Crip3 (cysteine-rich protein 3) - Rat Genome Database

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Gene: Crip3 (cysteine-rich protein 3) Rattus norvegicus
Analyze
Symbol: Crip3
Name: cysteine-rich protein 3
RGD ID: 1565018
Description: Predicted to enable metal ion binding activity. Predicted to act upstream of or within T cell proliferation. Predicted to be located in cytoplasm. Orthologous to human CRIP3 (cysteine rich protein 3); INTERACTS WITH bisphenol A; fipronil; gentamycin.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC501100; RGD1565018; similar to thymus LIM protein TLP-B
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8922,052,039 - 22,054,933 (-)NCBIGRCr8
mRatBN7.2914,554,450 - 14,557,344 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl914,554,450 - 14,557,302 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx923,137,647 - 23,140,497 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0928,201,068 - 28,203,910 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0926,501,026 - 26,503,876 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0916,931,862 - 16,934,714 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl916,931,862 - 16,934,714 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0915,828,909 - 15,831,761 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.499,940,850 - 9,943,702 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera912,301,636 - 12,304,478 (-)NCBICelera
Cytogenetic Map9q12NCBI
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

Biological Process

Cellular Component
cytoplasm  (ISO)
nucleus  (ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11713292  


Genomics

Comparative Map Data
Crip3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8922,052,039 - 22,054,933 (-)NCBIGRCr8
mRatBN7.2914,554,450 - 14,557,344 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl914,554,450 - 14,557,302 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx923,137,647 - 23,140,497 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0928,201,068 - 28,203,910 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0926,501,026 - 26,503,876 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0916,931,862 - 16,934,714 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl916,931,862 - 16,934,714 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0915,828,909 - 15,831,761 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.499,940,850 - 9,943,702 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera912,301,636 - 12,304,478 (-)NCBICelera
Cytogenetic Map9q12NCBI
CRIP3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38643,305,472 - 43,308,826 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl643,299,710 - 43,308,826 (-)EnsemblGRCh38hg38GRCh38
GRCh37643,273,210 - 43,276,564 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36643,381,189 - 43,384,508 (-)NCBINCBI36Build 36hg18NCBI36
Build 34643,381,681 - 43,384,508NCBI
Celera644,824,971 - 44,828,289 (-)NCBICelera
Cytogenetic Map6p21.1NCBI
HuRef642,991,716 - 42,995,034 (-)NCBIHuRef
CHM1_1643,276,157 - 43,279,475 (-)NCBICHM1_1
T2T-CHM13v2.0643,134,412 - 43,137,765 (-)NCBIT2T-CHM13v2.0
Crip3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391746,735,058 - 46,742,706 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1746,739,852 - 46,742,702 (+)EnsemblGRCm39 Ensembl
GRCm381746,428,195 - 46,431,780 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1746,428,926 - 46,431,776 (+)EnsemblGRCm38mm10GRCm38
MGSCv371746,565,891 - 46,568,720 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361745,892,131 - 45,894,960 (+)NCBIMGSCv36mm8
Celera1749,863,793 - 49,866,622 (+)NCBICelera
Cytogenetic Map17CNCBI
cM Map1722.9NCBI
Crip3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554379,210,901 - 9,215,471 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554379,210,901 - 9,215,471 (-)NCBIChiLan1.0ChiLan1.0
CRIP3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2557,805,606 - 57,818,391 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1653,675,445 - 53,688,226 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0642,891,980 - 42,901,666 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1644,183,770 - 44,193,629 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl644,189,327 - 44,193,629 (-)Ensemblpanpan1.1panPan2
CRIP3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11211,788,401 - 11,791,350 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1211,788,721 - 11,791,258 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1211,825,349 - 11,869,118 (-)NCBIDog10K_Boxer_Tasha
Dog10K_Boxer_Tasha1211,839,006 - 11,845,369 (-)NCBIDog10K_Boxer_Tasha
Dog10K_Boxer_Tasha1211,815,098 - 11,825,331 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01212,272,165 - 12,326,612 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1212,272,500 - 12,275,037 (-)EnsemblROS_Cfam_1.0 Ensembl
ROS_Cfam_1.0 Ensembl1212,297,256 - 12,326,612 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11211,797,905 - 11,808,137 (-)NCBIUMICH_Zoey_3.1
UMICH_Zoey_3.11211,808,155 - 11,852,127 (-)NCBIUMICH_Zoey_3.1
UMICH_Zoey_3.11211,821,842 - 11,828,225 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01211,882,106 - 11,936,580 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01211,977,198 - 12,031,780 (-)NCBIUU_Cfam_GSD_1.0
Crip3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494647,285,863 - 47,289,736 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647616,671,284 - 16,674,406 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647616,671,284 - 16,674,406 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CRIP3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl738,334,833 - 38,338,246 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1738,334,616 - 38,338,626 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2743,835,172 - 43,858,530 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CRIP3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11728,844,793 - 28,848,181 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604443,366,782 - 43,369,877 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Crip3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475416,273,242 - 16,275,400 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475416,269,979 - 16,275,755 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Crip3
9 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:46
Count of miRNA genes:44
Interacting mature miRNAs:44
Transcripts:ENSRNOT00000061503
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
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9510982642921101Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9510982650109826Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)9728325252283252Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)9795472022071169Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)9895256053952560Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9895256053952560Rat
1600365Mcs20Mammary carcinoma susceptibility QTL 203mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)91353377042791750Rat

