Human Gene RLIM (ENST00000332687.11_7) from GENCODE V47lift37
  Description: ring finger protein, LIM domain interacting, transcript variant 1 (from RefSeq NM_016120.4)
Gencode Transcript: ENST00000332687.11_7
Gencode Gene: ENSG00000131263.13_9
Transcript (Including UTRs)
   Position: hg19 chrX:73,802,811-73,834,459 Size: 31,649 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chrX:73,811,275-73,815,812 Size: 4,538 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:73,802,811-73,834,459)mRNA (may differ from genome)Protein (624 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RNF12_HUMAN
DESCRIPTION: RecName: Full=E3 ubiquitin-protein ligase RLIM; EC=6.3.2.-; AltName: Full=LIM domain-interacting RING finger protein; AltName: Full=RING finger LIM domain-binding protein; Short=R-LIM; AltName: Full=RING finger protein 12; AltName: Full=Renal carcinoma antigen NY-REN-43;
FUNCTION: E3 ubiquitin-protein ligase. Acts as a negative coregulator for LIM homeodomain transcription factors by mediating the ubiquitination and subsequent degradation of LIM cofactors LDB1 and LDB2 and by mediating the recruitment the SIN3a/histone deacetylase corepressor complex. Ubiquitination and degradation of LIM cofactors LDB1 and LDB2 allows DNA-bound LIM homeodomain transcription factors to interact with other protein partners such as RLIM. Plays a role in telomere length-mediated growth suppression by mediating the ubiquitination and degradation of TERF1. By targeting ZFP42 for degradation, acts as an activator of random inactivation of X chromosome in the embryo, a stochastic process in which one X chromosome is inactivated to minimize sex- related dosage differences of X-encoded genes in somatic cells of female placental mammals.
PATHWAY: Protein modification; protein ubiquitination.
SUBUNIT: Interacts with LIM/homeobox factors such as LHX3. Interacts with LDB1, LDB2 and SIN3A (By similarity). Interacts with LIMK1 (By similarity). Interacts (via N-terminus) with TERF1. Interacts (via C-terminus) with ESR1.
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Expressed in many tissues.
MISCELLANEOUS: Acts as a positive coregulator of ESR1-mediated transcription in breast cancer cells.
SIMILARITY: Belongs to the RNF12 family.
SIMILARITY: Contains 1 RING-type zinc finger.
SEQUENCE CAUTION: Sequence=AAD42875.1; Type=Frameshift; Positions=134, 142;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: RLIM
Diseases sorted by gene-association score: mental retardation, x-linked 61* (1230), x-linked non-specific intellectual disability* (350), syndromic x-linked intellectual disability (13)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 9.80 RPKM in Pituitary
Total median expression: 331.60 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -89.50226-0.396 Picture PostScript Text
3' UTR -2378.008464-0.281 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001841 - Znf_RING
IPR013083 - Znf_RING/FYVE/PHD

Pfam Domains:
PF00097 - Zinc finger, C3HC4 type (RING finger)
PF12678 - RING-H2 zinc finger domain
PF12861 - Anaphase-promoting complex subunit 11 RING-H2 finger
PF13639 - Ring finger domain
PF13923 - Zinc finger, C3HC4 type (RING finger)
PF17123 - RING-like zinc finger

SCOP Domains:
57850 - RING/U-box
57903 - FYVE/PHD zinc finger

ModBase Predicted Comparative 3D Structure on Q9NVW2
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003714 transcription corepressor activity
GO:0004842 ubiquitin-protein transferase activity
GO:0016740 transferase activity
GO:0046872 metal ion binding
GO:0061630 ubiquitin protein ligase activity

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0000209 protein polyubiquitination
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0016567 protein ubiquitination
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0043433 negative regulation of sequence-specific DNA binding transcription factor activity
GO:0045892 negative regulation of transcription, DNA-templated
GO:0060816 random inactivation of X chromosome
GO:1900095 regulation of dosage compensation by inactivation of X chromosome

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005829 cytosol
GO:0017053 transcriptional repressor complex


