Zcchc2 (zinc finger CCHC-type containing 2) - Rat Genome Database
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Gene: Zcchc2 (zinc finger CCHC-type containing 2) Rattus norvegicus
Analyze
Symbol: Zcchc2
Name: zinc finger CCHC-type containing 2
RGD ID: 1310626
Description: Predicted to have nucleic acid binding activity; phosphatidylinositol binding activity; and zinc ion binding activity. Predicted to localize to cytoplasm. Orthologous to human ZCCHC2 (zinc finger CCHC-type containing 2); INTERACTS WITH acetamide; flutamide; vinclozolin.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC304695; MGC112793; Tnfrsf11a; tumor necrosis factor receptor superfamily, member 11a; zinc finger CCHC domain-containing protein 2; zinc finger, CCHC domain containing 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21322,118,677 - 22,193,626 (+)NCBI
Rnor_6.0 Ensembl1325,966,428 - 26,013,338 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01325,961,762 - 26,052,472 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01331,122,293 - 31,210,284 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41312,148,072 - 12,196,570 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11312,148,071 - 12,196,570 (+)NCBI
Celera1321,988,903 - 22,034,139 (+)NCBICelera
Cytogenetic Map13p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IEA,ISO)

Molecular Function

References

Additional References at PubMed
PMID:12477932  


Genomics

Comparative Map Data
Zcchc2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21322,118,677 - 22,193,626 (+)NCBI
Rnor_6.0 Ensembl1325,966,428 - 26,013,338 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01325,961,762 - 26,052,472 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01331,122,293 - 31,210,284 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41312,148,072 - 12,196,570 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11312,148,071 - 12,196,570 (+)NCBI
Celera1321,988,903 - 22,034,139 (+)NCBICelera
Cytogenetic Map13p11NCBI
ZCCHC2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1862,523,025 - 62,587,709 (+)EnsemblGRCh38hg38GRCh38
GRCh381862,523,025 - 62,587,709 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371860,190,258 - 60,253,962 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh371860,190,658 - 60,254,942 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361858,357,894 - 58,396,798 (+)NCBINCBI36hg18NCBI36
Build 341858,357,893 - 58,396,796NCBI
Celera1856,910,014 - 56,965,120 (+)NCBI
Cytogenetic Map18q21.33NCBI
HuRef1856,901,978 - 56,956,933 (+)NCBIHuRef
CHM1_11860,186,189 - 60,248,511 (+)NCBICHM1_1
Zcchc2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391105,916,929 - 105,961,807 (+)NCBIGRCm39mm39
GRCm381105,990,390 - 106,034,077 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1105,990,406 - 106,034,074 (+)EnsemblGRCm38mm10GRCm38
MGSCv371107,886,983 - 107,930,654 (+)NCBIGRCm37mm9NCBIm37
MGSCv361107,817,953 - 107,861,621 (+)NCBImm8
Celera1108,839,603 - 108,883,221 (+)NCBICelera
Cytogenetic Map1E2.1NCBI
Zcchc2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540246,426,432 - 46,464,063 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540246,426,432 - 46,466,064 (+)NCBIChiLan1.0ChiLan1.0
ZCCHC2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11859,210,876 - 59,265,634 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1859,209,993 - 59,265,634 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01855,893,099 - 55,948,648 (+)NCBIMhudiblu_PPA_v0panPan3
ZCCHC2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl114,337,065 - 14,393,158 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1114,335,727 - 14,393,157 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Zcchc2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364972,785,508 - 2,844,181 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ZCCHC2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1158,962,511 - 159,022,072 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11158,964,816 - 159,022,143 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21176,374,309 - 176,412,878 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ZCCHC2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11817,186,456 - 17,244,639 (-)NCBI
ChlSab1.1 Ensembl1817,177,964 - 17,244,574 (-)Ensembl
Zcchc2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247928,239,931 - 8,298,508 (+)NCBI

Position Markers
RH137338  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01325,965,698 - 25,965,894NCBIRnor6.0
Rnor_5.01331,126,197 - 31,126,393UniSTSRnor5.0
RGSC_v3.41312,147,342 - 12,147,538UniSTSRGSC3.4
Celera1321,988,173 - 21,988,369UniSTS
Cytogenetic Map13p13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2317027Aia22Adjuvant induced arthritis QTL 222.29joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)13136779181Rat
738036Lnnr4Liver neoplastic nodule remodeling QTL 43.64liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)13147622148Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131107975663Rat
631672Iddm12Insulin dependent diabetes mellitus QTL 122.20.0032blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)13901674239373058Rat
61339Bp24Blood pressure QTL 240.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)13901674250513953Rat
1581554Pur11Proteinuria QTL 11urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13901690682995569Rat
1581573Uae36Urinary albumin excretion QTL 36urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13901690682995569Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1312193394108478121Rat
9589141Insul28Insulin level QTL 2810.820.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)131409633059096330Rat
7411662Foco29Food consumption QTL 2920.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)131409633059096330Rat
2303031Bp326Blood pressure QTL 326arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131427908126919398Rat
2317034Aia9Adjuvant induced arthritis QTL 94.62joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)131427908137124697Rat
2317044Aia23Adjuvant induced arthritis QTL 232.3joint integrity trait (VT:0010548)ankle joint diameter (CMO:0002148)131427908137124697Rat
1300163Cardf1Cardiac cell morphology QTL 14.18aorta morphology trait (VT:0000272)artery lesion measurement (CMO:0000975)131444158250799665Rat
2302275Gluco37Glucose level QTL 373.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)131444158251577031Rat
2317040Aia21Adjuvant induced arthritis QTL 212.75joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)131462463159624631Rat
2317046Aia8Adjuvant induced arthritis QTL 83.9700000286102295joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)131462463159624631Rat
631645Bp121Blood pressure QTL 1213.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131981081464810814Rat
9589164Gluco66Glucose level QTL 666.670.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)132005247765052477Rat
1331784Bp222Blood pressure QTL 2222.944arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)132148248158537177Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1324502279108770533Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:563
Count of miRNA genes:266
Interacting mature miRNAs:336
Transcripts:ENSRNOT00000003870, ENSRNOT00000061814
Prediction methods:Microtar, Miranda, 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.


