Human Gene SIX5 (uc002pdb.3) Description and Page Index
Description: Homo sapiens SIX homeobox 5 (SIX5), mRNA. RefSeq Summary (NM_175875): The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this gene are a cause of branchiootorenal syndrome type 2. [provided by RefSeq, Jul 2009]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR1163655.484181.1, AK074826.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA2155770, SAMEA2155984 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000317578.7/ ENSP00000316842.4 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END## Transcript (Including UTRs) Position: hg19 chr19:46,268,043-46,272,497 Size: 4,455 Total Exon Count: 3 Strand: - Coding Region Position: hg19 chr19:46,268,759-46,272,102 Size: 3,344 Coding Exon Count: 3
ID:SIX5_HUMAN DESCRIPTION: RecName: Full=Homeobox protein SIX5; AltName: Full=DM locus-associated homeodomain protein; AltName: Full=Sine oculis homeobox homolog 5; FUNCTION: Transcription factor that is thought to be involved in regulation of organogenesis. May be involved in determination and maintenance of retina formation. Binds a 5'-GGTGTCAG-3' motif present in the ARE regulatory element of ATP1A1. Binds a 5'- TCA[AG][AG]TTNC-3' motif present in the MEF3 element in the myogenin promoter, and in the IGFBP5 promoter (By similarity). Thought to be regulated by association with Dach and Eya proteins, and seems to be coactivated by EYA1, EYA2 and EYA3 (By similarity). SUBUNIT: Probably binds DNA dimer. Interacts with EYA3, and probably EYA1 and EYA2 (By similarity). INTERACTION: P54253:ATXN1; NbExp=4; IntAct=EBI-946167, EBI-930964; SUBCELLULAR LOCATION: Cytoplasm. Nucleus. TISSUE SPECIFICITY: Expressed in adult but not in fetal eyes. Found in corneal epithelium and endothelium, lens epithelium, ciliary body epithelia, cellular layers of the retina and the sclera. DEVELOPMENTAL STAGE: At the begin of fourth week of development detected in cytoplasm of somite cells, and at the end of fourth week is accumulated in the nucleus. Between the sixth and eighth week of development detected in the nucleus of limb bud cells. DISEASE: Defects in SIX5 are the cause of branchiootorenal syndrome type 2 (BOR2) [MIM:610896]. BOR is an autosomal dominant disorder manifested by various combinations of preauricular pits, branchial fistulae or cysts, lacrimal duct stenosis, hearing loss, structural defects of the outer, middle, or inner ear, and renal dysplasia. Associated defects include asthenic habitus, long narrow facies, constricted palate, deep overbite, and myopia. Hearing loss may be due to mondini type cochlear defect and stapes fixation. Penetrance of BOR syndrome is high, although expressivity can be extremely variable. SIMILARITY: Belongs to the SIX/Sine oculis homeobox family. SIMILARITY: Contains 1 homeobox DNA-binding domain. SEQUENCE CAUTION: Sequence=AAH33204.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing; Sequence=AK074826; Type=Erroneous termination; Positions=721; Note=Translated as Glu;
Genetic Association Studies of Complex Diseases and Disorders
Genetic Association Database (archive): SIX5 CDC HuGE Published Literature: SIX5
The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.
ModBase Predicted Comparative 3D Structure on Q8N196
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Orthologous Genes in Other Species
Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
Gene Ontology (GO) Annotations with Structured Vocabulary
Molecular Function: GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding GO:0003677 DNA binding GO:0005515 protein binding GO:0043565 sequence-specific DNA binding
Biological Process: GO:0002088 lens development in camera-type eye GO:0006351 transcription, DNA-templated GO:0006355 regulation of transcription, DNA-templated GO:0007275 multicellular organism development GO:0007286 spermatid development GO:0008285 negative regulation of cell proliferation GO:0045892 negative regulation of transcription, DNA-templated GO:0045944 positive regulation of transcription from RNA polymerase II promoter GO:1902723 negative regulation of skeletal muscle satellite cell proliferation