ANDSMAD4, ELP3, ESR1, EXT2, FOXO1, H3F3A, HNF1A, HNF4A, MAPK14, MECR, MED1, MED7ANDHAVCR2, MED10, MED14, MED16, MED17, MED21, MED23, MED24ANDSNORD124, NCOA1, NCOA2, NCOA6, NPPA, NR0B2, NR2C2, NR2F1, NRBF2, NRIP1, PABPC4ANDSNORA55, PNRC1, PNRC2, PPARGC1A, PPARGC1B, PRKAA2, PROX1, SIRT1, SMAD2, SMAD3, SMARCA4, SNCG, SP1, SREBF2, STK16, SUB1, TP53, TRIM24, UBE2I, ZNHIT3).
Protein coding potential: The 8 spliced and the unspliced mRNAs putatively encode good proteins, altogether 9 different isoforms (8 complete, 1 COOH complete), some containing domains Ligand-binding domain of nuclear hormone receptor, Zinc finger, C4 type (two domains) [Pfam].
Isoform HNF4A.cAug10 is annotated using as Met a Kozak-compatible a..TTG. start, thereby gaining 76 amino acids N-terminal to the first AUG. Finally proteins from this gene may be modulated by acetylation; phosphorylation; ubiquitination, 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 20, links to other databases and other names
Map: This gene HNF4A maps on chromosome 20, at 20q13.12 according to Entrez Gene. In AceView, it covers 75.95 kb, from 42984091 to 43060036 (NCBI 37, August 2010), on the direct strand.
Links to: manual annotations from OMIM_125853, OMIM_606391, OMIM_125850, GAD, KEGG_04950, PhosphoSite, the SNP view, gene overviews from Entrez Gene 3172, 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 HNF4A, RP5-1013A22.1, TCF, HNF4, MODY, MODY1, NR2A1, TCF14, HNF4a7, HNF4a8, HNF4a9, NR2A21, FLJ39654 or HNF4alpha, LOC3172. It has been described as hepatocyte nuclear factor 4-alpha, TCF-14, HNF-4-alpha, HNF4alpha10/11/12, transcription factor 14, transcription factor-14, transcription factor HNF-4, hepatic nuclear factor 4 alpha, nuclear receptor subfamily 2 group A member 1.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Hnf4a (e=2 10-47).
The closest C.elegans genes, according to BlastP, are the AceView/WormGenes nhr-64 (e=4 10-25), nhr-14 (e=3 10-24), nhr-69 (e=5 10-24), nhr-41 (e=2 10-23), nhr-88C (e=10-22), unc-55 (e=2 10-22), nhr-49 (e=5 10-22), nhr-62 (e=3 10-21), which may contain interesting functional annotation.
The closest A.thaliana gene, according to BlastP, is the AceView gene AT2G21850 (e=0.43), 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
HNF4A 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 70.2 86.5 0.12 3.10 23.2 61.1 0.04 0.04 0.32 0.48 49.7 70.2 70.2 70.2 0.13 65.5 0.10 106 92.7 0.16 0.14 0.09 0.14 43.2 40.3 0.10 43.2 0.11 0.10 0.68 1.26 0.11 0.13 122 0.45 0.10 0.11 61.1 0.34 106 0.05 37.6 0.10 53.2 0.08 75.3 40.3 0.12 0.59 0.07 0.09 65.5 0.10 65.5 0.14 40.3 0.12 0.09 70.2 0.11 0.14 28.5 0.04 0.08 43.2 0.10 0.07 0.06 57.1 86.5 0.16 0.18 46.3 0.08 0.12 46.3 0.10 46.3 0.13 0.11 92.7 57.1 0.14 0.16 0.18 0.14 4.10 0.36 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!.
Read more...
