Homo sapiens complex locus POU5F1, encoding POU class 5 homeobox 1.
SUMMARY back to top
RefSeq summary
[POU5F1] This gene encodes a transcription factor containing a POU homeodomain. This transcription factor plays a role in embryonic development, especially during early embryogenesis, and it is necessary for embryonic stem cell pluripotency. A translocation of this gene with the Ewing's sarcoma gene, t(6;22)(p21;q12), has been linked to tumor formation. Alternative splicing, as well as usage of alternative translation initiation codons, results in multiple isoforms, one of which initiates at a non-AUG (CUG) start codon. Related pseudogenes have been identified on chromosomes 1, 3, 8, 10, and 12. [provided by RefSeq].

RefSeq annotates 3 representative transcripts (NM included in AceView variants .a, .d and .e), 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 7 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, 1.8 times the average gene in this release. The sequence of this gene is defined by 200 GenBank accessions from 192 cDNA clones, some from embryonic stem cells, cell lines H1, H7, andh9 (seen 26 times), human embryonic stem cells (21), human embryonic stem cells differentiated toan early endodermal cell type (13), embryonic stem cells, WA01, passage 38 (12), blastocyst (10), pluripotent cell line derived fromblastocyst inner cell mass (10), ovary (6) and 30 other tissues. We annotate structural defects or features in one cDNA clone.
Alternative mRNA variants and regulation: The gene contains 6 distinct introns (4 gt-ag, 2 gc-ag). Transcription produces 8 different mRNAs, 7 alternatively spliced variants and 1 unspliced form. There are 3 probable alternative promotors, 2 non overlapping alternative last exons and 6 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, splicing versus retention of 2 introns. 782 bp of this gene are antisense to spliced gene TCF19, raising the possibility of regulated alternate expression.
Function: There are 138 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (Bone Neoplasms; Breast Neoplasms; Carcinoma; Genetic Predisposition to Disease; Hypertension, Pulmonary; Ischemia; Lupus Erythematosus, Systemic; Neoplasms; Ovarian Neoplasms; Salivary Gland Neoplasms; Sweat Gland Neoplasms; Testicular Neoplasms) and proposed to participate in processes (anatomical structure morphogenesis, BMP signaling pathway involved in heart induction, cardiac cell fate specification, cell fate commitment involved in the formation of primary germ layers, negative regulation of gene silencing by miRNA, positive regulation of catenin protein nuclear translocation, positive regulation of gene-specific transcription from RNA polymerase II promoter, positive regulation of SMAD protein nuclear translocation, regulation of canonical Wnt receptor signaling pathway involved in heart induction, regulation of gene expression, regulation of methylation-dependent chromatin silencing, regulation of transcription, DNA-dependent, response to wounding, somatic stem cell maintenance). Proteins are expected to have molecular functions (DNA binding, miRNA binding, promoter binding, protein binding, transcription factor activity, transcription factor binding, ubiquitin binding, sequence-specific DNA binding) and to localize in various compartments (cytoplasm, cytosol, nucleus, transcription factor complex, extracellular space). Putative protein interactors have been described (AR, ETS2, EWSR1, FOXD3, HMGB1, HMGB2, MNAT1, SOX2, SOX8, SOX10, SUMO1).
Protein coding potential: 7 spliced mRNAs putatively encode good proteins, altogether 5 different isoforms (4 complete, 1 COOH complete), some containing domains Homeobox domain, Pou domain - N-terminal to homeobox domain [Pfam], a coiled coil stretch [Psort2]; 1 of the 4 complete proteins appears to be secreted. The remaining mRNA variant (unspliced) appears not to encode a good protein.
Isoform POU5F1.bAug10 is annotated using as Met a Kozak-compatible a..ACG. start, thereby gaining 89 amino acids N-terminal to the first AUG. Finally proteins from this gene may be modulated by phosphorylation; sumoylation; 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 6, links to other databases and other names
Map: This gene POU5F1 maps on chromosome 6, at 6p21.31 according to Entrez Gene. In AceView, it covers 16.39 kb, from 31148506 to 31132113 (NCBI 37, August 2010), on the reverse strand.
Links to: , manual annotations from GAD, PhosphoSite, the SNP view, gene overviews from Entrez Gene 5460, 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 POU5F1, DADB-104B20.2, OCT3, OCT4, OTF3, OTF4, OTF-3, Oct-3, Oct-4, MGC22487, LOC5460 or shujaw, klerklobu. It has been described as POU domain, class 5, transcription factor 1, OTTHUMP00000221150, OTTHUMP00000221151, octamer-binding protein 3, octamer-binding protein 4, octamer-binding transcription factor 3, octamer-binding transcription factor-3, POU-type homeodomain-containing DNA-binding protein.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Pou5f1 (e=10-65).
The closest C.elegans genes, according to BlastP, are the AceView/WormGenes unc-86 (e=6 10-13), ceh-6 (e=7 10-13), ceh-18 (e=5 10-12), which may contain interesting functional annotation.
The closest A.thaliana genes, according to BlastP, are the AceView genes HDG11 (e=3 10-04), AT4G03250 (e=6 10-04), AT3G03260 (e=0.001), ANL2 (e=0.002), GL2 (e=0.004), HB-7 (e=0.005), AT2G32370 (e=0.005), ATML1 (e=0.005), PDF2 (e=0.005), HDG7 (e=0.006), AT1G05230 (e=0.008), 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
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!.
          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the Flash version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
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.
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
Downstream sequence
aAug10 1432 bp 360 aa 86 bp 263 bp 2kb possibly including promoter 6369 bp 1kb
bAug10 1038 bp 252 aa 30 bp 249 bp 2kb possibly including promoter 16378 bp 1kb
cAug10 691 bp 210 aa 38 bp 20 bp 2kb probably including promoter 4859 bp 1kb
dAug10 1246 bp 164 aa 488 bp 263 bp 21 bp 2kb possibly including promoter 2501 bp 1kb
eAug10 1732 bp 164 aa 974 bp 263 bp 21 bp 2kb possibly including promoter 2501 bp 1kb
fAug10 2275 bp 164 aa 1531 bp 249 bp 2kb possibly including promoter 2819 bp 1kb
gAug10 681 bp 143 aa 249 bp 2kb 941 bp 1kb
hAug10-unspliced 1801 bp 61 aa 1607 bp 8 bp 2kb including Promoter 2304 bp 1kb

Gene neighbors and Navigator on chromosome 6p21.31 back to top
ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications        
Annotated mRNA diagrams back to top
Bibliography:               138 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h-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'.

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