Zcrb1 (zinc finger CCHC-type and RNA binding motif containing 1) - Rat Genome Database

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Gene: Zcrb1 (zinc finger CCHC-type and RNA binding motif containing 1) Rattus norvegicus
Analyze
Symbol: Zcrb1
Name: zinc finger CCHC-type and RNA binding motif containing 1
RGD ID: 1309851
Description: Predicted to enable RNA binding activity and zinc ion binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be located in nucleoplasm. Predicted to be part of U12-type spliceosomal complex. Orthologous to human ZCRB1 (zinc finger CCHC-type and RNA binding motif containing 1); INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC362990; MGC124878; RGD1309851; similar to MADP-1 protein; U11/U12 small nuclear ribonucleoprotein 31 kDa protein; U11/U12 snRNP 31 kDa protein; zinc finger CCHC-type and RNA binding motif 1; zinc finger CCHC-type and RNA-binding motif-containing protein 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87126,404,675 - 126,418,012 (-)NCBIGRCr8
mRatBN7.27124,525,227 - 124,538,564 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7124,524,870 - 124,571,261 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7126,300,190 - 126,313,312 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07128,526,061 - 128,539,183 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07128,447,361 - 128,460,725 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.07134,588,902 - 134,602,239 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7134,588,903 - 134,602,239 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07134,255,942 - 134,269,279 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47131,852,634 - 131,865,971 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.17131,929,540 - 131,943,889 (-)NCBI
Celera7120,923,040 - 120,935,959 (-)NCBICelera
Cytogenetic Map7q35NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

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. 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:12477932   PMID:15146077   PMID:15489334   PMID:22658674   PMID:22681889  


Genomics

Comparative Map Data
Zcrb1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87126,404,675 - 126,418,012 (-)NCBIGRCr8
mRatBN7.27124,525,227 - 124,538,564 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7124,524,870 - 124,571,261 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7126,300,190 - 126,313,312 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07128,526,061 - 128,539,183 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07128,447,361 - 128,460,725 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.07134,588,902 - 134,602,239 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7134,588,903 - 134,602,239 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07134,255,942 - 134,269,279 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47131,852,634 - 131,865,971 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.17131,929,540 - 131,943,889 (-)NCBI
Celera7120,923,040 - 120,935,959 (-)NCBICelera
Cytogenetic Map7q35NCBI
ZCRB1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381242,312,086 - 42,326,094 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1242,312,086 - 42,326,257 (-)EnsemblGRCh38hg38GRCh38
GRCh371242,705,888 - 42,719,896 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361240,992,155 - 41,006,199 (-)NCBINCBI36Build 36hg18NCBI36
Celera1241,507,709 - 41,521,753 (-)NCBICelera
Cytogenetic Map12q12NCBI
HuRef1239,732,766 - 39,746,809 (-)NCBIHuRef
CHM1_11242,672,498 - 42,686,541 (-)NCBICHM1_1
T2T-CHM13v2.01242,270,020 - 42,284,029 (-)NCBIT2T-CHM13v2.0
Zcrb1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391593,283,987 - 93,296,218 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1593,283,978 - 93,296,215 (-)EnsemblGRCm39 Ensembl
GRCm381593,386,106 - 93,398,341 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1593,386,097 - 93,398,334 (-)EnsemblGRCm38mm10GRCm38
MGSCv371593,216,544 - 93,228,721 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361593,214,293 - 93,226,470 (-)NCBIMGSCv36mm8
Celera1595,530,863 - 95,543,026 (-)NCBICelera
Cytogenetic Map15E3NCBI
cM Map1547.53NCBI
Zcrb1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555001,684,562 - 1,782,905 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555001,684,003 - 1,784,075 (-)NCBIChiLan1.0ChiLan1.0
ZCRB1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21051,834,397 - 51,847,687 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11251,831,071 - 51,844,447 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01246,392,094 - 46,405,453 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11247,256,625 - 47,270,388 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1247,256,625 - 47,271,832 (+)Ensemblpanpan1.1panPan2
ZCRB1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12711,590,152 - 11,605,079 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2711,590,332 - 11,604,986 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2734,698,316 - 34,713,224 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02711,786,482 - 11,801,404 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2711,786,520 - 11,801,387 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12711,604,795 - 11,619,702 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02711,628,882 - 11,643,802 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02734,943,879 - 34,959,060 (-)NCBIUU_Cfam_GSD_1.0
Zcrb1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494572,107,398 - 72,119,942 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049365121,044,899 - 1,057,497 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ZCRB1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl573,538,985 - 73,556,233 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1573,538,982 - 73,556,240 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2576,457,402 - 76,468,361 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ZCRB1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11138,547,928 - 38,563,803 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1138,547,881 - 38,564,522 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037207,999,230 - 208,015,185 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:65
Count of miRNA genes:56
Interacting mature miRNAs:61
Transcripts:ENSRNOT00000006780
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
631529Tls2T-lymphoma susceptibility QTL 200.001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)782111382132099989Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7121393075137014596Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)798549867137014596Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7119280025135560836Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7104186212135371468Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)793302009131686183Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7110725024135371468Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)7100548246137014596Rat
61397Bw17Body weight QTL 176.3body mass (VT:0001259)body weight (CMO:0000012)795485047137014596Rat
1331746Kidm9Kidney mass QTL 93.934kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)782111245134948181Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7115313999136544683Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)7116269196132020414Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)746307490127866166Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)785043242130043242Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)785497398130497398Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)792362341137014596Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)771827901136544683Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)783626689128626689Rat


