Ints9 (integrator complex subunit 9) - Rat Genome Database

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Gene: Ints9 (integrator complex subunit 9) Rattus norvegicus
Analyze
Symbol: Ints9
Name: integrator complex subunit 9
RGD ID: 1311539
Description: Predicted to be involved in RNA polymerase II transcription initiation surveillance; negative regulation of transforming growth factor beta receptor signaling pathway; and snRNA 3'-end processing. Predicted to be located in cytosol. Predicted to be part of INTAC complex and integrator complex. Predicted to be active in nucleus. Orthologous to human INTS9 (integrator complex subunit 9); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; gentamycin; thioacetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: integrator complex subunit 9-like; LOC102549712; LOC290322; RGD1311539; similar to hypothetical protein FLJ10871
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81543,376,235 - 43,460,549 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1543,375,850 - 43,478,936 (+)EnsemblGRCr8
mRatBN7.21539,200,541 - 39,284,858 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1539,200,553 - 39,303,189 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1541,065,446 - 41,149,179 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01542,216,131 - 42,299,870 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01540,660,981 - 40,745,273 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01548,326,728 - 48,413,792 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1548,327,461 - 48,411,462 (+)Ensemblrn6Rnor6.0
Rnor_5.01552,074,082 - 52,160,485 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41544,305,731 - 44,389,322 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1538,876,823 - 38,960,851 (+)NCBICelera
RGSC_v3.11544,321,372 - 44,405,016 (+)NCBI
Cytogenetic Map15p12NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IEA,ISO)
cytosol  (IEA,ISO)
INTAC complex  (IEA,ISO)
integrator complex  (IBA,IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IEA,ISO)

Molecular Function

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16239144   PMID:23904267  


Genomics

Comparative Map Data
Ints9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81543,376,235 - 43,460,549 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1543,375,850 - 43,478,936 (+)EnsemblGRCr8
mRatBN7.21539,200,541 - 39,284,858 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1539,200,553 - 39,303,189 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1541,065,446 - 41,149,179 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01542,216,131 - 42,299,870 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01540,660,981 - 40,745,273 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01548,326,728 - 48,413,792 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1548,327,461 - 48,411,462 (+)Ensemblrn6Rnor6.0
Rnor_5.01552,074,082 - 52,160,485 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41544,305,731 - 44,389,322 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1538,876,823 - 38,960,851 (+)NCBICelera
RGSC_v3.11544,321,372 - 44,405,016 (+)NCBI
Cytogenetic Map15p12NCBI
INTS9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38828,767,661 - 28,889,969 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl828,767,661 - 28,890,242 (-)Ensemblhg38GRCh38
GRCh37828,625,178 - 28,747,486 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36828,681,099 - 28,803,398 (-)NCBIBuild 36Build 36hg18NCBI36
Celera827,585,025 - 27,707,519 (-)NCBICelera
Cytogenetic Map8p21.1NCBI
HuRef827,170,713 - 27,292,794 (-)NCBIHuRef
CHM1_1828,827,212 - 28,949,697 (-)NCBICHM1_1
T2T-CHM13v2.0829,045,883 - 29,168,153 (-)NCBIT2T-CHM13v2.0
Ints9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391465,187,494 - 65,277,284 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1465,187,494 - 65,277,284 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381464,950,045 - 65,039,835 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1464,950,045 - 65,039,832 (+)Ensemblmm10GRCm38
GRCm38.p6 Ensembl1464,950,045 - 65,039,835 (+)Ensemblmm10GRCm38
MGSCv371465,568,882 - 65,658,663 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361463,904,155 - 63,993,936 (+)NCBIMGSCv36mm8
Celera1462,711,961 - 62,802,247 (+)NCBICelera
Cytogenetic Map14D1NCBI
cM Map1433.81NCBI
Ints9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540351,109,751 - 51,199,136 (-)Ensembl
ChiLan1.0NW_00495540351,111,418 - 51,199,430 (-)NCBIChiLan1.0ChiLan1.0
INTS9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2747,311,623 - 47,435,019 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1823,024,615 - 23,148,007 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0828,049,858 - 28,173,046 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1825,247,565 - 25,369,907 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl825,247,565 - 25,369,907 (-)EnsemblpanPan2panpan1.1
INTS9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12528,679,470 - 28,779,931 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2528,679,465 - 28,904,332 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2529,327,374 - 29,428,497 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02528,835,218 - 28,935,751 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2528,835,487 - 28,935,746 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12528,795,031 - 28,896,165 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02528,680,435 - 28,781,769 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02528,842,816 - 28,944,349 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Ints9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049437,006,739 - 7,098,808 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366751,486,036 - 1,578,551 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366751,489,833 - 1,578,499 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
INTS9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1412,577,104 - 12,692,240 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11412,577,095 - 12,692,440 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21413,726,714 - 13,790,370 (-)NCBISscrofa10.2Sscrofa10.2susScr3
INTS9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1826,872,786 - 26,999,410 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl826,872,726 - 26,999,265 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605215,131,526 - 15,257,546 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ints9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475823,378,233 - 23,472,367 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462475823,378,362 - 23,472,415 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Ints9
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11259,375,718 - 59,460,661 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Ints9
364 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:73
Count of miRNA genes:68
Interacting mature miRNAs:72
Transcripts:ENSRNOT00000018071
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)15231575947315759Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15144836456Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15231575953331089Rat
152025253Hrtrt24Heart rate QTL 243.82heart pumping trait (VT:2000009)153185580392671517Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152852773273527732Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1525285835104695021Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)152233635152597086Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)1525285835104695021Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151915576287086765Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)15278592347785923Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)154046315285463152Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151492659471614418Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)152233635167336351Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)1525285835104695021Rat

