Cib4 (calcium and integrin binding family member 4) - Rat Genome Database

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Gene: Cib4 (calcium and integrin binding family member 4) Rattus norvegicus
Analyze
Symbol: Cib4
Name: calcium and integrin binding family member 4
RGD ID: 1584147
Description: Predicted to enable calcium ion binding activity and magnesium ion binding activity. Orthologous to human CIB4 (calcium and integrin binding family member 4); INTERACTS WITH acrylamide; bisphenol A; N,N-diethyl-m-toluamide.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: calcium and integrin-binding family member 4; LOC688819; rCG61337-like; similar to calcium and integrin binding family member 4
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
GRCr8631,560,105 - 31,623,403 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl631,562,489 - 31,623,464 (+)EnsemblGRCr8
mRatBN7.2625,842,605 - 25,903,509 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl625,842,622 - 25,917,206 (+)EnsemblmRatBN7.2
Rnor_6.0627,241,804 - 27,303,617 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl627,241,919 - 27,303,615 (+)Ensemblrn6Rnor6.0
Rnor_5.0637,058,400 - 37,115,989 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4625,825,158 - 25,887,430 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera625,324,446 - 25,382,084 (+)NCBICelera
Cytogenetic Map6q14NCBI
JBrowse:




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

Biological Process

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. 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:22779914  


Genomics

Comparative Map Data
Cib4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8631,560,105 - 31,623,403 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl631,562,489 - 31,623,464 (+)EnsemblGRCr8
mRatBN7.2625,842,605 - 25,903,509 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl625,842,622 - 25,917,206 (+)EnsemblmRatBN7.2
Rnor_6.0627,241,804 - 27,303,617 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl627,241,919 - 27,303,615 (+)Ensemblrn6Rnor6.0
Rnor_5.0637,058,400 - 37,115,989 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4625,825,158 - 25,887,430 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera625,324,446 - 25,382,084 (+)NCBICelera
Cytogenetic Map6q14NCBI
CIB4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38226,581,205 - 26,641,366 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl226,581,205 - 26,641,366 (-)Ensemblhg38GRCh38
GRCh37226,804,073 - 26,864,234 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36226,657,577 - 26,717,715 (-)NCBIBuild 36Build 36hg18NCBI36
Celera226,647,704 - 26,707,827 (-)NCBICelera
Cytogenetic Map2p23.3NCBI
HuRef226,543,509 - 26,603,418 (-)NCBIHuRef
CHM1_1226,734,122 - 26,794,199 (-)NCBICHM1_1
T2T-CHM13v2.0226,620,353 - 26,681,744 (-)NCBIT2T-CHM13v2.0
Cib4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39530,642,927 - 30,703,191 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl530,642,927 - 30,703,180 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38530,485,583 - 30,545,845 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl530,485,583 - 30,545,836 (-)Ensemblmm10GRCm38
MGSCv37530,787,957 - 30,848,209 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36530,762,164 - 30,822,417 (-)NCBIMGSCv36mm8
Celera527,963,768 - 28,024,353 (-)NCBICelera
Cytogenetic Map5B1NCBI
cM Map516.59NCBI
Cib4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554698,604,799 - 8,669,916 (-)Ensembl
ChiLan1.0NW_0049554698,604,866 - 8,669,890 (-)NCBIChiLan1.0ChiLan1.0
CIB4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21299,876,073 - 99,936,088 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A99,880,053 - 99,940,041 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A26,578,051 - 26,670,672 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A26,669,870 - 26,729,792 (-)NCBIPanPan1.1PanPan1.1panPan2
CIB4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11720,635,050 - 20,685,775 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1720,635,214 - 20,685,675 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1720,529,315 - 20,579,886 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01720,956,432 - 21,007,233 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1720,956,420 - 21,007,151 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11720,643,373 - 20,694,146 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01720,654,507 - 20,705,263 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01720,700,854 - 20,751,456 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Cib4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629264,945,208 - 64,996,761 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364935,842,964 - 5,894,306 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049364935,805,911 - 5,894,306 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CIB4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3112,406,908 - 112,457,138 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.13112,415,709 - 112,457,253 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23119,405,976 - 119,456,544 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CIB4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl1480,997,393 - 81,057,566 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Cib4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247388,718,687 - 8,771,025 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247388,704,726 - 8,813,441 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Cib4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1723,534,518 - 23,596,702 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Cib4
187 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:33
Count of miRNA genes:33
Interacting mature miRNAs:33
Transcripts:ENSRNOT00000013123
Prediction methods:Miranda, Rnahybrid
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
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6197587946975879Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)62009763565097635Rat
8552910Pigfal5Plasma insulin-like growth factor 1 level QTL 54.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)62265388967653889Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)62009763565097635Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6323998948239989Rat
1331779Rf38Renal function QTL 382.876kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)63118500276185002Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6197587946975879Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6197587946975879Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6144788383Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6197587946975879Rat
2292616Ept15Estrogen-induced pituitary tumorigenesis QTL 154.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)6144788383Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6197587946975879Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62661831486868070Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)620859430113082285Rat
2301964Bp323Blood pressure QTL 3234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6186868070Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6323998948239989Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6323998948239989Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62661831486868070Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6140163351Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)63093763275937632Rat
70199Coreg1Compensatory renal growth QTL 111.8kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)61459947363457687Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)61608937261967788Rat
1358190Ept1Estrogen-induced pituitary tumorigenesis QTL 14.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)6144788383Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6323998948239989Rat
1359023Bp272Blood pressure QTL 2722.5arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)62228825732981219Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)62228825767288257Rat