          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 HNF4A 5' 3' encoded on plus strand of chromosome 20 from 42,984,091 to 43,060,036 2389 4007 4133 4864 3562 3325 4718 3621 3318 a [NM] 2389 4007 4133 4864 3562 3325 4718 3621 514 b [NM] 1 22 4007 4133 4864 3562 3325 4718 3621 3318 c i-u 2389 4007 4133 4864 3562 3325 4718 d [NM] 341 4007 4133 4864 3562 3325 4718 3621 3318 e [NM] 341 4007 4133 4864 3562 3325 4718 3621 514 f [NM] 341 4007 4133 4864 3562 3325 4718 g [NM] 1 29 4007 h 1 2kb 0 204 bp exon 204 bp exon 4570 bp [gt-ag] intron 13 GenBank accessions 2376 RNA-seq supporting reads 1856 UHR pooled cells 6 Blood 514 Neuroblastoma (also 4574 Primates bodymap) 175 bp exon 1148 bp [gt-ag] intron 21 GenBank accessions 3986 RNA-seq supporting reads 3121 UHR pooled cells 4 Brain 4 Blood 857 Neuroblastoma (also 8658 Primates bodymap) 95 bp exon 6218 bp [gt-ag] intron 20 GenBank accessions 4113 RNA-seq supporting reads 3334 UHR pooled cells 3 Brain 7 Blood 769 Neuroblastoma (also 5800 Primates bodymap) 107 bp exon 706 bp [gt-ag] intron 19 GenBank accessions 4845 RNA-seq supporting reads 3876 UHR pooled cells 7 Brain 10 Blood 952 Neuroblastoma (also 6397 Primates bodymap) 156 bp exon 3762 bp [gt-ag] intron 25 GenBank accessions 3537 RNA-seq supporting reads 2783 UHR pooled cells 9 Brain 7 Blood 738 Neuroblastoma (also 5871 Primates bodymap) 88 bp exon 1208 bp [gt-ag] intron 25 GenBank accessions 3300 RNA-seq supporting reads 2674 UHR pooled cells 1 Brain 8 Blood 617 Neuroblastoma (also 4672 Primates bodymap) 156 bp exon 4141 bp [gt-ag] intron 28 GenBank accessions 4690 RNA-seq supporting reads 3860 UHR pooled cells 15 Brain 7 Blood 808 Neuroblastoma (also 6319 Primates bodymap) 237 bp exon 4080 bp [gt-ag] intron 13 GenBank accessions 3608 RNA-seq supporting reads 2818 UHR pooled cells 70 Brain 8 Blood 712 Neuroblastoma (also 6033 Primates bodymap) 153 bp exon 1035 bp [gt-ag] intron 8 GenBank accessions 3310 RNA-seq supporting reads 2608 UHR pooled cells 54 Brain 2 Blood 646 Neuroblastoma (also 5145 Primates bodymap) 1868 bp exon 5 accessions, NM_000457.3 some from liver (seen 2 times) colon (once) Validated 3' end, 1 accession 1868 bp exon 204 bp exon 204 bp exon 4570 bp [gt-ag] intron 13 GenBank accessions 2376 RNA-seq supporting reads 1856 UHR pooled cells 6 Blood 514 Neuroblastoma (also 4574 Primates bodymap) 175 bp exon 1148 bp [gt-ag] intron 21 GenBank accessions 3986 RNA-seq supporting reads 3121 UHR pooled cells 4 Brain 4 Blood 857 Neuroblastoma (also 8658 Primates bodymap) 95 bp exon 6218 bp [gt-ag] intron 20 GenBank accessions 4113 RNA-seq supporting reads 3334 UHR pooled cells 3 Brain 7 Blood 769 Neuroblastoma (also 5800 Primates bodymap) 107 bp exon 706 bp [gt-ag] intron 19 GenBank accessions 4845 RNA-seq supporting reads 3876 UHR pooled cells 7 Brain 10 Blood 952 Neuroblastoma (also 6397 Primates bodymap) 156 bp exon 3762 bp [gt-ag] intron 25 GenBank accessions 3537 RNA-seq supporting reads 2783 UHR pooled cells 9 Brain 7 Blood 738 Neuroblastoma (also 5871 Primates bodymap) 88 bp exon 1208 bp [gt-ag] intron 