Zc3h12a (zinc finger CCCH type containing 12A) - Rat Genome Database
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Gene: Zc3h12a (zinc finger CCCH type containing 12A) Rattus norvegicus
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Symbol: Zc3h12a
Name: zinc finger CCCH type containing 12A
RGD ID: 1306776
Description: Predicted to contribute to thiol-dependent ubiquitin-specific protease activity. Predicted to be involved in several processes, including cellular response to cytokine stimulus; negative regulation of gene expression; and positive regulation of cellular metabolic process. Predicted to localize to several cellular components, including P-body; endoplasmic reticulum; and nucleoplasm. Orthologous to human ZC3H12A (zinc finger CCCH-type containing 12A); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: bifunctional endoribonuclease and deubiquitinase ZC3H12A; endoribonuclease ZC3H12A; LOC313587; MCP-induced protein 1; MCPIP-1; MGC156729; monocyte chemotactic protein-induced protein 1; Reg1; regnase-1; RGD1306776; ribonuclease ZC3H12A; similar to hypothetical protein MGC41320; Zinc finger CCCH domain-containing protein 12A
Orthologs:
Homo sapiens (human) : ZC3H12A (zinc finger CCCH-type containing 12A)  HGNC  Alliance
Mus musculus (house mouse) : Zc3h12a (zinc finger CCCH type containing 12A)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Zc3h12a (zinc finger CCCH-type containing 12A)
Pan paniscus (bonobo/pygmy chimpanzee) : ZC3H12A (zinc finger CCCH-type containing 12A)
Canis lupus familiaris (dog) : ZC3H12A (zinc finger CCCH-type containing 12A)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Zc3h12a (zinc finger CCCH-type containing 12A)
Sus scrofa (pig) : ZC3H12A (zinc finger CCCH-type containing 12A)
Chlorocebus sabaeus (African green monkey) : ZC3H12A (zinc finger CCCH-type containing 12A)
Heterocephalus glaber (naked mole-rat) : Zc3h12a (zinc finger CCCH-type containing 12A)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.05143,111,342 - 143,120,131 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5143,111,074 - 143,120,165 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05146,878,968 - 146,887,760 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45144,457,753 - 144,467,275 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15144,468,090 - 144,476,486 (-)NCBI
Celera5135,894,447 - 135,903,150 (-)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
3'-UTR-mediated mRNA destabilization  (IBA,ISO,ISS)
angiogenesis  (IEA)
apoptotic process  (IEA)
cell differentiation  (IEA)
cellular response to chemokine  (ISO,ISS)
cellular response to DNA damage stimulus  (ISO,ISS)
cellular response to glucose starvation  (ISO)
cellular response to interleukin-1  (ISO)
cellular response to ionomycin  (ISO,ISS)
cellular response to lipopolysaccharide  (ISO,ISS)
cellular response to oxidative stress  (ISO)
cellular response to sodium arsenite  (ISO)
cellular response to tumor necrosis factor  (ISO,ISS)
cellular response to virus  (ISO)
immune response-activating signal transduction  (ISO,ISS)
inflammatory response  (IEA)
negative regulation by host of viral genome replication  (ISO)
negative regulation of cardiac muscle contraction  (ISO,ISS)
negative regulation of cytokine production involved in inflammatory response  (ISO,ISS)
negative regulation of gene expression  (ISO)
negative regulation of I-kappaB kinase/NF-kappaB signaling  (ISO,ISS)
negative regulation of interferon-gamma production  (ISO,ISS)
negative regulation of interleukin-1 beta production  (ISO,ISS)
negative regulation of interleukin-6 production  (ISO,ISS)
negative regulation of muscle cell apoptotic process  (ISO,ISS)
negative regulation of NF-kappaB transcription factor activity  (ISO)
negative regulation of NIK/NF-kappaB signaling  (ISO,ISS)
negative regulation of nitric oxide biosynthetic process  (ISO,ISS)
negative regulation of production of miRNAs involved in gene silencing by miRNA  (ISO,ISS)
negative regulation of protein phosphorylation  (ISO)
negative regulation of T-helper 17 cell differentiation  (ISO,ISS)
negative regulation of tumor necrosis factor production  (ISO,ISS)
nervous system development  (IEA)
nuclear-transcribed mRNA catabolic process, endonucleolytic cleavage-dependent decay  (IBA,ISO)
positive regulation of angiogenesis  (ISO,ISS)
positive regulation of autophagy  (ISO)
positive regulation of cell death  (ISO,ISS)
positive regulation of defense response to virus by host  (ISO)
positive regulation of endothelial cell migration  (ISO,ISS)
positive regulation of execution phase of apoptosis  (ISO)
positive regulation of fat cell differentiation  (ISO,ISS)
positive regulation of gene expression  (ISO)
positive regulation of lipid storage  (ISO)
positive regulation of miRNA catabolic process  (ISO,ISS)
positive regulation of mRNA catabolic process  (ISO,ISS)
positive regulation of p38MAPK cascade  (ISO)
positive regulation of protein deubiquitination  (ISO,ISS)
positive regulation of protein import into nucleus  (ISO)
positive regulation of reactive oxygen species metabolic process  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO,ISS)
protein complex oligomerization  (ISO,ISS)
protein deubiquitination  (ISO)
regulation of gene expression  (ISO)
RNA phosphodiester bond hydrolysis  (ISO,ISS)
RNA phosphodiester bond hydrolysis, endonucleolytic  (IBA,ISO,ISS)
RNA phosphodiester bond hydrolysis, exonucleolytic  (IEA)
T cell receptor signaling pathway  (ISO,ISS)