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 1 25 9 19 9 34 17 33 11
Low 2 43 32 32 32 8 11 40 18 8 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001122677 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001271042 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006249626 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090658 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090659 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090660 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090661 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090662 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090663 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090664 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090665 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090666 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090667 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001840776 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005492235 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005492236 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005492237 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC100090 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000242 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000003870   ⟹   ENSRNOP00000003870
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1325,966,428 - 26,013,338 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000061814   ⟹   ENSRNOP00000058528
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1325,966,428 - 26,000,768 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000086167   ⟹   ENSRNOP00000075165
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1325,966,810 - 26,011,355 (+)Ensembl
RefSeq Acc Id: NM_001122677   ⟹   NP_001116149
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21322,119,568 - 22,166,397 (+)NCBI
Rnor_6.01325,966,428 - 26,013,338 (+)NCBI
Rnor_5.01331,122,293 - 31,210,284 (+)NCBI
RGSC_v3.41312,148,072 - 12,196,570 (+)RGD
Celera1321,988,903 - 22,034,139 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001271042   ⟹   NP_001257971
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21322,119,568 - 22,153,909 (+)NCBI
Rnor_6.01325,966,428 - 26,000,769 (+)NCBI
Rnor_5.01331,122,293 - 31,210,284 (+)NCBI
Celera1321,988,903 - 22,023,239 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006249625   ⟹   XP_006249687
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01325,961,762 - 26,011,909 (+)NCBI
Rnor_5.01331,122,293 - 31,210,284 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006249626   ⟹   XP_006249688
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21322,118,677 - 22,166,397 (+)NCBI
Rnor_6.01325,961,762 - 26,014,926 (+)NCBI
Rnor_5.01331,122,293 - 31,210,284 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006249627   ⟹   XP_006249689
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01325,967,010 - 26,011,909 (+)NCBI
Rnor_5.01331,122,293 - 31,210,284 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006249628   ⟹   XP_006249690
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01325,967,010 - 26,011,909 (+)NCBI
Rnor_5.01331,122,293 - 31,210,284 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598783   ⟹   XP_017454272
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01325,961,762 - 26,026,271 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039090658   ⟹   XP_038946586
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21322,118,677 - 22,193,626 (+)NCBI
RefSeq Acc Id: XM_039090659   ⟹   XP_038946587
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21322,118,677 - 22,166,397 (+)NCBI
RefSeq Acc Id: XM_039090660   ⟹   XP_038946588
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21322,118,677 - 22,166,397 (+)NCBI
RefSeq Acc Id: XM_039090661   ⟹   XP_038946589
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21322,118,677 - 22,166,397 (+)NCBI
RefSeq Acc Id: XM_039090662   ⟹   XP_038946590
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21322,147,756 - 22,166,397 (+)NCBI
RefSeq Acc Id: XM_039090663   ⟹   XP_038946591
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21322,143,416 - 22,166,397 (+)NCBI
RefSeq Acc Id: XM_039090664   ⟹   XP_038946592
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21322,152,659 - 22,166,397 (+)NCBI
RefSeq Acc Id: XM_039090665   ⟹   XP_038946593
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21322,118,677 - 22,162,139 (+)NCBI
RefSeq Acc Id: XM_039090666   ⟹   XP_038946594
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21322,118,677 - 22,153,314 (+)NCBI
RefSeq Acc Id: XM_039090667   ⟹   XP_038946595
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21322,118,677 - 22,162,139 (+)NCBI
RefSeq Acc Id: XR_001840776
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21322,118,677 - 22,193,626 (+)NCBI
Rnor_6.01325,961,762 - 26,052,472 (+)NCBI
Sequence:
RefSeq Acc Id: XR_005492235
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21322,118,677 - 22,162,110 (+)NCBI
RefSeq Acc Id: XR_005492236
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21322,118,677 - 22,159,756 (+)NCBI
RefSeq Acc Id: XR_005492237
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21322,118,677 - 22,162,103 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001116149   ⟸   NM_001122677
- Peptide Label: isoform 1
- UniProtKB: A0A0H2UHB2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001257971   ⟸   NM_001271042
- Peptide Label: isoform 2
- UniProtKB: Q498S6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006249688   ⟸   XM_006249626
- Peptide Label: isoform X1
- UniProtKB: Q498S6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006249687   ⟸   XM_006249625
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006249690   ⟸   XM_006249628
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006249689   ⟸   XM_006249627
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017454272   ⟸   XM_017598783
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000058528   ⟸   ENSRNOT00000061814
RefSeq Acc Id: ENSRNOP00000003870   ⟸   ENSRNOT00000003870
RefSeq Acc Id: ENSRNOP00000075165   ⟸   ENSRNOT00000086167
RefSeq Acc Id: XP_038946586   ⟸   XM_039090658
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038946589   ⟸   XM_039090661
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038946588   ⟸   XM_039090660
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038946587   ⟸   XM_039090659
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038946593   ⟸   XM_039090665
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038946595   ⟸   XM_039090667
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038946594   ⟸   XM_039090666
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038946591   ⟸   XM_039090663
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038946590   ⟸   XM_039090662
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038946592   ⟸   XM_039090664
- Peptide Label: isoform X7
Protein Domains
CCHC-type

Transcriptome

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

Promoters
RGD ID:13698747
Promoter ID:EPDNEW_R9272
Type:multiple initiation site
Name:Zcchc2_1
Description:zinc finger CCHC-type containing 2
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_6.01325,966,466 - 25,966,526EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310626 AgrOrtholog
Ensembl Genes ENSRNOG00000002882 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000003870 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000058528 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000075165 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000003870 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000061814 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000086167 UniProtKB/Swiss-Prot
Gene3D-CATH 3.30.1520.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro PX_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZCCHC2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_CCHC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_CCHC_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:304695 UniProtKB/Swiss-Prot
NCBI Gene 304695 ENTREZGENE
PANTHER PTHR46939 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam zf-CCHC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Zcchc2 PhenoGen
PROSITE ZF_CCHC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART ZnF_C2HC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF57756 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF64268 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0H2UHB2 ENTREZGENE, UniProtKB/TrEMBL
  Q498S6 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Zcchc2  zinc finger CCHC-type containing 2  Zcchc2  zinc finger, CCHC domain containing 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-04 Zcchc2  zinc finger, CCHC domain containing 2  Tnfrsf11a  tumor necrosis factor receptor superfamily, member 11a  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Tnfrsf11a  tumor necrosis factor receptor superfamily, member 11a  Tnfrsf11a_predicted  tumor necrosis factor receptor superfamily, member 11a (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Tnfrsf11a_predicted  tumor necrosis factor receptor superfamily, member 11a (predicted)      Symbol and Name status set to approved 70820 APPROVED