25 GenBank accessions 3300 RNA-seq supporting reads 2674 UHR pooled cells 1 Brain 8 Blood 617 Neuroblastoma (also 4672 Primates bodymap) 156 bp exon 4141 bp [gt-ag] intron 28 GenBank accessions 4690 RNA-seq supporting reads 3860 UHR pooled cells 15 Brain 7 Blood 808 Neuroblastoma (also 6319 Primates bodymap) 237 bp exon 4080 bp [gt-ag] intron 13 GenBank accessions 3608 RNA-seq supporting reads 2818 UHR pooled cells 70 Brain 8 Blood 712 Neuroblastoma (also 6033 Primates bodymap) 123 bp exon 1065 bp [gt-ag] intron 6 GenBank accessions 508 RNA-seq supporting reads 315 UHR pooled cells 3 Brain 3 Blood 187 Neuroblastoma (also 2839 Primates bodymap) 1868 bp exon 24 accessions, NM_178849.1 some from liver and spleen (seen 5 times) kidney (3), colon (2) colon normal (2), corresponding non cancerous liver tissue (2) Validated 3' end, 2 accessions 1868 bp exon 218 bp exon 1068 bp [gt-at] fuzzy intron 1 GenBank accession 89 bp exon 89 bp exon 3413 bp [gt-ag] intron 1 GenBank accession 21 RNA-seq supporting reads 3 UHR pooled cells 18 Neuroblastoma 175 bp exon 1148 bp [gt-ag] intron 21 GenBank accessions 3986 RNA-seq supporting reads 3121 UHR pooled cells 4 Brain 4 Blood 857 Neuroblastoma (also 8658 Primates bodymap) 95 bp exon 6218 bp [gt-ag] intron 20 GenBank accessions 4113 RNA-seq supporting reads 3334 UHR pooled cells 3 Brain 7 Blood 769 Neuroblastoma (also 5800 Primates bodymap) 107 bp exon 706 bp [gt-ag] intron 19 GenBank accessions 4845 RNA-seq supporting reads 3876 UHR pooled cells 7 Brain 10 Blood 952 Neuroblastoma (also 6397 Primates bodymap) 156 bp exon 3762 bp [gt-ag] intron 25 GenBank accessions 3537 RNA-seq supporting reads 2783 UHR pooled cells 9 Brain 7 Blood 738 Neuroblastoma (also 5871 Primates bodymap) 88 bp exon 1208 bp [gt-ag] intron 25 GenBank accessions 3300 RNA-seq supporting reads 2674 UHR pooled cells 1 Brain 8 Blood 617 Neuroblastoma (also 4672 Primates bodymap) 156 bp exon 4141 bp [gt-ag] intron 28 GenBank accessions 4690 RNA-seq supporting reads 3860 UHR pooled cells 15 Brain 7 Blood 808 Neuroblastoma (also 6319 Primates bodymap) 237 bp exon 4080 bp [gt-ag] intron 13 GenBank accessions 3608 RNA-seq supporting reads 2818 UHR pooled cells 70 Brain 8 Blood 712 Neuroblastoma (also 6033 Primates bodymap) 153 bp exon 1035 bp [gt-ag] intron 8 GenBank accessions 3310 RNA-seq supporting reads 2608 UHR pooled cells 54 Brain 2 Blood 646 Neuroblastoma (also 5145 Primates bodymap) 820 bp exon 1 accession from kidney 820 bp exon 2684 bp exon 2684 bp exon 135 bp uORF 2684 bp exon 2684 bp exon 5 accessions, some from small intestine (seen 2 times) denis drash (once), liver (once) liver and spleen (once) capped 5' end, 1 accession 2684 bp exon 232 bp exon 4570 bp [gt-ag] intron 13 GenBank accessions 2376 RNA-seq supporting reads 1856 UHR pooled cells 6 Blood 514 Neuroblastoma (also 4574 Primates bodymap) 175 bp exon 1148 bp [gt-ag] intron 21 GenBank accessions 3986 RNA-seq supporting reads 3121 UHR pooled cells 4 Brain 4 Blood 857 Neuroblastoma (also 8658 Primates bodymap) 95 bp exon 6218 bp [gt-ag] intron 20 GenBank accessions 4113 RNA-seq supporting reads 3334 UHR pooled cells 3 Brain 7 Blood 769 Neuroblastoma (also 5800 Primates bodymap) 107 bp exon 706 bp [gt-ag] intron 19 GenBank accessions 4845 RNA-seq supporting reads 3876 UHR pooled cells 7 Brain 10 Blood 952 Neuroblastoma (also 6397 Primates bodymap) 156 bp exon 3762 bp [gt-ag] intron 25 GenBank accessions 3537 RNA-seq supporting reads 2783 UHR pooled cells 9 Brain 7 Blood 738 Neuroblastoma (also 5871 Primates bodymap) 88 bp exon 1208 bp [gt-ag] intron 25 GenBank accessions 3300 RNA-seq supporting reads 2674 UHR pooled cells 1 Brain 8 Blood 617 Neuroblastoma (also 4672 Primates bodymap) 156 bp exon 4141 bp [gt-ag] intron 28 GenBank accessions 4690 RNA-seq supporting reads 3860 UHR pooled cells 15 Brain 7 Blood 808 Neuroblastoma (also 6319 Primates bodymap) 622 bp exon 6 accessions, NM_178850.1 some from pooled, cerebellum kidney, placenta,testis lung, colon, liver, heart thyroid, bladder,uterus PCR rescued clones (seen 2 times) kidney (once), liver (once) 622 bp exon 53 bp exon 53 bp exon 50204 bp [gt-ag] intron 6 GenBank accessions 335 RNA-seq supporting reads 296 UHR pooled cells 39 Neuroblastoma (also 201 Primates bodymap) 175 bp exon 1148 bp [gt-ag] intron 21 GenBank accessions 3986 RNA-seq supporting reads 3121 UHR pooled cells 4 Brain 4 Blood 857 Neuroblastoma (also 8658 Primates bodymap) 95 bp exon 6218 bp [gt-ag] intron 20 GenBank accessions 4113 RNA-seq supporting reads 3334 UHR pooled cells 3 Brain 7 Blood 769 Neuroblastoma (also 5800 Primates bodymap) 107 bp exon 706 bp [gt-ag] intron 19 GenBank accessions 4845 RNA-seq supporting reads 3876 UHR pooled cells 7 Brain 10 Blood 952 Neuroblastoma (also 6397 Primates bodymap) 156 bp exon 3762 bp [gt-ag] intron 25 GenBank accessions 3537 RNA-seq supporting reads 2783 UHR pooled cells 9 Brain 7 Blood 738 Neuroblastoma (also 5871 Primates bodymap) 88 bp exon 1208 bp [gt-ag] intron 25 GenBank accessions 3300 RNA-seq supporting reads 2674 UHR pooled cells 1 Brain 8 Blood 617 Neuroblastoma (also 4672 Primates bodymap) 156 bp exon 4141 bp [gt-ag] intron 28 GenBank accessions 4690 RNA-seq supporting reads 3860 UHR pooled cells 15 Brain 7 Blood 808 Neuroblastoma (also 6319 Primates bodymap) 237 bp exon 4080 bp [gt-ag] intron 13 GenBank accessions 3608 RNA-seq supporting reads 2818 UHR pooled cells 70 Brain 8 Blood 712 Neuroblastoma (also 6033 Primates bodymap) 153 bp exon 1035 bp [gt-ag] intron 8 GenBank accessions 3310 RNA-seq supporting reads 2608 UHR pooled cells 54 Brain 2 Blood 646 Neuroblastoma (also 5145 Primates bodymap) 149 bp exon 2 accessions, NM_175914.3 149 bp exon 53 bp exon 53 bp exon 50204 bp [gt-ag] intron 6 GenBank accessions 335 RNA-seq supporting reads 296 UHR pooled cells 39 Neuroblastoma (also 201 Primates bodymap) 175 bp exon 1148 bp [gt-ag] intron 21 GenBank accessions 3986 RNA-seq supporting reads 3121 UHR pooled cells 4 Brain 4 Blood 857 Neuroblastoma (also 8658 Primates bodymap) 95 bp exon 6218 bp [gt-ag] intron 20 GenBank accessions 4113 RNA-seq supporting reads 3334 UHR pooled cells 3 Brain 7 