IRX6 (iroquois homeobox 6) - Rat Genome Database

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Gene: IRX6 (iroquois homeobox 6) Sus scrofa
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Symbol: IRX6
Name: iroquois homeobox 6
RGD ID: 13942037
Description: ENCODES a protein that exhibits DNA-binding transcription repressor activity, RNA polymerase II-specific (ortholog); INVOLVED IN detection of visible light (ortholog); negative regulation of DNA-templated transcription (ortholog); positive regulation of DNA-templated transcription (ortholog); ASSOCIATED WITH genetic disease (ortholog); Joubert syndrome 1 (ortholog); FOUND IN nucleus (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: iroquois-class homeodomain protein IRX-6
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 Ensembl630,198,956 - 30,205,319 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1630,198,948 - 30,204,587 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2627,666,518 - 27,672,096 (-)NCBISscrofa10.2Sscrofa10.2susScr3
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
IRX6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl630,198,956 - 30,205,319 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1630,198,948 - 30,204,587 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2627,666,518 - 27,672,096 (-)NCBISscrofa10.2Sscrofa10.2susScr3
IRX6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381655,324,203 - 55,330,756 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1655,324,203 - 55,330,756 (+)EnsemblGRCh38hg38GRCh38
GRCh371655,358,115 - 55,364,668 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361653,915,972 - 53,922,173 (+)NCBINCBI36Build 36hg18NCBI36
Build 341653,915,971 - 53,922,172NCBI
Celera1639,872,722 - 39,878,927 (+)NCBICelera
Cytogenetic Map16q12.2NCBI
HuRef1641,244,432 - 41,250,656 (+)NCBIHuRef
CHM1_11656,765,742 - 56,771,956 (+)NCBICHM1_1
T2T-CHM13v2.01661,122,362 - 61,128,939 (+)NCBIT2T-CHM13v2.0
Irx6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39893,400,917 - 93,407,584 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl893,400,916 - 93,407,584 (+)EnsemblGRCm39 Ensembl
GRCm38892,674,289 - 92,680,956 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl892,674,288 - 92,680,956 (+)EnsemblGRCm38mm10GRCm38
MGSCv37895,198,301 - 95,203,979 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36895,563,530 - 95,569,208 (+)NCBIMGSCv36mm8
Celera897,001,163 - 97,006,835 (+)NCBICelera
Cytogenetic Map8C5NCBI
cM Map844.99NCBI
Irx6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81930,503,416 - 30,509,396 (-)NCBIGRCr8
mRatBN7.21914,330,440 - 14,336,403 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1914,330,440 - 14,336,403 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1916,026,560 - 16,032,511 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01921,221,366 - 21,227,321 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01924,167,163 - 24,173,104 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01915,726,633 - 15,733,442 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1915,727,514 - 15,733,412 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01926,812,637 - 26,819,392 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41915,433,142 - 15,439,105 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1914,246,025 - 14,251,980 (-)NCBICelera
Cytogenetic Map19p11NCBI
Irx6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543312,889,001 - 12,895,121 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543312,889,025 - 12,895,090 (+)NCBIChiLan1.0ChiLan1.0
IRX6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21864,752,187 - 64,758,915 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11670,670,684 - 70,677,639 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01635,556,558 - 35,563,568 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11654,662,732 - 54,669,745 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1654,662,732 - 54,669,745 (+)Ensemblpanpan1.1panPan2
IRX6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1260,630,688 - 60,636,285 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl260,630,447 - 60,636,416 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha257,265,053 - 57,270,525 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0261,169,456 - 61,174,927 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl261,169,219 - 61,174,825 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1257,997,933 - 58,003,402 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0259,022,212 - 59,027,683 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0259,900,508 - 59,905,979 (-)NCBIUU_Cfam_GSD_1.0
Irx6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934951,916,943 - 51,924,125 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364757,665,841 - 7,670,582 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364757,665,100 - 7,672,132 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
IRX6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1541,104,302 - 41,112,663 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl541,105,631 - 41,109,866 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604735,258,091 - 35,263,434 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Irx6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247571,619,023 - 1,622,800 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247571,617,674 - 1,623,928 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in IRX6
141 total Variants

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
Low 14
Below cutoff 1 1 7

Sequence


RefSeq Acc Id: ENSSSCT00000003131   ⟹   ENSSSCP00000003050
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl630,198,956 - 30,205,319 (-)Ensembl
RefSeq Acc Id: XM_013994643   ⟹   XP_013850097
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1630,198,948 - 30,204,587 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_013850097 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSSCP00000003050
  ENSSSCP00000003050.4
  ENSSSCP00045012660.1
  ENSSSCP00055012924.1
  ENSSSCP00065003614.1
RefSeq Acc Id: XP_013850097   ⟸   XM_013994643
- UniProtKB: A0A8D1H4B4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000003050   ⟸   ENSSSCT00000003131
Protein Domains
Homeobox


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000002830 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00045010801 UniProtKB/TrEMBL
  ENSSSCG00055008400 UniProtKB/TrEMBL
  ENSSSCG00065006355 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000003131 ENTREZGENE
  ENSSSCT00000003131.5 UniProtKB/TrEMBL
  ENSSSCT00045018354.1 UniProtKB/TrEMBL
  ENSSSCT00055016403.1 UniProtKB/TrEMBL
  ENSSSCT00065008558.1 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
  Iroquois_homeo UniProtKB/TrEMBL
NCBI Gene IRX6 ENTREZGENE
PANTHER IROQUOIS-CLASS HOMEODOMAIN PROTEIN IRX UniProtKB/TrEMBL
  IROQUOIS-CLASS HOMEODOMAIN PROTEIN IRX-6 UniProtKB/TrEMBL
Pfam Homeobox_KN UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
SMART HOX UniProtKB/TrEMBL
  IRO UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/TrEMBL
UniProt A0A8D1H4B4 ENTREZGENE, UniProtKB/TrEMBL
  F1RF02_PIG UniProtKB/TrEMBL
VGNC ID VGNC:89220 ENTREZGENE