Markers in Region
RH126495  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21539,284,617 - 39,284,849 (+)MAPPERmRatBN7.2
Rnor_6.01548,540,379 - 48,540,610NCBIRnor6.0
Rnor_6.01548,411,232 - 48,411,463NCBIRnor6.0
Rnor_5.01552,158,054 - 52,158,285UniSTSRnor5.0
Rnor_5.01552,286,416 - 52,286,647UniSTSRnor5.0
RGSC_v3.41544,389,082 - 44,389,313UniSTSRGSC3.4
Celera1538,960,611 - 38,960,842UniSTS
Cytogenetic Map15p12UniSTS
RH133202  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21539,225,747 - 39,225,929 (+)MAPPERmRatBN7.2
Rnor_6.01548,352,577 - 48,352,758NCBIRnor6.0
Rnor_5.01552,099,399 - 52,099,580UniSTSRnor5.0
RGSC_v3.41544,330,912 - 44,331,093UniSTSRGSC3.4
Celera1538,901,995 - 38,902,176UniSTS
RH 3.4 Map15290.3UniSTS
Cytogenetic Map15p12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
19 13 80 208 91 90 59 153 59 6 462 276 22 186 100 122 31 30 30

Sequence


Ensembl Acc Id: ENSRNOT00000018071   ⟹   ENSRNOP00000018071
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1543,375,850 - 43,458,757 (+)Ensembl
mRatBN7.2 Ensembl1539,200,553 - 39,284,853 (+)Ensembl
Rnor_6.0 Ensembl1548,327,461 - 48,411,462 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000095720   ⟹   ENSRNOP00000080797
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1543,375,850 - 43,478,936 (+)Ensembl
mRatBN7.2 Ensembl1539,200,553 - 39,303,189 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000096924   ⟹   ENSRNOP00000088568
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1543,376,427 - 43,460,549 (+)Ensembl
mRatBN7.2 Ensembl1539,224,445 - 39,284,853 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000119472   ⟹   ENSRNOP00000085699
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1543,375,850 - 43,460,544 (+)Ensembl
mRatBN7.2 Ensembl1539,200,779 - 39,284,802 (+)Ensembl
RefSeq Acc Id: NM_001402259   ⟹   NP_001389188
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81543,376,235 - 43,460,549 (+)NCBI
mRatBN7.21539,200,541 - 39,284,858 (+)NCBI
RefSeq Acc Id: XM_063274137   ⟹   XP_063130207
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81543,401,021 - 43,460,486 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001389188 (Get FASTA)   NCBI Sequence Viewer  
  XP_063130207 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL85348 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000018071.7
  ENSRNOP00000080797.1
  ENSRNOP00000085699.2
  ENSRNOP00000088568
  ENSRNOP00000088568.2
Ensembl Acc Id: ENSRNOP00000018071   ⟸   ENSRNOT00000018071
Ensembl Acc Id: ENSRNOP00000088568   ⟸   ENSRNOT00000096924
Ensembl Acc Id: ENSRNOP00000080797   ⟸   ENSRNOT00000095720