Blood 769 Neuroblastoma (also 5800 Primates bodymap) 107 bp exon 706 bp [gt-ag] intron 19 GenBank accessions 4845 RNA-seq supporting reads 3876 UHR pooled cells 7 Brain 10 Blood 952 Neuroblastoma (also 6397 Primates bodymap) 156 bp exon 3762 bp [gt-ag] intron 25 GenBank accessions 3537 RNA-seq supporting reads 2783 UHR pooled cells 9 Brain 7 Blood 738 Neuroblastoma (also 5871 Primates bodymap) 88 bp exon 1208 bp [gt-ag] intron 25 GenBank accessions 3300 RNA-seq supporting reads 2674 UHR pooled cells 1 Brain 8 Blood 617 Neuroblastoma (also 4672 Primates bodymap) 156 bp exon 4141 bp [gt-ag] intron 28 GenBank accessions 4690 RNA-seq supporting reads 3860 UHR pooled cells 15 Brain 7 Blood 808 Neuroblastoma (also 6319 Primates bodymap) 237 bp exon 4080 bp [gt-ag] intron 13 GenBank accessions 3608 RNA-seq supporting reads 2818 UHR pooled cells 70 Brain 8 Blood 712 Neuroblastoma (also 6033 Primates bodymap) 123 bp exon 1065 bp [gt-ag] intron 6 GenBank accessions 508 RNA-seq supporting reads 315 UHR pooled cells 3 Brain 3 Blood 187 Neuroblastoma (also 2839 Primates bodymap) 149 bp exon 12 accessions, NM_001030003.1 some from colon (seen 3 times) colon est (3), pooled germ cell tumors (3) adenocarcinoma cell line (once) colon ins (once) 149 bp exon 53 bp exon 53 bp exon 50204 bp [gt-ag] intron 6 GenBank accessions 335 RNA-seq supporting reads 296 UHR pooled cells 39 Neuroblastoma (also 201 Primates bodymap) 175 bp exon 1148 bp [gt-ag] intron 21 GenBank accessions 3986 RNA-seq supporting reads 3121 UHR pooled cells 4 Brain 4 Blood 857 Neuroblastoma (also 8658 Primates bodymap) 95 bp exon 6218 bp [gt-ag] intron 20 GenBank accessions 4113 RNA-seq supporting reads 3334 UHR pooled cells 3 Brain 7 Blood 769 Neuroblastoma (also 5800 Primates bodymap) 107 bp exon 706 bp [gt-ag] intron 19 GenBank accessions 4845 RNA-seq supporting reads 3876 UHR pooled cells 7 Brain 10 Blood 952 Neuroblastoma (also 6397 Primates bodymap) 156 bp exon 3762 bp [gt-ag] intron 25 GenBank accessions 3537 RNA-seq supporting reads 2783 UHR pooled cells 9 Brain 7 Blood 738 Neuroblastoma (also 5871 Primates bodymap) 88 bp exon 1208 bp [gt-ag] intron 25 GenBank accessions 3300 RNA-seq supporting reads 2674 UHR pooled cells 1 Brain 8 Blood 617 Neuroblastoma (also 4672 Primates bodymap) 156 bp exon 4141 bp [gt-ag] intron 28 GenBank accessions 4690 RNA-seq supporting reads 3860 UHR pooled cells 15 Brain 7 Blood 808 Neuroblastoma (also 6319 Primates bodymap) 2 accessions, NM_001030004.1 362 bp exon 49 bp exon 102 bp uORF 34604 bp [gt-ag] intron 1 GenBank accession 102 bp uORF 222 bp exon 222 bp exon 222 bp exon 15378 bp [gt-ag] intron 1 GenBank accession 28 RNA-seq supporting reads 28 Neuroblastoma 175 bp exon 175 bp exon 1148 bp [gt-ag] intron 21 GenBank accessions 3986 RNA-seq supporting reads 3121 UHR pooled cells 4 Brain 4 Blood 857 Neuroblastoma (also 8658 Primates bodymap) 815 bp exon 815 bp exon 815 bp exon Sequence gap 3457 bp 4 accessions, some from hepatoblastoma (seen once) kidney (once), ovary (once) 369 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.
