Isx (intestine-specific homeobox) - Rat Genome Database

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Gene: Isx (intestine-specific homeobox) Rattus norvegicus
Analyze
Symbol: Isx
Name: intestine-specific homeobox
RGD ID: 1592776
Description: Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within negative regulation of intestinal absorption and regulation of vitamin A metabolic process. Predicted to be located in nucleus. Orthologous to human ISX (intestine specific homeobox); INTERACTS WITH bisphenol A; methoxychlor; 1,2-dimethylhydrazine (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC682968; similar to Retinal homeobox protein Rx (DRx1) (DRx)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81913,222,834 - 13,245,506 (+)NCBIGRCr8
mRatBN7.21913,217,637 - 13,239,754 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1913,218,552 - 13,239,760 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1913,192,658 - 13,214,362 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01913,957,905 - 13,979,607 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01913,239,598 - 13,260,417 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01914,198,899 - 14,219,269 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1914,198,899 - 14,218,531 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01925,312,031 - 25,333,241 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1913,089,232 - 13,110,157 (+)NCBICelera
Cytogenetic Map19p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IEA)

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:18093975   PMID:25701869  


Genomics

Comparative Map Data
Isx
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81913,222,834 - 13,245,506 (+)NCBIGRCr8
mRatBN7.21913,217,637 - 13,239,754 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1913,218,552 - 13,239,760 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1913,192,658 - 13,214,362 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01913,957,905 - 13,979,607 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01913,239,598 - 13,260,417 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01914,198,899 - 14,219,269 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1914,198,899 - 14,218,531 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01925,312,031 - 25,333,241 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1913,089,232 - 13,110,157 (+)NCBICelera
Cytogenetic Map19p11NCBI
ISX
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382235,066,158 - 35,087,387 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2235,066,136 - 35,087,387 (+)EnsemblGRCh38hg38GRCh38
GRCh372235,462,151 - 35,483,380 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362233,792,130 - 33,813,380 (+)NCBINCBI36Build 36hg18NCBI36
Celera2219,264,831 - 19,286,082 (+)NCBICelera
Cytogenetic Map22q12.3NCBI
HuRef2218,424,658 - 18,445,908 (+)NCBIHuRef
CHM1_12235,420,993 - 35,442,242 (+)NCBICHM1_1
T2T-CHM13v2.02235,524,914 - 35,546,195 (+)NCBIT2T-CHM13v2.0
Isx
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39875,599,326 - 75,620,134 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl875,599,801 - 75,620,134 (+)EnsemblGRCm39 Ensembl
GRCm38874,873,174 - 74,893,506 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl874,873,173 - 74,893,506 (+)EnsemblGRCm38mm10GRCm38
MGSCv37877,397,073 - 77,417,405 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36877,768,789 - 77,789,578 (+)NCBIMGSCv36mm8
Celera879,169,160 - 79,189,471 (+)NCBICelera
Cytogenetic Map8C1NCBI
cM Map835.54NCBI
Isx
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495540542,979,063 - 43,015,561 (+)NCBIChiLan1.0ChiLan1.0
ISX
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22345,004,839 - 45,026,076 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12247,701,590 - 47,722,834 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02216,071,117 - 16,095,029 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12233,917,642 - 33,938,908 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2233,917,642 - 33,938,908 (+)Ensemblpanpan1.1panPan2
ISX
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11028,993,515 - 29,011,736 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1028,993,795 - 29,011,640 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1028,929,188 - 28,948,497 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01029,779,524 - 29,798,838 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1029,779,924 - 29,797,781 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11029,503,201 - 29,522,502 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01029,811,951 - 29,831,872 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01029,991,729 - 30,011,036 (-)NCBIUU_Cfam_GSD_1.0
Isx
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494512,234,407 - 12,250,365 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364925,245,211 - 5,265,419 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364925,245,211 - 5,265,419 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ISX
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa10.259,957,450 - 9,975,312 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ISX
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11917,827,274 - 17,850,296 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1917,828,177 - 17,852,069 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666045108,100,487 - 108,122,703 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Isx
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624750468,316 - 482,716 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624750460,058 - 483,303 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Isx
172 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:47
Count of miRNA genes:43
Interacting mature miRNAs:46
Transcripts:ENSRNOT00000061079
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19131963836Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19136824771Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19128982497Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19136824771Rat
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191032318023069265Rat
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127355345Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191082797043544039Rat
7411590Foco7Food consumption QTL 76.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)19124688055Rat
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19128982497Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19136824771Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19136824771Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19997775339654489Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
reproductive system
respiratory system
9 6 32 31 27 13 8 13 6 49 27 19 49 14

Sequence


Ensembl Acc Id: ENSRNOT00000061079   ⟹   ENSRNOP00000057796
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1913,218,552 - 13,239,760 (+)Ensembl
Rnor_6.0 Ensembl1914,198,899 - 14,218,531 (+)Ensembl
RefSeq Acc Id: NM_001400999   ⟹   NP_001387928
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81913,223,385 - 13,245,501 (+)NCBI
mRatBN7.21913,217,637 - 13,239,754 (+)NCBI
RefSeq Acc Id: NM_001401000   ⟹   NP_001387929
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81913,223,385 - 13,245,501 (+)NCBI
mRatBN7.21913,217,637 - 13,239,754 (+)NCBI
RefSeq Acc Id: XM_039098196   ⟹   XP_038954124
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81913,222,834 - 13,245,506 (+)NCBI
mRatBN7.21913,236,022 - 13,239,754 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001387928 (Get FASTA)   NCBI Sequence Viewer  
  NP_001387929 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954124 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL87370 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000057796.3
Ensembl Acc Id: ENSRNOP00000057796   ⟸   ENSRNOT00000061079
RefSeq Acc Id: XP_038954124   ⟸   XM_039098196
- Peptide Label: isoform X1
RefSeq Acc Id: NP_001387928   ⟸   NM_001400999
- Peptide Label: isoform 2
- UniProtKB: F1M478 (UniProtKB/TrEMBL),   A6JY92 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001387929   ⟸   NM_001401000
- Peptide Label: isoform 1
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M478-F1-model_v2 AlphaFold F1M478 1-242 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1592776 AgrOrtholog
BioCyc Gene G2FUF-6438 BioCyc
Ensembl Genes ENSRNOG00000039808 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000061079.3 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro Homeobox UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  Paired_Homeobox_TFs UniProtKB/TrEMBL
NCBI Gene 682968 ENTREZGENE
PANTHER HOMEOBOX PROTEIN ARISTALESS UniProtKB/TrEMBL
  INTESTINE-SPECIFIC HOMEOBOX UniProtKB/TrEMBL
Pfam Homeobox UniProtKB/TrEMBL
PhenoGen Isx PhenoGen
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000039808 RatGTEx
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt A6JY92 ENTREZGENE, UniProtKB/TrEMBL
  F1M478 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-08-13 Isx  intestine-specific homeobox  LOC682968  similar to Retinal homeobox protein Rx (DRx1) (DRx)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC682968  similar to Retinal homeobox protein Rx (DRx1) (DRx)      Symbol and Name status set to provisional 70820 PROVISIONAL