Six2 (SIX homeobox 2) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Six2 (SIX homeobox 2) Heterocephalus glaber
Analyze
Symbol: Six2
Name: SIX homeobox 2
RGD ID: 18930823
Description: ENCODES a protein that exhibits DNA-binding transcription activator activity, RNA polymerase II-specific (ortholog); DNA-binding transcription factor activity (ortholog); protein-containing complex binding (ortholog); INVOLVED IN anterior/posterior axis specification (ortholog); cell migration (ortholog); cell population proliferation (ortholog); ASSOCIATED WITH amyotrophic lateral sclerosis type 1 (ortholog); CAKUT (ortholog); chronic kidney disease (ortholog); FOUND IN nucleus (inferred); transcription regulator complex (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: Homeobox protein SIX2
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: HetGla 1.0 - Naked Mole-Rat female 1.0 Assembly
Position:
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473826,442,965 - 26,446,942 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473826,442,935 - 26,447,100 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References
Additional References at PubMed
PMID:21993625   PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
Six2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473826,442,965 - 26,446,942 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473826,442,935 - 26,447,100 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2
SIX2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38245,005,182 - 45,009,452 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl245,005,182 - 45,009,452 (-)EnsemblGRCh38hg38GRCh38
GRCh37245,232,321 - 45,236,591 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36245,085,847 - 45,090,026 (-)NCBINCBI36Build 36hg18NCBI36
Build 34245,143,994 - 45,148,173NCBI
Celera245,070,945 - 45,075,163 (-)NCBICelera
Cytogenetic Map2p21NCBI
HuRef244,969,941 - 44,974,159 (-)NCBIHuRef
CHM1_1245,162,931 - 45,167,149 (-)NCBICHM1_1
T2T-CHM13v2.0245,010,408 - 45,014,884 (-)NCBIT2T-CHM13v2.0
Six2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391785,970,276 - 85,995,682 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1785,991,705 - 85,995,702 (-)EnsemblGRCm39 Ensembl
GRCm381785,662,736 - 85,688,254 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1785,684,277 - 85,688,274 (-)EnsemblGRCm38mm10GRCm38
MGSCv371786,083,608 - 86,087,594 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361785,592,594 - 85,596,573 (-)NCBIMGSCv36mm8
MGSCv361784,980,193 - 84,984,172 (-)NCBIMGSCv36mm8
Celera1790,046,891 - 90,050,640 (-)NCBICelera
Cytogenetic Map17E4NCBI
cM Map1755.72NCBI
Six2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8614,727,756 - 14,734,219 (+)NCBIGRCr8
mRatBN7.268,974,859 - 8,981,345 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl68,967,157 - 8,981,193 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx69,252,089 - 9,255,407 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.069,561,498 - 9,564,816 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.069,089,205 - 9,092,512 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.068,952,572 - 8,955,893 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl68,952,572 - 8,956,276 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.068,875,432 - 8,878,685 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.469,094,655 - 9,097,973 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.169,095,089 - 9,098,000 (-)NCBI
Celera68,702,767 - 8,705,759 (+)NCBICelera
Cytogenetic Map6q12NCBI
Six2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544112,029,480 - 12,033,214 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495544112,029,530 - 12,033,214 (-)NCBIChiLan1.0ChiLan1.0
SIX2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21281,393,947 - 81,398,443 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A81,397,915 - 81,402,411 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A45,109,414 - 45,113,887 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A46,040,067 - 46,044,029 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A46,039,582 - 46,044,035 (-)Ensemblpanpan1.1panPan2
SIX2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11047,399,152 - 47,403,503 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1047,400,034 - 47,403,509 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1047,259,008 - 47,263,037 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01048,278,170 - 48,282,199 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1048,279,055 - 48,282,792 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11047,986,666 - 47,990,695 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01048,275,743 - 48,279,772 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01048,458,612 - 48,462,641 (-)NCBIUU_Cfam_GSD_1.0
Six2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629235,619,153 - 35,623,120 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365087,047,304 - 7,051,732 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365087,047,563 - 7,051,129 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SIX2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl395,459,945 - 95,463,251 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1395,460,046 - 95,463,428 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23101,507,697 - 101,511,756 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SIX2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11462,212,920 - 62,219,976 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1462,213,115 - 62,220,069 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604549,662,672 - 49,667,207 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSHGLT00000025528   ⟹   ENSHGLP00000025306
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla_female_1.0 EnsemblNW_00462473826,442,965 - 26,446,942 (-)Ensembl
RefSeq Acc Id: XM_004839390   ⟹   XP_004839447
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462473826,443,013 - 26,447,100 (-)NCBI
RefSeq Acc Id: XM_021253814   ⟹   XP_021109473
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462473826,442,935 - 26,447,100 (-)NCBI
Protein Sequences
Protein RefSeqs XP_004839447 (Get FASTA)   NCBI Sequence Viewer  
  XP_021109473 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EHB18301 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSHGLP00000025306
RefSeq Acc Id: XP_021109473   ⟸   XM_021253814
- Peptide Label: isoform X1
RefSeq Acc Id: XP_004839447   ⟸   XM_004839390
- Peptide Label: isoform X2
- UniProtKB: G5C9U0 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSHGLP00000025306   ⟸   ENSHGLT00000025528


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSHGLG00000018034 Ensembl, ENTREZGENE
Ensembl Transcript ENSHGLT00000025528 ENTREZGENE
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro Homeobox-like_sf UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/TrEMBL
  SIX1_SD UniProtKB/TrEMBL
KEGG Report hgl:101698682 UniProtKB/TrEMBL
NCBI Gene Six2 ENTREZGENE
PANTHER HOMEOBOX PROTEIN SIX UniProtKB/TrEMBL
  HOMEOBOX PROTEIN SIX2 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 G5C9U0 ENTREZGENE, UniProtKB/TrEMBL