Rlim (ring finger protein, LIM domain interacting) - Rat Genome Database
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Gene: Rlim (ring finger protein, LIM domain interacting) Rattus norvegicus
Analyze
Symbol: Rlim
Name: ring finger protein, LIM domain interacting
RGD ID: 1559832
Description: Predicted to have ubiquitin protein ligase activity. Predicted to be involved in cellular protein metabolic process and regulation of gene expression. Predicted to localize to cytosol and nucleoplasm. Orthologous to human RLIM (ring finger protein, LIM domain interacting); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: E3 ubiquitin-protein ligase RLIM; ring finger protein 12; Rnf12
RGD Orthologs
Human
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
NCBI Annotation Information: Note: GeneIDs: 317241 and 100910646 are annotated independently on Rnor_6.0 but may be redundant loci. [17 Feb 2015]
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X68,983,259 - 69,004,368 (-)NCBI
Rnor_6.0 EnsemblX74,843,186 - 74,847,379 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 EnsemblX73,762,691 - 73,778,674 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X73,757,664 - 73,778,763 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X75,641,176 - 75,662,560 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X91,969,453 - 91,985,349 (-)NCBIRGSC3.4rn4RGSC3.4
CeleraX70,345,584 - 70,361,477 (-)NCBICelera
Cytogenetic MapXq22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IBA)
cytosol  (ISO)
nucleoplasm  (IBA,ISO)

Molecular Function

References

Additional References at PubMed
PMID:19028597   PMID:19945382   PMID:30988473  


Genomics

Comparative Map Data
Rlim
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X68,983,259 - 69,004,368 (-)NCBI
Rnor_6.0 EnsemblX74,843,186 - 74,847,379 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 EnsemblX73,762,691 - 73,778,674 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X73,757,664 - 73,778,763 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X75,641,176 - 75,662,560 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X91,969,453 - 91,985,349 (-)NCBIRGSC3.4rn4RGSC3.4
CeleraX70,345,584 - 70,361,477 (-)NCBICelera
Cytogenetic MapXq22NCBI
RLIM
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX74,582,976 - 74,614,624 (-)EnsemblGRCh38hg38GRCh38
GRCh38X74,582,976 - 74,614,624 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X73,802,811 - 73,834,459 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh37X73,802,811 - 73,834,461 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X73,726,765 - 73,751,168 (-)NCBINCBI36hg18NCBI36
Build 34X73,593,066 - 73,617,464NCBI
CeleraX74,086,277 - 74,117,928 (-)NCBI
Cytogenetic MapXq13.2NCBI
HuRefX67,437,612 - 67,469,342 (-)NCBIHuRef
CHM1_1X73,695,686 - 73,727,336 (-)NCBICHM1_1
RLIM
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX59,893,146 - 59,920,182 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X59,889,799 - 59,920,464 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X67,848,216 - 67,878,753 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RLIM
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X64,178,159 - 64,205,759 (-)NCBI
Rlim
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248366,257,740 - 6,290,054 (+)NCBI

Position Markers
RH143323  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X73,764,220 - 73,764,331NCBIRnor6.0
Rnor_6.0X74,844,715 - 74,844,826NCBIRnor6.0
Rnor_5.0X75,647,732 - 75,647,843UniSTSRnor5.0
Rnor_5.0X74,569,172 - 74,569,283UniSTSRnor5.0
RGSC_v3.4X91,970,895 - 91,971,006UniSTSRGSC3.4
CeleraX70,347,026 - 70,347,137UniSTS
Cytogenetic MapXq31UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X15688119127888215Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X44320616158345622Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX44557974120045269Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X70352120127888215Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:171
Count of miRNA genes:120
Interacting mature miRNAs:129
Transcripts:ENSRNOT00000003782, ENSRNOT00000067009
Prediction methods:Microtar, Miranda, Pita, 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.


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
Low 1 23 34 18 18 18 1 1 70 21 41 11 1
Below cutoff 2 20 23 23 1 23 7 9 4 13 7

Sequence


Reference Sequences
RefSeq Acc Id: NM_001024892   ⟹   NP_001020063
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X68,988,373 - 69,004,271 (-)NCBI
Rnor_6.0X73,762,778 - 73,778,674 (-)NCBI
Rnor_5.0X75,641,176 - 75,662,560 (-)NCBI
RGSC_v3.4X91,969,453 - 91,985,349 (-)RGD
CeleraX70,345,584 - 70,361,477 (-)RGD
Sequence:
RefSeq Acc Id: XM_006257141   ⟹   XP_006257203
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X68,983,259 - 69,004,368 (-)NCBI
Rnor_6.0X73,757,664 - 73,778,763 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017602050   ⟹   XP_017457539
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X73,757,664 - 73,778,542 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017602051   ⟹   XP_017457540
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X73,757,664 - 73,775,066 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017602052   ⟹   XP_017457541
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X73,757,664 - 73,768,885 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001020063 (Get FASTA)   NCBI Sequence Viewer  
  XP_006257203 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH97491 (Get FASTA)   NCBI Sequence Viewer  
  EDM07168 (Get FASTA)   NCBI Sequence Viewer  
  EDM07169 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001020063   ⟸   NM_001024892
- UniProtKB: Q4V889 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257203   ⟸   XM_006257141
- Peptide Label: isoform X1
- UniProtKB: Q4V889 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457539   ⟸   XM_017602050
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457540   ⟸   XM_017602051
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457541   ⟸   XM_017602052
- Peptide Label: isoform X1
- Sequence:
Protein Domains
RING-type

Transcriptome

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

Promoters
RGD ID:13701891
Promoter ID:EPDNEW_R12412
Type:multiple initiation site
Name:Rlim_1
Description:ring finger protein, LIM domain interacting
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_6.0X73,778,751 - 73,778,811EPDNEW

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)
Visual CSV TAB Printer
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)
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
F344/NRrrc (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
FHH/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)
FHH/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
FHL/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)
FHL/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
GH/OmrMcwi (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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
MHS/Gib (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
MNS/Gib (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
MR/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
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/Ygl (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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/NHsd (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
SHRSP/Gcrc (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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WKY/Gcrc (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
WKY/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
WKY/NCrl (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
WKY/NHsd (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
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1559832 AgrOrtholog
Ensembl Genes ENSRNOG00000002824 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000045695 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000003782 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000059093 UniProtKB/TrEMBL
  ENSRNOP00000068204 UniProtKB/TrEMBL
  ENSRNOP00000068504 UniProtKB/TrEMBL
  ENSRNOP00000072115 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003782 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000067009 UniProtKB/TrEMBL
  ENSRNOT00000075926 UniProtKB/TrEMBL
  ENSRNOT00000076081 UniProtKB/TrEMBL
  ENSRNOT00000091325 UniProtKB/TrEMBL
Gene3D-CATH 3.30.40.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7461011 IMAGE-MGC_LOAD
InterPro Znf_RING UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
KEGG Report rno:108348168 UniProtKB/TrEMBL
  rno:317241 UniProtKB/TrEMBL
MGC_CLONE MGC:114563 IMAGE-MGC_LOAD
NCBI Gene 317241 ENTREZGENE
Pfam zf-RING_2 UniProtKB/TrEMBL
PhenoGen Rlim PhenoGen
PROSITE ZF_RING_2 UniProtKB/TrEMBL
SMART RING UniProtKB/TrEMBL
UniProt A0A096MJN9_RAT UniProtKB/TrEMBL
  A0A096MKG3_RAT UniProtKB/TrEMBL
  Q4V889 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary D4A8S6 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-05-25 Rlim  ring finger protein, LIM domain interacting  Rnf12  ring finger protein 12  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Rnf12  ring finger protein 12      Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 Rnf12  ring finger protein 12      Symbol and Name status set to provisional 70820 PROVISIONAL