Ensembl Acc Id: ENSRNOP00000085699   ⟸   ENSRNOT00000119472
RefSeq Acc Id: NP_001389188   ⟸   NM_001402259
- UniProtKB: F1M365 (UniProtKB/TrEMBL),   A0A8I6A9P4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063130207   ⟸   XM_063274137
- Peptide Label: isoform X1
- UniProtKB: A6K6I8 (UniProtKB/TrEMBL)
Protein Domains
Beta-Casp

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M365-F1-model_v2 AlphaFold F1M365 1-658 view protein structure

Transcriptome

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

Promoters
RGD ID:13699788
Promoter ID:EPDNEW_R10310
Type:multiple initiation site
Name:Ints9_1
Description:integrator complex subunit 9
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01548,327,611 - 48,327,671EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311539 AgrOrtholog
BioCyc Gene G2FUF-13368 BioCyc
Ensembl Genes ENSRNOG00000013459 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018071.9 UniProtKB/TrEMBL
  ENSRNOT00000095720.2 UniProtKB/TrEMBL
  ENSRNOT00000096924 ENTREZGENE
  ENSRNOT00000096924.2 UniProtKB/TrEMBL
  ENSRNOT00000119472.2 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.10890 UniProtKB/TrEMBL
  3.60.15.10 UniProtKB/TrEMBL
InterPro Beta_Casp UniProtKB/TrEMBL
  Integrator_9su UniProtKB/TrEMBL
  IntS9-like_C UniProtKB/TrEMBL
  Metallo-B-lactamas UniProtKB/TrEMBL
  Metallo-hydrolase/OxRdtase UniProtKB/TrEMBL
NCBI Gene 290322 ENTREZGENE
PANTHER INTEGRATOR COMPLEX SUBUNIT 9 UniProtKB/TrEMBL
  PTHR46094 UniProtKB/TrEMBL
Pfam Beta-Casp UniProtKB/TrEMBL
  IntS9_C UniProtKB/TrEMBL
  Lactamase_B_6 UniProtKB/TrEMBL
PhenoGen Ints9 PhenoGen
RatGTEx ENSRNOG00000013459 RatGTEx
SMART Beta-Casp UniProtKB/TrEMBL
Superfamily-SCOP SSF56281 UniProtKB/TrEMBL
UniProt A0A8I5ZQE1_RAT UniProtKB/TrEMBL
  A0A8I6A4F2_RAT UniProtKB/TrEMBL
  A0A8I6A9P4 ENTREZGENE, UniProtKB/TrEMBL
  A6K6I8 ENTREZGENE, UniProtKB/TrEMBL
  F1M365 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Ints9  integrator complex subunit 9  LOC102549712  integrator complex subunit 9-like  Data merged from RGD:7692244 737654 PROVISIONAL
2013-12-18 LOC102549712  integrator complex subunit 9-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-02-27 Ints9  integrator complex subunit 9  RGD1311539_predicted  similar to hypothetical protein FLJ10871 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1311539_predicted  similar to hypothetical protein FLJ10871 (predicted)  LOC290322_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC290322_predicted  similar to hypothetical protein FLJ10871 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL