SIX1 (SIX homeobox 1) - Rat Genome Database

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Gene: SIX1 (SIX homeobox 1) Chlorocebus sabaeus
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Symbol: SIX1
Name: SIX homeobox 1
RGD ID: 18403907
Description: ENCODES a protein that exhibits transcription coactivator binding (ortholog); INVOLVED IN aorta morphogenesis (ortholog); branching involved in ureteric bud morphogenesis (ortholog); cellular response to 3,3',5-triiodo-L-thyronine (ortholog); ASSOCIATED WITH 22q11 Deletion Syndrome (ortholog); autosomal dominant nonsyndromic deafness (ortholog); autosomal dominant nonsyndromic deafness 23 (ortholog); FOUND IN cytoplasm (inferred); nucleolus (inferred); nucleoplasm (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: homeobox protein SIX1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: ChlSab1.1 - Green Monkey 1.1 Assembly
Position:
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12437,840,399 - 37,855,801 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2437,840,309 - 37,845,192 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605326,090,242 - 26,095,370 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

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

Cellular Component

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
SIX1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12437,840,399 - 37,855,801 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2437,840,309 - 37,845,192 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605326,090,242 - 26,095,370 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
SIX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381460,643,421 - 60,649,477 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1460,643,421 - 60,658,259 (-)EnsemblGRCh38hg38GRCh38
GRCh371461,110,139 - 61,116,195 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361460,182,506 - 60,185,933 (-)NCBINCBI36Build 36hg18NCBI36
Build 341460,182,505 - 60,185,933NCBI
Celera1441,161,682 - 41,166,417 (-)NCBICelera
Cytogenetic Map14q23.1NCBI
HuRef1441,274,621 - 41,279,356 (-)NCBIHuRef
CHM1_11461,050,553 - 61,055,290 (-)NCBICHM1_1
T2T-CHM13v2.01454,849,879 - 54,855,949 (-)NCBIT2T-CHM13v2.0
Six1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391273,088,601 - 73,093,486 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1273,086,789 - 73,100,661 (-)EnsemblGRCm39 Ensembl
GRCm381273,041,827 - 73,046,712 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1273,040,015 - 73,053,887 (-)EnsemblGRCm38mm10GRCm38
MGSCv371274,142,814 - 74,147,699 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361273,960,668 - 73,965,302 (-)NCBIMGSCv36mm8
Celera1274,158,405 - 74,163,290 (-)NCBICelera
Cytogenetic Map12C3NCBI
cM Map1230.34NCBI
Six1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8697,482,617 - 97,487,853 (-)NCBIGRCr8
mRatBN7.2691,746,739 - 91,751,975 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl691,746,739 - 91,751,975 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx692,137,046 - 92,142,281 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0692,436,544 - 92,441,778 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0691,864,445 - 91,869,679 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
NHGRI_mPanPan1-v21561,782,374 - 61,786,732 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11460,997,057 - 61,003,141 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01441,250,512 - 41,256,567 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11459,515,324 - 59,518,740 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1459,515,324 - 59,527,494 (-)Ensemblpanpan1.1panPan2
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0835,909,922 - 35,912,747 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl835,909,922 - 35,913,208 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1835,522,041 - 35,524,863 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0835,599,806 - 35,602,627 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0835,960,733 - 35,963,565 (-)NCBIUU_Cfam_GSD_1.0
Six1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864069,348,816 - 69,353,683 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364954,838,051 - 4,842,994 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364954,839,496 - 4,842,906 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
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
(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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473440,453,445 - 40,457,551 (+)NCBIHetGla_female_1.0HetGla 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

endocrine system hemolymphoid system nervous system
High
Medium 20 20
Low 1 10
Below cutoff 15 7 37

Sequence


RefSeq Acc Id: ENSCSAT00000012270   ⟹   ENSCSAP00000010313
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1 Ensembl2437,840,309 - 37,845,192 (-)Ensembl
RefSeq Acc Id: XM_007986884   ⟹   XP_007985075
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.12437,840,399 - 37,845,811 (-)NCBI
Vero_WHO_p1.0NW_02366605326,090,242 - 26,095,370 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_007985075 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCSAP00000010313
  ENSCSAP00000010313.1
RefSeq Acc Id: XP_007985075   ⟸   XM_007986884
- UniProtKB: A0A0D9RNX4 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCSAP00000010313   ⟸   ENSCSAT00000012270


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCSAG00000014174 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCSAT00000012270.1 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro Homeobox-like_sf UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/TrEMBL
  Homeobox_KN_domain UniProtKB/TrEMBL
  SIX1_SD UniProtKB/TrEMBL
NCBI Gene SIX1 ENTREZGENE
PANTHER HOMEOBOX PROTEIN SIX UniProtKB/TrEMBL
  PTHR10390:SF13 UniProtKB/TrEMBL
Pfam Homeobox_KN 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 A0A0D9RNX4 ENTREZGENE, UniProtKB/TrEMBL