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:12477932   PMID:15489334   PMID:16574901   PMID:18178554   PMID:18364357   PMID:19322177   PMID:19666473   PMID:19909337   PMID:20356868   PMID:21616078   PMID:21971051   PMID:22055188  
PMID:22739135   PMID:23185455   PMID:23355615   PMID:24048733   PMID:25282160   PMID:25861989   PMID:26000482   PMID:26134560   PMID:26255671   PMID:26812136   PMID:26865670   PMID:27044405  
PMID:30631045   PMID:31323531  


Genomics

Comparative Map Data
Zc3h12a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.05143,111,342 - 143,120,131 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5143,111,074 - 143,120,165 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05146,878,968 - 146,887,760 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45144,457,753 - 144,467,275 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15144,468,090 - 144,476,486 (-)NCBI
Celera5135,894,447 - 135,903,150 (-)NCBICelera
Cytogenetic Map5q36NCBI
ZC3H12A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl137,474,580 - 37,484,377 (+)EnsemblGRCh38hg38GRCh38
GRCh38137,474,518 - 37,484,377 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37137,940,119 - 37,949,978 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36137,712,706 - 37,722,565 (+)NCBINCBI36hg18NCBI36
Celera136,218,067 - 36,227,926 (+)NCBI
Cytogenetic Map1p34.3NCBI
HuRef136,057,283 - 36,067,022 (+)NCBIHuRef
CHM1_1138,056,246 - 38,066,105 (+)NCBICHM1_1
Zc3h12a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394125,012,207 - 125,021,674 (-)NCBI
GRCm384125,118,414 - 125,127,881 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4125,118,423 - 125,127,840 (-)EnsemblGRCm38mm10GRCm38
MGSCv374124,795,658 - 124,805,125 (-)NCBIGRCm37mm9NCBIm37
MGSCv364124,620,727 - 124,630,144 (-)NCBImm8
Celera4123,439,822 - 123,449,288 (-)NCBICelera
Cytogenetic Map4D2.2NCBI
Zc3h12a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545215,305,775 - 15,314,959 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545215,306,398 - 15,314,959 (+)NCBIChiLan1.0ChiLan1.0
ZC3H12A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1138,093,036 - 38,103,556 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl138,093,917 - 38,103,556 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0136,743,341 - 36,753,261 (+)NCBIMhudiblu_PPA_v0panPan3
ZC3H12A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl154,972,956 - 4,980,371 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1154,972,369 - 4,984,218 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Zc3h12a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493647419,714,145 - 19,722,512 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ZC3H12A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl693,541,334 - 93,551,195 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1693,541,334 - 93,551,200 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
ZC3H12A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl2095,388,477 - 95,397,960 (-)Ensembl
ChlSab1.12095,388,469 - 95,398,305 (-)NCBI
Zc3h12a
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476420,224,919 - 20,234,108 (+)NCBI

Position Markers
BE101710  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.05143,106,201 - 143,106,356NCBIRnor6.0
Rnor_5.05146,873,830 - 146,873,985UniSTSRnor5.0
RGSC_v3.45144,452,612 - 144,452,767UniSTSRGSC3.4
Celera5135,889,306 - 135,889,461UniSTS
Cytogenetic Map5q36UniSTS
RH 3.4 Map5897.4UniSTS
RH135324  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.05143,112,688 - 143,112,887NCBIRnor6.0
Rnor_5.05146,880,317 - 146,880,516UniSTSRnor5.0
RGSC_v3.45144,459,099 - 144,459,298UniSTSRGSC3.4
Celera5135,895,793 - 135,895,992UniSTS
Cytogenetic Map5q36UniSTS
RH 3.4 Map5897.4UniSTS
RH141495  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.05143,102,824 - 143,103,029NCBIRnor6.0
Rnor_5.05146,870,453 - 146,870,658UniSTSRnor5.0
RGSC_v3.45144,449,235 - 144,449,440UniSTSRGSC3.4
Cytogenetic Map5q36UniSTS
RH 3.4 Map5891.0UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535788756147487820Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540777918154732375Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)547745646167946134Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)551418671147487820Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)561086525149030144Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)561612600168109659Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)571552569157225114Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)584963058173504662Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)597921932149030144Rat
1331796Thshl2Thyroid stimulating hormone level QTL 22.3blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)5100723739153577831Rat
1358187Emca1Estrogen-induced mammary cancer QTL 14.4mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)5102945579154732228Rat
1578673Bmd13Bone mineral density QTL 134.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)5107119214152119214Rat
2317056Wbc3White blood cell count QTL 32.510.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)5111278451156278451Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5112279412157279412Rat
7207481Bss106Bone structure and strength QTL 1067.9femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5112279412157279412Rat
7207486Bss109Bone structure and strength QTL 109femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)5112279412157279412Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5112279412157279412Rat
7207491Bss112Bone structure and strength QTL 1127femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)5112279412157279412Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5114140832159140832Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5114140832159140832Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5116767924161767924Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5116767924161767924Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5116767924161767924Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5116767924161767924Rat
1581510Cm54Cardiac mass QTL 543.40.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)5125455818149568944Rat
2293642Bss37Bone structure and strength QTL 374.640.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5125455818157225114Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5128687766173687766Rat
1300122Wbc1White blood cell count QTL 12.75leukocyte quantity (VT:0000217)total white blood cell count (CMO:0000365)5130531300145726262Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5131077716173707219Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5132551937173707219Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5133943857173707219Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5133943857173707219Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5134197905173707219Rat
1331803Rf32Renal function QTL 322.798kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)5134502121149030144Rat
70156Niddm30Non-insulin dependent diabetes mellitus QTL 303.98blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)5134502140157212422Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5134712342173707219Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5134712342173707219Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5136354114173707219Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5136640731173707219Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5138154677172402610Rat
7411722Strs6Sensitivity to stroke QTL 63.9cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)5140387005143846157Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5142307322173707219Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5142309061173707219Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:215
Count of miRNA genes:144
Interacting mature miRNAs:157
Transcripts:ENSRNOT00000012314
Prediction methods:Microtar, 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.


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 3 7 1
Low 43 57 41 12 41 8 11 71 35 34 11 8
Below cutoff 3 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000012314   ⟹   ENSRNOP00000012314
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl5143,111,074 - 143,120,165 (-)Ensembl
RefSeq Acc Id: NM_001077671   ⟹   NP_001071139
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05143,111,342 - 143,120,131 (-)NCBI
Rnor_5.05146,878,968 - 146,887,760 (-)NCBI
RGSC_v3.45144,457,753 - 144,467,275 (-)RGD
Celera5135,894,447 - 135,903,150 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001071139 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein A0JPN4 (Get FASTA)   NCBI Sequence Viewer  
  AAI27517 (Get FASTA)   NCBI Sequence Viewer  
  EDL80428 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001071139   ⟸   NM_001077671
- UniProtKB: A0JPN4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000012314   ⟸   ENSRNOT00000012314

Transcriptome

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

Promoters
RGD ID:13694024
Promoter ID:EPDNEW_R4548
Type:initiation region
Name:Zc3h12a_1
Description:zinc finger CCCH type containing 12A
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_6.05143,120,138 - 143,120,198EPDNEW

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)
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
Buf/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
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:1306776 AgrOrtholog
Ensembl Genes ENSRNOG00000009131 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000012314 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000012314 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7102954 IMAGE-MGC_LOAD
InterPro Rege-1_UBA-like UniProtKB/Swiss-Prot
  Regnase_1/ZC3H12_C UniProtKB/Swiss-Prot
  RNase_Zc3h12_NYN UniProtKB/Swiss-Prot
KEGG Report rno:313587 UniProtKB/Swiss-Prot
MGC_CLONE MGC:156729 IMAGE-MGC_LOAD
NCBI Gene 313587 ENTREZGENE
Pfam Regnase_1_C UniProtKB/Swiss-Prot
  RNase_Zc3h12a UniProtKB/Swiss-Prot
  UBA_6 UniProtKB/Swiss-Prot
PhenoGen Zc3h12a PhenoGen
UniGene Rn.234344 ENTREZGENE
UniProt A0JPN4 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Zc3h12a  zinc finger CCCH type containing 12A   Zc3h12a_predicted  zinc finger CCCH type containing 12A (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Zc3h12a_predicted  zinc finger CCCH type containing 12A (predicted)  RGD1306776_predicted  similar to hypothetical protein MGC41320 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1306776_predicted  similar to hypothetical protein MGC41320 (predicted)  LOC313587_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC313587_predicted  similar to hypothetical protein MGC41320 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL