SIX1 (SIX homeobox 1) - Rat Genome Database

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Gene: SIX1 (SIX homeobox 1) Sus scrofa
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Symbol: SIX1
Name: SIX homeobox 1
RGD ID: 13972080
Description: ENCODES a protein that exhibits DNA-binding transcription factor activity (ortholog); sequence-specific DNA binding (ortholog); transcription coactivator binding (ortholog); INVOLVED IN anatomical structure development (ortholog); aorta morphogenesis (ortholog); branching involved in ureteric bud morphogenesis (ortholog); ASSOCIATED WITH 22q11 Deletion Syndrome (ortholog); autosomal dominant nonsyndromic deafness (ortholog); autosomal dominant nonsyndromic deafness 23 (ortholog); FOUND IN nucleus (ortholog); transcription regulator complex (ortholog)
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: homeobox protein SIX1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1189,619,855 - 189,624,651 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11189,620,430 - 189,624,652 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21210,729,818 - 210,734,041 (-)NCBISscrofa10.2Sscrofa10.2susScr3
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
anatomical structure development  (IEA,ISO)
aorta morphogenesis  (IEA,ISO)
apoptotic process  (IEA)
branching involved in ureteric bud morphogenesis  (IEA,ISO,ISS)
cellular response to 3,3',5-triiodo-L-thyronine  (ISO)
cochlea morphogenesis  (IEA,ISO)
embryonic cranial skeleton morphogenesis  (IEA,ISO,ISS)
embryonic skeletal system morphogenesis  (IEA,ISO,ISS)
endothelin receptor signaling pathway  (IEA)
epithelial cell differentiation  (IEA,ISO,ISS)
facial nerve morphogenesis  (IEA,ISO)
fungiform papilla morphogenesis  (IEA)
gene expression  (IEA)
generation of neurons  (IEA,ISS)
inner ear development  (IEA,ISS)
inner ear morphogenesis  (IEA,ISO,ISS)
kidney development  (IEA,ISS)
mesenchymal cell proliferation involved in ureter development  (IEA,ISO)
mesonephric tubule formation  (IEA,ISS)
metanephric mesenchyme development  (IEA,ISS)
middle ear morphogenesis  (IEA,ISO)
myoblast migration  (IEA,ISO,ISS)
myoblast proliferation  (IEA,ISO)
myotome development  (IEA)
negative regulation of apoptotic process  (IEA)
negative regulation of DNA-templated transcription  (IEA)
negative regulation of neuron apoptotic process  (IEA,ISS)
negative regulation of transcription by RNA polymerase II  (IEA,ISO)
neural crest cell differentiation  (IEA)
neurogenesis  (IEA)
neuron fate specification  (IEA,ISO)
Notch signaling pathway  (IEA)
olfactory placode formation  (IEA)
organ induction  (IEA,ISO,ISS)
otic vesicle development  (IEA,ISO)
outflow tract morphogenesis  (IEA,ISO)
pattern specification process  (IEA,ISO,ISS)
pharyngeal system development  (IEA,ISO)
positive regulation of branching involved in ureteric bud morphogenesis  (IEA,ISO,ISS)
positive regulation of brown fat cell differentiation  (IEA)
positive regulation of DNA-templated transcription  (IEA,ISS)
positive regulation of mesenchymal cell proliferation involved in ureter development  (IEA,ISO)
positive regulation of myoblast proliferation  (IEA,ISO)
positive regulation of secondary heart field cardioblast proliferation  (IEA,ISO)
positive regulation of transcription by RNA polymerase II  (IEA,ISO,ISS)
positive regulation of ureteric bud formation  (IEA,ISS)
protein localization to nucleus  (IEA)
regulation of branch elongation involved in ureteric bud branching  (IEA,ISS)
regulation of DNA-templated transcription  (IEA,ISO,ISS)
regulation of epithelial cell proliferation  (IEA)
regulation of gene expression  (IEA,ISO)
regulation of neuron differentiation  (IEA,ISO,ISS)
regulation of protein localization  (IEA,ISO)
regulation of skeletal muscle cell differentiation  (IEA)
regulation of skeletal muscle cell proliferation  (IBA)
regulation of skeletal muscle satellite cell proliferation  (IEA)
regulation of synaptic assembly at neuromuscular junction  (IEA,ISO)
regulation of transcription by RNA polymerase II  (IBA)
sensory perception of sound  (IEA,ISO)
skeletal muscle fiber development  (IBA)
skeletal muscle tissue development  (IEA,ISO,ISS)
skeletal system morphogenesis  (IEA,ISO)
thymus development  (IEA,ISO,ISS)
thyroid gland development  (IEA,ISO,ISS)
tongue development  (IEA)
trigeminal ganglion development  (IEA)
ureter smooth muscle cell differentiation  (IEA,ISO)
ureteric bud development  (IEA,ISO,ISS)

Cellular Component
cytoplasm  (IEA)
nucleolus  (IEA)
nucleoplasm  (IEA)
nucleus  (IBA,IEA,ISO,ISS)
transcription regulator complex  (IBA,IEA,ISS)

References
Additional References at PubMed
PMID:21082258   PMID:22752728  


Genomics

Comparative Map Data
SIX1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1189,619,855 - 189,624,651 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11189,620,430 - 189,624,652 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21210,729,818 - 210,734,041 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SIX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381460,643,421 - 60,649,477 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1460,643,421 - 60,658,259 (-)EnsemblGRCh38hg38GRCh38
GRCh371461,110,139 - 61,116,195 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361460,182,506 - 60,185,933 (-)NCBINCBI36hg18NCBI36
Build 341460,182,505 - 60,185,933NCBI
Celera1441,161,682 - 41,166,417 (-)NCBI
Cytogenetic Map14q23.1NCBI
HuRef1441,274,621 - 41,279,356 (-)NCBIHuRef
CHM1_11461,050,553 - 61,055,290 (-)NCBICHM1_1
T2T-CHM13v2.01454,849,879 - 54,855,934 (-)NCBI
Six1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391273,088,601 - 73,093,486 (-)NCBIGRCm39mm39
GRCm39 Ensembl1273,086,789 - 73,100,661 (-)Ensembl
GRCm381273,041,827 - 73,046,712 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1273,040,015 - 73,053,887 (-)EnsemblGRCm38mm10GRCm38
MGSCv371274,142,814 - 74,147,699 (-)NCBIGRCm37mm9NCBIm37
MGSCv361273,960,668 - 73,965,302 (-)NCBImm8
Celera1274,158,405 - 74,163,290 (-)NCBICelera
Cytogenetic Map12C3NCBI
cM Map1230.34NCBI
Six1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2691,746,739 - 91,751,975 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl691,746,739 - 91,751,975 (-)Ensembl
Rnor_6.0695,929,060 - 95,934,296 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl695,929,060 - 95,934,296 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06105,364,372 - 105,369,608 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4695,470,153 - 95,475,389 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1695,475,346 - 95,478,212 (-)NCBI
Celera690,209,553 - 90,214,789 (-)NCBICelera
Cytogenetic Map6q24NCBI
Six1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554668,961,597 - 8,966,069 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554668,961,597 - 8,966,069 (+)NCBIChiLan1.0ChiLan1.0
SIX1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11459,515,324 - 59,518,740 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1459,515,324 - 59,527,494 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01441,250,512 - 41,256,567 (-)NCBIMhudiblu_PPA_v0panPan3
SIX1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1835,676,705 - 35,679,534 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl835,676,479 - 35,679,534 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha835,430,686 - 35,433,517 (-)NCBI
ROS_Cfam_1.0835,909,922 - 35,912,747 (-)NCBI
ROS_Cfam_1.0 Ensembl835,909,922 - 35,913,208 (-)Ensembl
UMICH_Zoey_3.1835,522,041 - 35,524,863 (-)NCBI
UNSW_CanFamBas_1.0835,599,806 - 35,602,627 (-)NCBI
UU_Cfam_GSD_1.0835,960,733 - 35,963,565 (-)NCBI
Six1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864069,348,816 - 69,353,683 (+)NCBI
SpeTri2.0NW_0049364954,839,496 - 4,842,906 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SIX1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12437,840,399 - 37,855,801 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2437,840,309 - 37,845,192 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605326,090,242 - 26,095,370 (-)NCBIVero_WHO_p1.0
Six1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473440,453,420 - 40,459,671 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462473440,453,445 - 40,457,551 (+)NCBIHetGla_female_1.0hetGla2


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system hemolymphoid system musculoskeletal system nervous system renal system reproductive system
High
Medium 3 2 3
Low 1 1 1
Below cutoff 1 1 1 3 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSSSCT00000005607   ⟹   ENSSSCP00000005467
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1189,619,855 - 189,624,651 (-)Ensembl
RefSeq Acc Id: NM_001199718   ⟹   NP_001186647
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11189,620,430 - 189,624,652 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001186647 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein ADQ54113 (Get FASTA)   NCBI Sequence Viewer  
  ADQ54114 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001186647   ⟸   NM_001199718
- UniProtKB: E5DCJ4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000005467   ⟸   ENSSSCT00000005607
Protein Domains
Homeobox


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000005087 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00015031412 UniProtKB/TrEMBL
  ENSSSCG00025054475 UniProtKB/TrEMBL
  ENSSSCG00030012294 UniProtKB/TrEMBL
  ENSSSCG00035003116 UniProtKB/TrEMBL
  ENSSSCG00040039180 UniProtKB/TrEMBL
  ENSSSCG00045034119 UniProtKB/TrEMBL
  ENSSSCG00050061285 UniProtKB/TrEMBL
  ENSSSCG00055008613 UniProtKB/TrEMBL
  ENSSSCG00060004189 UniProtKB/TrEMBL
  ENSSSCG00065069245 UniProtKB/TrEMBL
  ENSSSCG00070030519 UniProtKB/TrEMBL
Ensembl Protein ENSSSCP00000005467 ENTREZGENE
  ENSSSCP00000005467.2 UniProtKB/TrEMBL
  ENSSSCP00015016446.1 UniProtKB/TrEMBL
  ENSSSCP00025032281.1 UniProtKB/TrEMBL
  ENSSSCP00030007586.1 UniProtKB/TrEMBL
  ENSSSCP00035001313.1 UniProtKB/TrEMBL
  ENSSSCP00040021777.1 UniProtKB/TrEMBL
  ENSSSCP00045040796.1 UniProtKB/TrEMBL
  ENSSSCP00050035851.1 UniProtKB/TrEMBL
  ENSSSCP00055013281.1 UniProtKB/TrEMBL
  ENSSSCP00060001741.1 UniProtKB/TrEMBL
  ENSSSCP00065041572.1 UniProtKB/TrEMBL
  ENSSSCP00070052383.1 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000005607 ENTREZGENE
  ENSSSCT00000005607.4 UniProtKB/TrEMBL
  ENSSSCT00015041623.1 UniProtKB/TrEMBL
  ENSSSCT00025074526.1 UniProtKB/TrEMBL
  ENSSSCT00030016898.1 UniProtKB/TrEMBL
  ENSSSCT00035003875.1 UniProtKB/TrEMBL
  ENSSSCT00040052425.1 UniProtKB/TrEMBL
  ENSSSCT00045058356.1 UniProtKB/TrEMBL
  ENSSSCT00050083512.1 UniProtKB/TrEMBL
  ENSSSCT00055016829.1 UniProtKB/TrEMBL
  ENSSSCT00060005193.1 UniProtKB/TrEMBL
  ENSSSCT00065095058.1 UniProtKB/TrEMBL
  ENSSSCT00070061439.1 UniProtKB/TrEMBL
InterPro Homeobox-like_sf UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/TrEMBL
  SIX1 UniProtKB/TrEMBL
  SIX1_SD UniProtKB/TrEMBL
KEGG Report ssc:100156847 UniProtKB/TrEMBL
NCBI Gene SIX1 ENTREZGENE
PANTHER PTHR10390:SF13 UniProtKB/TrEMBL
Pfam Homeodomain UniProtKB/TrEMBL
  SIX1_SD UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/TrEMBL
UniProt A0A4X1WCT7_PIG UniProtKB/TrEMBL
  E5DCJ4 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:92892 ENTREZGENE