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
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000006780   ⟹   ENSRNOP00000006780
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7124,524,870 - 124,538,571 (-)Ensembl
Rnor_6.0 Ensembl7134,588,903 - 134,602,239 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000094501   ⟹   ENSRNOP00000087642
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7124,525,228 - 124,571,261 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000111421   ⟹   ENSRNOP00000082475
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7124,524,870 - 124,537,480 (-)Ensembl
RefSeq Acc Id: NM_001034940   ⟹   NP_001030112
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87126,404,675 - 126,418,012 (-)NCBI
mRatBN7.27124,525,227 - 124,538,564 (-)NCBI
Rnor_6.07134,588,902 - 134,602,239 (-)NCBI
Rnor_5.07134,255,942 - 134,269,279 (-)NCBI
RGSC_v3.47131,852,634 - 131,865,971 (-)RGD
Celera7120,923,040 - 120,935,959 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001030112 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH99747 (Get FASTA)   NCBI Sequence Viewer  
  EDL76624 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000006780.6
  ENSRNOP00000082475.1
  ENSRNOP00000087642.1
GenBank Protein Q499V6 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001030112   ⟸   NM_001034940
- UniProtKB: Q499V6 (UniProtKB/Swiss-Prot),   A6K7T1 (UniProtKB/TrEMBL),   A0A8I6A866 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000006780   ⟸   ENSRNOT00000006780
Ensembl Acc Id: ENSRNOP00000087642   ⟸   ENSRNOT00000094501
Ensembl Acc Id: ENSRNOP00000082475   ⟸   ENSRNOT00000111421
Protein Domains
CCHC-type   RRM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q499V6-F1-model_v2 AlphaFold Q499V6 1-217 view protein structure

Transcriptome

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

Promoters
RGD ID:13695602
Promoter ID:EPDNEW_R6127
Type:initiation region
Name:Zcrb1_1
Description:zinc finger CCHC-type and RNA binding motif containing 1
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_6.07134,602,274 - 134,602,334EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309851 AgrOrtholog
BioCyc Gene G2FUF-32337 BioCyc
Ensembl Genes ENSRNOG00000004996 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006780.6 UniProtKB/TrEMBL
  ENSRNOT00000094501.1 UniProtKB/TrEMBL
  ENSRNOT00000111421.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.330 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Zinc finger, CCHC-type UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:5598773 IMAGE-MGC_LOAD
InterPro Nucleotide-bd_a/b_plait_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RRM_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RRM_dom_euk UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZCRB1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZCRB1_RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_CCHC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_CCHC_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:362990 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:124878 IMAGE-MGC_LOAD
NCBI Gene 362990 ENTREZGENE
PANTHER PTHR46259 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZINC FINGER CCHC-TYPE AND RNA-BINDING MOTIF-CONTAINING PROTEIN 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam RRM_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-CCHC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Zcrb1 PhenoGen
PROSITE RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_CCHC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000004996 RatGTEx
SMART RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RRM_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZnF_C2HC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF54928 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF57756 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I5ZVC7_RAT UniProtKB/TrEMBL
  A0A8I6A866 ENTREZGENE, UniProtKB/TrEMBL
  A0A8L2Q3N7_RAT UniProtKB/TrEMBL
  A6K7T1 ENTREZGENE, UniProtKB/TrEMBL
  Q499V6 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Zcrb1  zinc finger CCHC-type and RNA binding motif containing 1  Zcrb1  zinc finger CCHC-type and RNA binding motif 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Zcrb1  zinc finger CCHC-type and RNA binding motif 1  RGD1309851  similar to MADP-1 protein  Symbol and Name updated 1299863 APPROVED
2005-12-06 RGD1309851  similar to MADP-1 protein  RGD1309851_predicted  similar to MADP-1 protein (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1309851_predicted  similar to MADP-1 protein (predicted)  LOC362990_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC362990_predicted  similar to MADP-1 protein (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL