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. Predicted to act upstream of or within spermatogenesis. 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: VALIDATED
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 (+)EnsemblRnor_6.0 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:




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

Molecular Function
calcium ion binding  (IBA,IEA,ISO)
magnesium ion binding  (IBA,IEA,ISO)

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 (+)EnsemblRnor_6.0 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 Ensembl226,579,428 - 26,641,366 (-)EnsemblGRCh38.p14 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 Ensembl530,642,290 - 30,703,196 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38530,485,583 - 30,545,845 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl530,485,583 - 30,545,836 (-)EnsemblGRCm38.p6 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 (-)EnsemblChiLan1.0 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 (-)EnsemblCanFam3.1 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
mIctTri1.hap112101,064,439 - 101,174,219 (+)NCBImIctTri1.hap1
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 (+)EnsemblSscrofa11.1 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
mChlSab1.0.hap11426,257,567 - 26,318,107 (-)NCBImChlSab1.0.hap1
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 1.0NW_0046247388,704,726 - 8,813,441 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
HetGla_female_1.0 EnsemblNW_0046247388,718,687 - 8,771,025 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
Naked mole-rat maternal Ensembl4119,379,310 - 119,480,894 (-)Ensembl
Cib4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1723,534,518 - 23,596,702 (+)NCBIRrattus_CSIRO_v1Rrattus_CSIRO_v1

Variants

.
Variants in Cib4
335 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

adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
entire extraembryonic component
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
pharyngeal arch
renal system
reproductive system
respiratory system
sensory system
visual system
30 12 3 62 144 46 227 12 13 21 13 2 176 143 5 130 4 47 208 220 11 11

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 NP_001433865 (Get FASTA)   NCBI Sequence Viewer  
  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)
- 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 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 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