Markers in Region
D9Uwm3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2914,554,555 - 14,554,654 (+)MAPPERmRatBN7.2
Rnor_6.0916,931,968 - 16,932,066NCBIRnor6.0
Rnor_5.0915,829,015 - 15,829,113UniSTSRnor5.0
RGSC_v3.499,940,955 - 9,941,054RGDRGSC3.4
RGSC_v3.499,940,956 - 9,941,054UniSTSRGSC3.4
RGSC_v3.199,938,277 - 9,938,376RGD
Celera912,301,742 - 12,301,830UniSTS
Cytogenetic Map9q12UniSTS


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
Low 1 21 8 18 8 1 1 59 8 22 11 1
Below cutoff 2 21 14 11 1 11 7 9 15 27 15 7

Sequence


RefSeq Acc Id: ENSRNOT00000061503   ⟹   ENSRNOP00000058221
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl914,554,450 - 14,557,302 (-)Ensembl
Rnor_6.0 Ensembl916,931,862 - 16,934,714 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000097550   ⟹   ENSRNOP00000091049
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl914,554,879 - 14,557,302 (-)Ensembl
RefSeq Acc Id: NM_001109303   ⟹   NP_001102773
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8922,052,039 - 22,054,891 (-)NCBI
mRatBN7.2914,554,450 - 14,557,302 (-)NCBI
Rnor_6.0916,931,862 - 16,934,714 (-)NCBI
Rnor_5.0915,828,909 - 15,831,761 (-)NCBI
RGSC_v3.499,940,850 - 9,943,702 (-)RGD
Celera912,301,636 - 12,304,478 (-)RGD
Sequence:
RefSeq Acc Id: XM_039084062   ⟹   XP_038939990
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8922,052,043 - 22,054,933 (-)NCBI
mRatBN7.2914,554,454 - 14,557,344 (-)NCBI
RefSeq Acc Id: XM_039084063   ⟹   XP_038939991
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8922,052,043 - 22,054,929 (-)NCBI
mRatBN7.2914,554,454 - 14,557,340 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001102773 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939990 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939991 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM18821 (Get FASTA)   NCBI Sequence Viewer  
  EDM18822 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000058221
  ENSRNOP00000058221.2
  ENSRNOP00000091049.1
RefSeq Acc Id: NP_001102773   ⟸   NM_001109303
- UniProtKB: D3ZNQ0 (UniProtKB/TrEMBL),   A6JIR0 (UniProtKB/TrEMBL),   A6JIR1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000058221   ⟸   ENSRNOT00000061503
RefSeq Acc Id: XP_038939990   ⟸   XM_039084062
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038939991   ⟸   XM_039084063
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000091049   ⟸   ENSRNOT00000097550
Protein Domains
LIM zinc-binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZNQ0-F1-model_v2 AlphaFold D3ZNQ0 1-204 view protein structure

Transcriptome

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

Promoters
RGD ID:13696522
Promoter ID:EPDNEW_R7047
Type:single initiation site
Name:Crip3_1
Description:cysteine-rich protein 3
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_6.0916,934,800 - 16,934,860EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565018 AgrOrtholog
BioCyc Gene G2FUF-28225 BioCyc
Ensembl Genes ENSRNOG00000018613 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000061503 ENTREZGENE
  ENSRNOT00000061503.3 UniProtKB/TrEMBL
  ENSRNOT00000097550.1 UniProtKB/TrEMBL
Gene3D-CATH Cysteine Rich Protein UniProtKB/TrEMBL
InterPro Znf_LIM UniProtKB/TrEMBL
KEGG Report rno:501100 UniProtKB/TrEMBL
NCBI Gene 501100 ENTREZGENE
PANTHER CYSTEINE-RICH PROTEIN 3 UniProtKB/TrEMBL
  CYSTEINE-RICH PROTEIN CRIP FAMILY MEMBER UniProtKB/TrEMBL
Pfam LIM UniProtKB/TrEMBL
PhenoGen Crip3 PhenoGen
PROSITE LIM_DOMAIN_1 UniProtKB/TrEMBL
  LIM_DOMAIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000018613 RatGTEx
SMART LIM UniProtKB/TrEMBL
Superfamily-SCOP Glucocorticoid receptor-like (DNA-binding domain) UniProtKB/TrEMBL
UniProt A0A8I6AEM2_RAT UniProtKB/TrEMBL
  A6JIR0 ENTREZGENE, UniProtKB/TrEMBL
  A6JIR1 ENTREZGENE, UniProtKB/TrEMBL
  D3ZNQ0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Crip3  cysteine-rich protein 3  RGD1565018_predicted  similar to thymus LIM protein TLP-B (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1565018_predicted  similar to thymus LIM protein TLP-B (predicted)  LOC501100  similar to thymus LIM protein TLP-B  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC501100  similar to thymus LIM protein TLP-B      Symbol and Name status set to provisional 70820 PROVISIONAL