Read more...
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 3239 bp 474 aa 89 bp 1725 bp 2kb probably including promoter 30107 bp 1kb
bAug10 3209 bp 464 aa 89 bp 1725 bp 2kb probably including promoter 30107 bp 1kb
cAug10 2294 bp 457 aa 243 bp 677 bp 2kb probably including promoter 29073 bp 1kb
dAug10 1631 bp 456 aa 260 bp 2kb 23384 bp 1kb
eAug10 1369 bp 452 aa 4 bp 6 bp 2kb probably including promoter 73871 bp 1kb
fAug10 1339 bp 442 aa 4 bp 6 bp 2kb probably including promoter 73871 bp 1kb
gAug10 1192 bp 395 aa 4 bp 2kb probably including promoter 68579 bp 1kb
hAug10 2658 bp 133 aa 231 bp 2025 bp 99 bp 2kb probably including promoter 56217 bp 1kb
iAug10-unspliced 2684 bp 132 aa 354 bp 1931 bp 132 bp 2kb including Promoter 2684 bp 1kb

Gene neighbors and Navigator on chromosome 20q13.12 back to top
TOX2 C I R P R GDAP1L1 D C R P R3HDML C R HNF4A D C I R P R TTPAL C I R P PKIG C I R P C WISP2 D C I R P KCNK15 C I R P R C I R P JPH2 D C R P C20orf111 C C P FITM2 R R R R P C20orf62 D P RPL37AP1 R C I R P SERINC3 D C I R P ADA G R C R P RIMS4 100kb 0 snoty, 8 accessions TOX2, 124 accessions, 13 variants ruyaru, 111 accessions 15 variants GDAP1L1, 222 accessions 12 variants R3HDML, 3 accessions HNF4A, 64 accessions, 9 variants swerky, 32 accessions TTPAL, 156 accessions 8 variants PKIG, 387 accessions, 17 variants targey, 1 accession WISP2, 137 accessions 7 variants KCNK15, 46 accessions 4 variants jatoy, 1 accession jeytoy, 1 accession jortoy, 1 accession katoy, 1 accession lorkee, 1 accession kytoy, 1 accession pogey, 1 accession kartoy, 1 accession keetoy, 1 accession sukeri, 1 accession koytoy, 1 accession maper, 1 accession latoy, 1 accession lartoy, 1 accession garsabu, 1 accession gawsabu, 2 accessions moper, 1 accession moyper, 1 accession rygey, 1 accession jasabu, 1 accession pytoy, 1 accession poper, 1 accession putoy, 1 accession jusabu, 1 accession potoy, 1 accession jarsabu, 1 accession poytoy, 1 accession perper, 2 accessions taper, 1 accession rawtoy, 1 accession rortoy, 3 accessions teyper, 1 accession sotoy, 1 accession seetoy, 3 accessions pukee, 1 accession tortoy, 2 accessions vytoy, 2 accessions vutoy, 2 accessions seygey, 1 accession vawtoy, 1 accession kosabu, 1 accession tereru, 10 accessions veytoy, 3 accessions watoy, 3 accessions wutoy, 1 accession weetoy, 1 accession keesabu, 2 accessions woytoy, 1 accession zutoy, 1 accession zeetoy, 2 accessions zertoy, 1 accession zortoy, 1 accession zeesobo, 1 accession cheetoy, 1 accession stawty, 2 accessions shytoy, 2 accessions lysabu, 1 accession shartoy, 1 accession sheytoy, 3 accessions zersobo, 1 accession shoytoy, 1 accession storty, 5 accessions bleyper, 1 accession zygey, 1 accession flutoy, 1 accession zugey, 1 accession snarty, 1 accession kotoy, 1 accession keytoy, 1 accession lytoy, 1 accession lutoy, 1 accession gosabu, 2 accessions pargey, 1 accession kakori, 2 accessions, 2 variants mawtoy, 2 accessions mawkee, 1 accession meetoy, 2 accessions gersabu, 2 accessions norper, 3 accessions geysabu, 1 accession moytoy, 2 accessions nytoy, 1 accession gorsabu, 1 accession neetoy, 2 accessions morvey, 3 accessions neytoy, 1 accession goysabu, 2 accessions zeybaw, 1 accession jysabu, 1 accession navey, 1 accession muwaru, 2 accessions, 2 variants patoy, 1 accession rararu, 2 accessions sterky, 2 accessions pawtoy, 5 accessions portoy, 1 accession jeesabu, 1 accession rytoy, 2 accessions peeper, 1 accession rogey, 1 accession jersabu, 1 accession rotoy, 1 accession senaru, 87 accessions niraru, 7 accessions tiruru, 7 accessions jeysabu, 1 accession rartoy, 1 accession reygey, 3 accessions, 2 variants reytoy, 1 accession reyaru, 34 accessions sytoy, 1 accession joysabu, 1 accession kasabu, 2 accessions nykee, 2 accessions kleevaw, 1 accession weeper, 1 accession soytoy, 2 accessions kusabu, 5 accessions sagey, 1 accession zuper, 1 accession zorper, 1 accession wytoy, 1 accession karsabu, 1 accession wotoy, 2 accessions wawtoy, 3 accessions chyper, 1 accession wertoy, 1 accession zawsobo, 2 accessions keysabu, 1 accession choper, 1 accession charper, 1 accession cheeper, 1 accession chotoy, 1 accession torgey, 1 accession toygey, 1 accession chawtoy, 2 accessions mesura, 1 accession chertoy, 1 accession chortoy, 1 accession cheyper, 1 accession shatoy, 3 accessions shawtoy, 1 accession sheetoy, 1 accession losabu, 1 accession blatoy, 1 accession vorgey, 1 accession wagey, 1 accession zagey, 17 accessions larsabu, 1 accession blartoy, 1 accession chorper, 1 accession lersabu, 2 accessions sureru, 1 accession bleytoy, 1 accession karoru, 2 accessions, 2 variants blortoy, 1 accession leysabu, 1 accession meyvey, 6 accessions JPH2, 84 accessions, 4 variants C20orf111, 525 accessions 12 variants josabu, 2 accessions FITM2, 20 accessions, 2 variants sputy, 13 accessions, 4 variants jorpa, 13 accessions, 5 variants staty, 5 accessions, 2 variants C20orf62, 5 accessions 2 variants RPL37AP1, 16 accessions perkee, 18 accessions SERINC3, 429 accessions 14 variants ADA, 221 accessions, 13 variants LOC79015, 56 accessions 15 variants RIMS4, 160 accessions 2 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               247 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h, .i-u Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DCI

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 !