Rint1 (RAD50 interactor 1) - Rat Genome Database

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Gene: Rint1 (RAD50 interactor 1) Rattus norvegicus
Analyze
Symbol: Rint1
Name: RAD50 interactor 1
RGD ID: 1560433
Description: Predicted to be involved in mitotic G2 DNA damage checkpoint signaling; regulation of ER to Golgi vesicle-mediated transport; and retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum. Predicted to be located in endoplasmic reticulum. Predicted to be part of Dsl1/NZR complex. Human ortholog(s) of this gene implicated in infantile liver failure syndrome. Orthologous to human RINT1 (RAD50 interactor 1); INTERACTS WITH bisphenol A; cobalt dichloride; gentamycin.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC296750; RAD50-interacting protein 1; RGD1560433; similar to 1500019C06Rik protein
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
GRCr8412,211,806 - 12,248,117 (-)NCBIGRCr8
mRatBN7.2411,319,416 - 11,355,740 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl411,320,955 - 11,355,736 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx416,472,326 - 16,506,568 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0412,297,437 - 12,331,722 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0410,644,302 - 10,678,548 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.047,851,602 - 7,885,446 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl47,852,224 - 7,885,301 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.047,859,660 - 7,893,315 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.446,691,863 - 6,728,969 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera46,934,752 - 6,968,412 (-)NCBICelera
Cytogenetic Map4q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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:11096100   PMID:15029241   PMID:16571679   PMID:20462495  


Genomics

Comparative Map Data
Rint1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8412,211,806 - 12,248,117 (-)NCBIGRCr8
mRatBN7.2411,319,416 - 11,355,740 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl411,320,955 - 11,355,736 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx416,472,326 - 16,506,568 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0412,297,437 - 12,331,722 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0410,644,302 - 10,678,548 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.047,851,602 - 7,885,446 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl47,852,224 - 7,885,301 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.047,859,660 - 7,893,315 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.446,691,863 - 6,728,969 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera46,934,752 - 6,968,412 (-)NCBICelera
Cytogenetic Map4q11NCBI
RINT1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh387105,532,201 - 105,567,677 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl7105,532,169 - 105,567,677 (+)EnsemblGRCh38hg38GRCh38
GRCh377105,172,648 - 105,208,124 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 367104,959,768 - 104,995,360 (+)NCBINCBI36Build 36hg18NCBI36
Celera799,977,643 - 100,013,242 (+)NCBICelera
Cytogenetic Map7q22.3NCBI
HuRef799,530,826 - 99,566,401 (+)NCBIHuRef
CHM1_17105,105,839 - 105,141,438 (+)NCBICHM1_1
T2T-CHM13v2.07106,846,396 - 106,881,882 (+)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v27104,533,083 - 104,568,680 (+)NCBI
Rint1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39523,992,700 - 24,028,582 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl523,992,709 - 24,025,367 (+)EnsemblGRCm39 Ensembl
GRCm38523,787,698 - 23,823,584 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl523,787,711 - 23,820,369 (+)EnsemblGRCm38mm10GRCm38
MGSCv37523,293,562 - 23,326,187 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36523,297,809 - 23,330,434 (+)NCBIMGSCv36mm8
Celera520,736,899 - 20,771,775 (+)NCBICelera
Cytogenetic Map5A3NCBI
cM Map510.45NCBI
Rint1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541010,121,219 - 10,144,748 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541010,121,322 - 10,144,748 (+)NCBIChiLan1.0ChiLan1.0
RINT1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v26142,382,888 - 142,418,404 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan17190,652,860 - 190,689,673 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0797,522,208 - 97,567,897 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.17110,252,778 - 110,287,708 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7110,252,776 - 110,287,702 (+)Ensemblpanpan1.1panPan2
RINT1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11814,843,820 - 14,877,334 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1814,843,829 - 14,877,607 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1814,494,854 - 14,528,503 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01815,146,297 - 15,179,923 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1815,144,991 - 15,179,914 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11814,932,259 - 14,966,162 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01814,855,205 - 14,888,884 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01815,135,240 - 15,169,303 (-)NCBIUU_Cfam_GSD_1.0
Rint1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511857,188,240 - 57,216,438 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647918,311,699 - 18,340,816 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647918,311,698 - 18,334,946 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RINT1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl9105,392,864 - 105,430,160 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.19105,392,853 - 105,430,198 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29116,160,107 - 116,194,692 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RINT1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12174,454,916 - 74,491,057 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2174,454,947 - 74,490,768 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604229,425,277 - 29,462,578 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rint1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473924,008,072 - 24,039,215 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473924,011,327 - 24,039,146 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rint1
212 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:113
Count of miRNA genes:76
Interacting mature miRNAs:80
Transcripts:ENSRNOT00000035034, ENSRNOT00000050789
Prediction methods:Microtar, 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
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829457114705Rat
8552903Pigfal2Plasma insulin-like growth factor 1 level QTL 27.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)4131934116Rat
724557Plsm1Polydactyly-luxate syndrome (PLS) morphotypes QTL 10.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)4127716890Rat
9590100Sffal4Serum free fatty acids level QTL 47.360.05blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)4131934116Rat
8552906Pigfal3Plasma insulin-like growth factor 1 level QTL 3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)41008408955084089Rat
1357341Gluco5Glucose level QTL 56.4adipocyte free fatty acid secretion trait (VT:0010465)absolute change in adipocyte free fatty acid secretion per unit volume (CMO:0001446)4133250345Rat
1357343Gluco4Glucose level QTL 40.00002adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake to basal glucose uptake ratio (CMO:0000874)4133250345Rat
6478766Anxrr47Anxiety related response QTL 470.09637locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)41008408955084089Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521917856647776Rat
6478769Anxrr48Anxiety related response QTL 480.02514locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)41008408955084089Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41081417091360527Rat
61333Gluco16Glucose level QTL 164.30.00001adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)4130372989Rat
634323Hc2Hypercalciuria QTL 22.15urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)421079645210796Rat
61408Scl23Serum cholesterol level QTL 230.0005blood HDL phospholipid amount (VT:0010504)serum high density lipoprotein phospholipid level (CMO:0001567)4127716890Rat
631209Bw2Body weight QTL24.2retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)4994088544463908Rat
8694374Bw155Body weight QTL 1553.390.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)41008408955084089Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
9589046Scfw2Subcutaneous fat weight QTL 25.540.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)4131934116Rat
6478724Anxrr35Anxiety related response QTL 350.00449defecation behavior trait (VT:0010462)defecation measurement (CMO:0000997)41008408955084089Rat
61351Bp33Blood pressure QTL 330.0018arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4127716890Rat
61415Eae11Experimental allergic encephalomyelitis QTL 112.9nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)4139505420Rat
1641905Colcr1Colorectal carcinoma resistance QTL 14.30.0003intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)4129494328Rat
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
1358201Gluco12Glucose level QTL121.6adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake (CMO:0000870)4521839229593287Rat
738021Hcar13Hepatocarcinoma resistance QTL 134.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)4132584199Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829465958103Rat
9590304Scort17Serum corticosterone level QTL 174.960.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)41008408955084089Rat
9589097Slep11Serum leptin concentration QTL 115.090.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)4131934116Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
1300141Bp178Blood pressure QTL 178arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)41002490139524530Rat

Markers in Region
BI286700  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.047,869,126 - 7,869,297NCBIRnor6.0
Celera46,951,907 - 6,952,066UniSTS
RH 3.4 Map411.4UniSTS
Cytogenetic Map4q11UniSTS


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 26 54 39 19 39 74 24 33 11
Low 17 3 2 2 8 11 11 8 8
Below cutoff

Sequence


Ensembl Acc Id: ENSRNOT00000035034   ⟹   ENSRNOP00000030177
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl411,320,955 - 11,355,736 (-)Ensembl
Rnor_6.0 Ensembl47,852,224 - 7,885,301 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000106589   ⟹   ENSRNOP00000082957
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl411,320,955 - 11,355,736 (-)Ensembl
RefSeq Acc Id: NM_001399263   ⟹   NP_001386192
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8412,213,156 - 12,248,117 (-)NCBI
mRatBN7.2411,320,775 - 11,355,740 (-)NCBI
RefSeq Acc Id: NM_001399264   ⟹   NP_001386193
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8412,213,156 - 12,248,117 (-)NCBI
mRatBN7.2411,320,775 - 11,355,740 (-)NCBI
RefSeq Acc Id: XM_039108555   ⟹   XP_038964483
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8412,211,806 - 12,232,476 (-)NCBI
mRatBN7.2411,319,416 - 11,340,096 (-)NCBI
RefSeq Acc Id: XM_063285696   ⟹   XP_063141766
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8412,211,806 - 12,241,636 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001386192 (Get FASTA)   NCBI Sequence Viewer  
  NP_001386193 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964483 (Get FASTA)   NCBI Sequence Viewer  
  XP_063141766 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL99392 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000030177.7
  ENSRNOP00000082957.1
Ensembl Acc Id: ENSRNOP00000030177   ⟸   ENSRNOT00000035034
RefSeq Acc Id: XP_038964483   ⟸   XM_039108555
- Peptide Label: isoform X2
Ensembl Acc Id: ENSRNOP00000082957   ⟸   ENSRNOT00000106589
RefSeq Acc Id: NP_001386193   ⟸   NM_001399264
- Peptide Label: isoform 2
RefSeq Acc Id: NP_001386192   ⟸   NM_001399263
- Peptide Label: isoform 1
- UniProtKB: A0A8I5ZVY6 (UniProtKB/TrEMBL),   D4A4T6 (UniProtKB/TrEMBL),   A6K582 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063141766   ⟸   XM_063285696
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A4T6-F1-model_v2 AlphaFold D4A4T6 1-735 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:1560433 AgrOrtholog
BioCyc Gene G2FUF-46014 BioCyc
Ensembl Genes ENSRNOG00000022182 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000035034.7 UniProtKB/TrEMBL
  ENSRNOT00000106589.1 UniProtKB/TrEMBL
Gene3D-CATH 1.20.58.670 UniProtKB/TrEMBL
InterPro EXOC6PINT-1/Sec15/Tip20_C_dom2 UniProtKB/TrEMBL
  RINT1_TIP1 UniProtKB/TrEMBL
NCBI Gene 296750 ENTREZGENE
PANTHER PTHR13520 UniProtKB/TrEMBL
  RAD50-INTERACTING PROTEIN 1 UniProtKB/TrEMBL
Pfam RINT1_TIP1 UniProtKB/TrEMBL
PhenoGen Rint1 PhenoGen
PROSITE RINT1_TIP20 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000022182 RatGTEx
UniProt A0A8I5ZVY6 ENTREZGENE, UniProtKB/TrEMBL
  A6K582 ENTREZGENE, UniProtKB/TrEMBL
  D4A4T6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-10-11 Rint1  RAD50 interactor 1  RGD1560433  similar to 1500019C06Rik protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1560433  similar to 1500019C06Rik protein   RGD1560433_predicted  similar to 1500019C06Rik protein (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1560433_predicted  similar to 1500019C06Rik protein (predicted)  LOC296750  similar to 1500019C06Rik protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC296750  similar to 1500019C06Rik protein      Symbol and Name status set to provisional 70820 PROVISIONAL