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 enable ubiquitin protein ligase activity. Predicted to be involved in protein ubiquitination; random inactivation of X chromosome; and ubiquitin-dependent protein catabolic process. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in Tonne-Kalscheuer syndrome. 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
Previously known as: E3 ubiquitin-protein ligase RLIM; ring finger protein 12; ring finger protein, LIM domain interacting-like 1; Rliml1; Rnf12
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X73,048,983 - 73,070,302 (-)NCBIGRCr8
mRatBN7.2X68,983,259 - 69,004,368 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX68,988,375 - 69,004,271 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX70,497,482 - 70,513,377 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X73,997,771 - 74,013,666 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X71,558,959 - 71,574,855 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X73,757,664 - 73,778,763 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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_5.0X75,641,176 - 75,662,560 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X91,969,453 - 91,985,349 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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

Biological Process

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

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:10431247   PMID:11882901   PMID:16204183   PMID:19028597   PMID:19945382   PMID:24613346   PMID:30988473  


Genomics

Comparative Map Data
Rlim
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X73,048,983 - 73,070,302 (-)NCBIGRCr8
mRatBN7.2X68,983,259 - 69,004,368 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX68,988,375 - 69,004,271 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX70,497,482 - 70,513,377 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X73,997,771 - 74,013,666 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X71,558,959 - 71,574,855 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X73,757,664 - 73,778,763 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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_5.0X75,641,176 - 75,662,560 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X91,969,453 - 91,985,349 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX70,345,584 - 70,361,477 (-)NCBICelera
Cytogenetic MapXq22NCBI
RLIM
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X74,582,976 - 74,614,624 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX74,582,976 - 74,614,624 (-)EnsemblGRCh38hg38GRCh38
GRCh37X73,802,811 - 73,834,459 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X73,726,765 - 73,751,168 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X73,593,066 - 73,617,464NCBI
CeleraX74,086,277 - 74,117,928 (-)NCBICelera
Cytogenetic MapXq13.2NCBI
HuRefX67,437,612 - 67,469,342 (-)NCBIHuRef
CHM1_1X73,695,686 - 73,727,336 (-)NCBICHM1_1
T2T-CHM13v2.0X73,016,616 - 73,048,268 (-)NCBIT2T-CHM13v2.0
Rlim
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X103,000,770 - 103,024,886 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX103,000,769 - 103,024,890 (-)EnsemblGRCm39 Ensembl
GRCm38X103,957,163 - 103,981,296 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX103,957,163 - 103,981,284 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X101,152,506 - 101,176,623 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X100,159,886 - 100,184,003 (-)NCBIMGSCv36mm8
CeleraX90,856,674 - 90,880,735 (-)NCBICelera
Cytogenetic MapXDNCBI
cM MapX46.42NCBI
Rlim
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955562510,739 - 531,830 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955562508,723 - 531,699 (-)NCBIChiLan1.0ChiLan1.0
RLIM
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X74,266,972 - 74,296,319 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X74,270,836 - 74,299,929 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X63,834,345 - 63,865,874 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X73,952,928 - 73,982,412 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX73,959,365 - 73,982,412 (-)Ensemblpanpan1.1panPan2
RLIM
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X57,879,749 - 57,905,805 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX57,885,123 - 57,889,253 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX49,058,848 - 49,084,812 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X59,093,206 - 59,119,165 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX59,093,226 - 59,118,999 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X56,838,049 - 56,864,001 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X58,417,151 - 58,443,102 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X58,024,547 - 58,050,513 (-)NCBIUU_Cfam_GSD_1.0
Rlim
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X43,985,980 - 44,017,247 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936683934,338 - 961,863 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936683930,537 - 961,792 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0

Variants

.
Variants in Rlim
20 total Variants
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.


QTLs in Region (mRatBN7.2)
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)X14843113120568734Rat
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)X41052407146860749Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat

Markers in Region
RH143323  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X68,989,814 - 68,989,926 (+)MAPPERmRatBN7.2
Rnor_6.0X74,844,715 - 74,844,826NCBIRnor6.0
Rnor_6.0X73,764,220 - 73,764,331NCBIRnor6.0
Rnor_5.0X74,569,172 - 74,569,283UniSTSRnor5.0
Rnor_5.0X75,647,732 - 75,647,843UniSTSRnor5.0
RGSC_v3.4X91,970,895 - 91,971,006UniSTSRGSC3.4
CeleraX70,347,026 - 70,347,137UniSTS
Cytogenetic MapXq31UniSTS


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: ENSRNOT00000003782   ⟹   ENSRNOP00000003782
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX68,988,375 - 69,004,271 (-)Ensembl
Rnor_6.0 EnsemblX73,762,778 - 73,778,674 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000067009   ⟹   ENSRNOP00000059093
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX74,843,186 - 74,847,379 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000075926   ⟹   ENSRNOP00000068204
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX73,764,136 - 73,778,614 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076081   ⟹   ENSRNOP00000068504
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX73,765,565 - 73,778,595 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091325   ⟹   ENSRNOP00000072115
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX73,762,691 - 73,766,885 (-)Ensembl
RefSeq Acc Id: NM_001024892   ⟹   NP_001020063
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X73,054,096 - 73,069,992 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X73,048,983 - 73,070,231 (-)NCBI
mRatBN7.2X68,983,259 - 69,004,368 (-)NCBI
Rnor_6.0X73,757,664 - 73,778,763 (-)NCBI
Sequence:
RefSeq Acc Id: XM_063280026   ⟹   XP_063136096
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X73,048,983 - 73,070,228 (-)NCBI
RefSeq Acc Id: XM_063280027   ⟹   XP_063136097
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X73,048,983 - 73,070,231 (-)NCBI
RefSeq Acc Id: XM_063280028   ⟹   XP_063136098
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X73,048,983 - 73,070,302 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001020063   ⟸   NM_001024892
- UniProtKB: Q4V889 (UniProtKB/TrEMBL),   D4A8S6 (UniProtKB/TrEMBL),   F7EY25 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257203   ⟸   XM_006257141
- Peptide Label: isoform X1
- UniProtKB: Q4V889 (UniProtKB/TrEMBL),   D4A8S6 (UniProtKB/TrEMBL),   F7EY25 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000068204   ⟸   ENSRNOT00000075926
RefSeq Acc Id: ENSRNOP00000003782   ⟸   ENSRNOT00000003782
RefSeq Acc Id: ENSRNOP00000068504   ⟸   ENSRNOT00000076081
RefSeq Acc Id: ENSRNOP00000059093   ⟸   ENSRNOT00000067009
RefSeq Acc Id: ENSRNOP00000072115   ⟸   ENSRNOT00000091325
RefSeq Acc Id: XP_063136098   ⟸   XM_063280028
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063136097   ⟸   XM_063280027
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063136096   ⟸   XM_063280026
- Peptide Label: isoform X1
Protein Domains
RING-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q4V889-F1-model_v2 AlphaFold Q4V889 1-603 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1559832 AgrOrtholog
BioCyc Gene G2FUF-2001 BioCyc
Ensembl Genes ENSRNOG00000002824 Ensembl
  ENSRNOG00000045695 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003782 ENTREZGENE
  ENSRNOT00000003782.8 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:317241 UniProtKB/TrEMBL
MGC_CLONE MGC:114563 IMAGE-MGC_LOAD
NCBI Gene 317241 ENTREZGENE
PANTHER E3 UBIQUITIN-PROTEIN LIGASE RLIM UniProtKB/TrEMBL
  SI:CH211-59O9.10 UniProtKB/TrEMBL
Pfam zf-RING_2 UniProtKB/TrEMBL
PhenoGen Rlim PhenoGen
PROSITE ZF_RING_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000002824 RatGTEx
  ENSRNOG00000045695 RatGTEx
SMART RING UniProtKB/TrEMBL
Superfamily-SCOP RING/U-box UniProtKB/TrEMBL
UniProt D4A8S6 ENTREZGENE
  F7EY25 ENTREZGENE, 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
2022-04-18 Rlim  ring finger protein, LIM domain interacting  Rliml1  ring finger protein, LIM domain interacting-like 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2021-11-05 Rliml1  ring finger protein, LIM domain interacting-like 1  Rlim  ring finger protein, LIM domain interacting  Name and Symbol changed 629549 APPROVED
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