Markers in Region
D6Got17  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8631,593,412 - 31,593,617 (+)Marker Load Pipeline
mRatBN7.2625,873,516 - 25,873,721 (+)MAPPERmRatBN7.2
Rnor_6.0627,269,817 - 27,270,021NCBIRnor6.0
Rnor_5.0637,086,838 - 37,087,042UniSTSRnor5.0
RGSC_v3.4625,856,187 - 25,856,392RGDRGSC3.4
RGSC_v3.4625,856,188 - 25,856,392UniSTSRGSC3.4
Celera625,353,028 - 25,353,232UniSTS
RGSC_v3.1625,859,141 - 25,859,345RGD
RH 3.4 Map697.9RGD
RH 3.4 Map697.9UniSTS
RH 2.0 Map6210.4RGD
Cytogenetic Map6q14UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
7 2 7 24 30 24 7 6 7 46 27 11 3 31 17

Sequence


Ensembl Acc Id: ENSRNOT00000013123   ⟹   ENSRNOP00000013123
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl631,562,489 - 31,623,464 (+)Ensembl
mRatBN7.2 Ensembl625,842,622 - 25,903,508 (+)Ensembl
Rnor_6.0 Ensembl627,241,919 - 27,303,615 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000095942   ⟹   ENSRNOP00000096540
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl625,842,622 - 25,902,008 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000113134   ⟹   ENSRNOP00000092694
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl625,842,622 - 25,917,206 (+)Ensembl
RefSeq Acc Id: XM_001068424   ⟹   XP_001068424
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8631,560,105 - 31,623,403 (+)NCBI
mRatBN7.2625,842,605 - 25,903,509 (+)NCBI
Rnor_6.0627,241,804 - 27,303,617 (+)NCBI
Rnor_5.0637,058,400 - 37,115,989 (+)NCBI
RGSC_v3.4625,825,158 - 25,887,430 (+)RGD
Sequence:
RefSeq Acc Id: XM_039113093   ⟹   XP_038969021
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8631,560,105 - 31,623,403 (+)NCBI
mRatBN7.2625,842,612 - 25,903,509 (+)NCBI
Protein Sequences
Protein RefSeqs XP_001068424 (Get FASTA)   NCBI Sequence Viewer  
  XP_038969021 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM02988 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000013123
  ENSRNOP00000013123.3
RefSeq Acc Id: XP_001068424   ⟸   XM_001068424
- Peptide Label: isoform X1
- UniProtKB: D3ZX64 (UniProtKB/TrEMBL),   A6HAD3 (UniProtKB/TrEMBL),   A0A8I6B4C8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000013123   ⟸   ENSRNOT00000013123
RefSeq Acc Id: XP_038969021   ⟸   XM_039113093
- Peptide Label: isoform X2
Ensembl Acc Id: ENSRNOP00000096540   ⟸   ENSRNOT00000095942
Ensembl Acc Id: ENSRNOP00000092694   ⟸   ENSRNOT00000113134
Protein Domains
EF-hand

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZX64-F1-model_v2 AlphaFold D3ZX64 1-185 view protein structure

Transcriptome

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

Promoters
RGD ID:13694469
Promoter ID:EPDNEW_R4987
Type:multiple initiation site
Name:Cib4_1
Description:calcium and integrin binding family member 4
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_6.0627,241,928 - 27,241,988EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1584147 AgrOrtholog
BioCyc Gene G2FUF-38311 BioCyc
Ensembl Genes ENSRNOG00000009898 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000013123 ENTREZGENE
  ENSRNOT00000013123.7 UniProtKB/TrEMBL
Gene3D-CATH EF-hand UniProtKB/TrEMBL
InterPro CIBP UniProtKB/TrEMBL
  EF-hand-like_dom UniProtKB/TrEMBL
  EF_Hand_1_Ca_BS UniProtKB/TrEMBL
  EF_hand_Ca-bd UniProtKB/TrEMBL
KEGG Report rno:688819 UniProtKB/TrEMBL
NCBI Gene 688819 ENTREZGENE
PANTHER CALCIUM AND INTEGRIN BINDING FAMILY MEMBER 2 UniProtKB/TrEMBL
  CALCIUM AND INTEGRIN-BINDING FAMILY MEMBER 4 UniProtKB/TrEMBL
Pfam EF_hand_5 UniProtKB/TrEMBL
PhenoGen Cib4 PhenoGen
PROSITE EF_HAND_1 UniProtKB/TrEMBL
  EF_HAND_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000009898 RatGTEx
SMART EFh UniProtKB/TrEMBL
Superfamily-SCOP SSF47473 UniProtKB/TrEMBL
UniProt A0A8I6B4C8 ENTREZGENE
  A6HAD3 ENTREZGENE, UniProtKB/TrEMBL
  D3ZX64 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-05-24 Cib4  calcium and integrin binding family member 4  LOC100365160  rCG61337-like  Data merged from RGD:2319614 1643240 APPROVED
2010-05-05 LOC100365160  rCG61337-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-03-06 Cib4  calcium and integrin binding family member 4  LOC688819  similar to calcium and integrin binding family member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC688819  similar to calcium and integrin binding family member 4  LOC684260  similar to calcium and integrin binding family member 4  Data merged from RGD:1592687 1643240 APPROVED
2006-11-20 LOC684260  similar to calcium and integrin binding family member 4      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC688819  similar to calcium and integrin binding family member 4      Symbol and Name status set to provisional 70820 PROVISIONAL