Six4 (SIX homeobox 4) - Rat Genome Database

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Gene: Six4 (SIX homeobox 4) Ictidomys tridecemlineatus
Analyze
Symbol: Six4
Name: SIX homeobox 4
RGD ID: 12593643
Description: ENCODES a protein that exhibits DNA binding (inferred); DNA-binding transcription activator activity, RNA polymerase II-specific (inferred); DNA-binding transcription factor activity (inferred); INVOLVED IN embryonic cranial skeleton morphogenesis (ortholog); embryonic skeletal system morphogenesis (ortholog); inner ear morphogenesis (ortholog); ASSOCIATED WITH Branchiootic Syndrome 3 (ortholog); genetic disease (ortholog); FOUND IN cytoplasm (inferred); nucleus (inferred); transcription regulator complex (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: homeobox protein SIX4; SIX homeobox 4, transcript variant X1; SIX homeobox 4, transcript variant X2
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: SpeTri2.0 - Squirrel SpeTri2.0 Assembly
Position:
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864069,291,248 - 69,302,270 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364954,887,718 - 4,900,198 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364954,887,718 - 4,900,198 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
embryonic cranial skeleton morphogenesis  (IEA,ISO)
embryonic skeletal system morphogenesis  (IEA,ISO)
fungiform papilla morphogenesis  (IEA)
generation of neurons  (IEA)
inner ear morphogenesis  (IEA,ISO)
male gonad development  (IEA)
male sex determination  (IEA)
male sex differentiation  (IEA)
metanephric mesenchyme development  (IEA)
myoblast migration  (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)
negative regulation of satellite cell differentiation  (IEA)
olfactory placode formation  (IEA)
pharyngeal system development  (IEA)
positive regulation of branching involved in ureteric bud morphogenesis  (IEA)
positive regulation of DNA-templated transcription  (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)
regulation of epithelial cell proliferation  (IEA)
regulation of gene expression  (IEA,ISO)
regulation of protein localization  (IEA,ISO)
regulation of synaptic assembly at neuromuscular junction  (IEA,ISO)
regulation of transcription by RNA polymerase II  (IEA)
sarcomere organization  (IEA)
skeletal muscle fiber differentiation  (IEA)
skeletal muscle tissue development  (IEA,ISO)
thymus development  (IEA,ISO)
tongue development  (IEA)
trigeminal ganglion development  (IEA)

Cellular Component

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
Six4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864069,291,248 - 69,302,270 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364954,887,718 - 4,900,198 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364954,887,718 - 4,900,198 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SIX4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381460,709,539 - 60,724,351 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1460,709,539 - 60,724,351 (-)EnsemblGRCh38hg38GRCh38
GRCh371461,176,257 - 61,191,069 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361460,246,009 - 60,260,545 (-)NCBINCBI36Build 36hg18NCBI36
Build 341460,249,877 - 60,260,482NCBI
Celera1441,226,507 - 41,241,110 (-)NCBICelera
Cytogenetic Map14q23.1NCBI
HuRef1441,338,950 - 41,376,872 (-)NCBIHuRef
CHM1_11461,115,577 - 61,130,176 (-)NCBICHM1_1
T2T-CHM13v2.01454,916,015 - 54,930,882 (-)NCBIT2T-CHM13v2.0
Six4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391273,146,383 - 73,160,201 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1273,146,383 - 73,160,230 (-)EnsemblGRCm39 Ensembl
GRCm381273,099,609 - 73,114,031 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1273,099,609 - 73,113,456 (-)EnsemblGRCm38mm10GRCm38
MGSCv371274,201,246 - 74,214,232 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361274,019,097 - 74,032,083 (-)NCBIMGSCv36mm8
Celera1274,211,796 - 74,224,743 (-)NCBICelera
Cytogenetic Map12C3NCBI
cM Map1230.36NCBI
Six4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8697,538,202 - 97,551,872 (-)NCBIGRCr8
mRatBN7.2691,802,328 - 91,816,002 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl691,802,329 - 91,815,992 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx692,192,313 - 92,205,976 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0692,491,810 - 92,505,473 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0691,919,712 - 91,933,375 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0695,984,868 - 95,999,709 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl695,984,868 - 95,998,529 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06105,420,180 - 105,433,894 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4695,526,293 - 95,539,953 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1695,533,549 - 95,543,176 (-)NCBI
Celera690,265,300 - 90,278,960 (-)NCBICelera
Cytogenetic Map6q24NCBI
Six4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554668,902,517 - 8,915,723 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554668,902,728 - 8,915,685 (+)NCBIChiLan1.0ChiLan1.0
LOC100981746
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21561,847,361 - 61,862,181 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11461,063,874 - 61,078,684 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01441,316,169 - 41,332,160 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11459,580,587 - 59,592,654 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1459,580,587 - 59,594,014 (-)Ensemblpanpan1.1panPan2
SIX4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1835,735,893 - 35,748,976 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl835,737,058 - 35,748,893 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha835,489,928 - 35,502,823 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0835,969,183 - 35,982,082 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl835,970,354 - 35,982,196 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1835,581,305 - 35,594,193 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0835,658,978 - 35,671,679 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0836,020,222 - 36,033,117 (-)NCBIUU_Cfam_GSD_1.0
SIX4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1189,670,390 - 189,682,577 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11189,670,390 - 189,682,378 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21210,780,397 - 210,792,387 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SIX4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12437,899,463 - 37,911,875 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2437,900,909 - 37,911,612 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605326,152,002 - 26,164,077 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Six4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473440,397,559 - 40,409,997 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473440,397,276 - 40,409,951 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSSTOT00000024469   ⟹   ENSSTOP00000019004
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_0049364954,887,718 - 4,900,198 (-)Ensembl
RefSeq Acc Id: XM_005322765   ⟹   XP_005322822
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440864069,291,469 - 69,302,270 (+)NCBI
SpeTri2.0NW_0049364954,887,718 - 4,900,198 (-)NCBI
Sequence:
RefSeq Acc Id: XM_013357510   ⟹   XP_013212964
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440864069,291,468 - 69,302,270 (+)NCBI
SpeTri2.0NW_0049364954,887,718 - 4,900,198 (-)NCBI
Sequence:
RefSeq Acc Id: XM_040275868   ⟹   XP_040131802
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440864069,291,248 - 69,302,270 (+)NCBI
Protein Sequences
Protein RefSeqs XP_005322822 (Get FASTA)   NCBI Sequence Viewer  
  XP_013212964 (Get FASTA)   NCBI Sequence Viewer  
  XP_040131802 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSTOP00000019004.1
GenBank Protein KAG3261336 (Get FASTA)   NCBI Sequence Viewer  
  KAG3261337 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: XP_013212964   ⟸   XM_013357510
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_005322822   ⟸   XM_005322765
- Peptide Label: isoform X1
- UniProtKB: I3N3Q8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_040131802   ⟸   XM_040275868
- Peptide Label: isoform X2
RefSeq Acc Id: ENSSTOP00000019004   ⟸   ENSSTOT00000024469
Protein Domains
Homeobox


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSTOG00000029039 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSSTOT00000024469.2 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro Homeobox-like_sf UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/TrEMBL
  SIX1_SD UniProtKB/TrEMBL
NCBI Gene Six4 ENTREZGENE
PANTHER HOMEOBOX PROTEIN SIX UniProtKB/TrEMBL
  HOMEOBOX PROTEIN SIX4 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 I3N3Q8 ENTREZGENE, UniProtKB/TrEMBL