SIX5 SIX homeobox 5 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SIX5provided by HGNC
Official Full Name: SIX homeobox 5provided by HGNC
Primary source: HGNC:HGNC:10891
See related: Ensembl:ENSG00000177045 MIM:600963; AllianceGenome:HGNC:10891
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: BOR2; DMAHP
Summary: 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]
Expression: Ubiquitous expression in ovary (RPKM 8.6), prostate (RPKM 7.4) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19q13.32

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (45764785..45769252, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (48592320..48596787, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (46268043..46272510, complement)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotype-genotype correlation in patients with typical and atypical branchio-oto-renal syndrome.
Title: Phenotype-genotype correlation in patients with typical and atypical branchio-oto-renal syndrome.
the higher expressions of SIX1-5 were associated with the greater possibility of the tumorigenesis in lung neoplasms
Title: The expression profile and clinic significance of the SIX family in non-small cell lung cancer.
Three causative genes for BOR syndrome have been reported thus far: EYA1, SIX1, and SIX5, but the causative genes for approximately half of all BOR patients remain unknown.[review]
Title: Branchio-oto-renal syndrome: comprehensive review based on nationwide surveillance in Japan.
In East Asian populations, a SIX1 mutation has been reported in a Japanese family with branchio-oto (BO) syndrome,yet SIX5 mutations have never been reported.
Title: Mutation screening of the EYA1, SIX1, and SIX5 genes in an East Asian cohort with branchio-oto-renal syndrome.
Study reports a screening of 140 patients from 124 families with Branchio-oto-renal and identified 36 EYA1 mutations in 42 unrelated patients, 2 mutations, and 1 change of unknown significance in SIX1 in 3 unrelated patients, but no mutation in SIX5.
Title: Mutation screening of the EYA1, SIX1, and SIX5 genes in a large cohort of patients harboring branchio-oto-renal syndrome calls into question the pathogenic role of SIX5 mutations.
Observational study of gene-disease association. (HuGE Navigator)
Title: Association of genetic variants with hemorrhagic stroke in Japanese individuals.
Transcription factor SIX5 is mutated in patients with branchio-oto-renal syndrome.
Title: Transcription factor SIX5 is mutated in patients with branchio-oto-renal syndrome.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Branchiootorenal syndrome 2 MedGen: C1970479 OMIM: 610896 GeneReviews: Branchiootorenal Spectrum Disorder	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

PMC104374P1 (e-PCR)
- UniSTS:270110

RH11440 (e-PCR)
- UniSTS:35122

D19S261 (e-PCR)
- UniSTS:147775

NoName (e-PCR)
- UniSTS:495167

D19S201 (e-PCR)
- UniSTS:147034

GDB:186209 (e-PCR)
- UniSTS:155482

GDB:186796 (e-PCR)
- UniSTS:155505

STS-N23083 (e-PCR)
- UniSTS:51570

G64289 (e-PCR)
- UniSTS:158663

G15898 (e-PCR)
- UniSTS:34269

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in Leydig cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in lens development in camera-type eye	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of skeletal muscle satellite cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in spermatid development	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info
part_of chromatin	ISA Inferred from Sequence Alignment more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
part_of transcription regulator complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: homeobox protein SIX5

Names: DM locus-associated homeodomain protein; dystrophia myotonica-associated homeodomain protein; sine oculis homeobox homolog 5

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_012745.2 RefSeqGene

Range

5000..9467

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_175875.5 → NP_787071.3 homeobox protein SIX5

Status: REVIEWED

Source sequence(s)

AC074212

Consensus CDS

CCDS12673.1

UniProtKB/Swiss-Prot

Q8N196

Related

ENSP00000316842.4, ENST00000317578.7

Conserved Domains (3) summary

cd00086
Location:206 → 257

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam16878
Location:86 → 195

SIX1_SD; Transcriptional regulator, SIX1, N-terminal SD domain

cl26464
Location:424 → 663

Atrophin-1; Atrophin-1 family