-  Descriptions from all associated GenBank mRNAs
  AK127880 - Homo sapiens cDNA FLJ45986 fis, clone PUAEN2000594.
DQ584635 - Homo sapiens piRNA piR-51747, complete sequence.
JD135566 - Sequence 116590 from Patent EP1572962.
JD165738 - Sequence 146762 from Patent EP1572962.
JD384741 - Sequence 365765 from Patent EP1572962.
JD396146 - Sequence 377170 from Patent EP1572962.
JD426708 - Sequence 407732 from Patent EP1572962.
JD255951 - Sequence 236975 from Patent EP1572962.
JD488997 - Sequence 470021 from Patent EP1572962.
JD488996 - Sequence 470020 from Patent EP1572962.
JD409250 - Sequence 390274 from Patent EP1572962.
BX648613 - Homo sapiens mRNA; cDNA DKFZp686N06224 (from clone DKFZp686N06224).
AK124877 - Homo sapiens cDNA FLJ42887 fis, clone BRHIP3007834.
AK098789 - Homo sapiens cDNA FLJ25923 fis, clone CBR05077.
AK123088 - Homo sapiens cDNA FLJ41093 fis, clone ASTRO2005423.
JD071444 - Sequence 52468 from Patent EP1572962.
JD535553 - Sequence 516577 from Patent EP1572962.
JD463282 - Sequence 444306 from Patent EP1572962.
JD035116 - Sequence 16140 from Patent EP1572962.
JD152351 - Sequence 133375 from Patent EP1572962.
JD562773 - Sequence 543797 from Patent EP1572962.
JD566071 - Sequence 547095 from Patent EP1572962.
JD155370 - Sequence 136394 from Patent EP1572962.
JD166122 - Sequence 147146 from Patent EP1572962.
JD280974 - Sequence 261998 from Patent EP1572962.
JD101309 - Sequence 82333 from Patent EP1572962.
JD107529 - Sequence 88553 from Patent EP1572962.
JD505763 - Sequence 486787 from Patent EP1572962.
JD476979 - Sequence 458003 from Patent EP1572962.
JD256639 - Sequence 237663 from Patent EP1572962.
JD256640 - Sequence 237664 from Patent EP1572962.
JD333190 - Sequence 314214 from Patent EP1572962.
JD242826 - Sequence 223850 from Patent EP1572962.
JD333189 - Sequence 314213 from Patent EP1572962.
JD364164 - Sequence 345188 from Patent EP1572962.
JD418652 - Sequence 399676 from Patent EP1572962.
JD132782 - Sequence 113806 from Patent EP1572962.
JD514197 - Sequence 495221 from Patent EP1572962.
JD514195 - Sequence 495219 from Patent EP1572962.
JD514196 - Sequence 495220 from Patent EP1572962.
AF086467 - Homo sapiens full length insert cDNA clone ZD86G12.
AF155109 - Homo sapiens putative ring zinc finger protein NY-REN-43 antigen mRNA, complete cds.
BC013357 - Homo sapiens ring finger protein, LIM domain interacting, mRNA (cDNA clone MGC:15161 IMAGE:3834870), complete cds.
AK001334 - Homo sapiens cDNA FLJ10472 fis, clone NT2RP2000054.
JD113977 - Sequence 95001 from Patent EP1572962.
JD074054 - Sequence 55078 from Patent EP1572962.
JD437321 - Sequence 418345 from Patent EP1572962.
JD280681 - Sequence 261705 from Patent EP1572962.
AK314760 - Homo sapiens cDNA, FLJ95628, Homo sapiens ring finger protein 12 (RNF12), mRNA.
DQ893500 - Synthetic construct clone IMAGE:100006130; FLH194883.01X; RZPDo839G0180D ring finger protein 12 (RNF12) gene, encodes complete protein.
KJ893830 - Synthetic construct Homo sapiens clone ccsbBroadEn_03224 RLIM gene, encodes complete protein.
DQ896498 - Synthetic construct Homo sapiens clone IMAGE:100010958; FLH194879.01L; RZPDo839G0170D ring finger protein 12 (RNF12) gene, encodes complete protein.
AB587388 - Synthetic construct DNA, clone: pF1KB5545, Homo sapiens RNF12 gene for ring finger protein, LIM domain interacting, without stop codon, in Flexi system.
BC002451 - Homo sapiens ring finger protein 12, mRNA (cDNA clone IMAGE:3343080), **** WARNING: chimeric clone ****.
CU680578 - Synthetic construct Homo sapiens gateway clone IMAGE:100019958 5' read RNF12 mRNA.
JD329958 - Sequence 310982 from Patent EP1572962.
JD083021 - Sequence 64045 from Patent EP1572962.
JD266758 - Sequence 247782 from Patent EP1572962.
JD172526 - Sequence 153550 from Patent EP1572962.
JD468625 - Sequence 449649 from Patent EP1572962.
JD263636 - Sequence 244660 from Patent EP1572962.
JD139596 - Sequence 120620 from Patent EP1572962.
JD336421 - Sequence 317445 from Patent EP1572962.
JD081147 - Sequence 62171 from Patent EP1572962.
JD228957 - Sequence 209981 from Patent EP1572962.
JD231811 - Sequence 212835 from Patent EP1572962.
JD258153 - Sequence 239177 from Patent EP1572962.
JD251153 - Sequence 232177 from Patent EP1572962.
JD288813 - Sequence 269837 from Patent EP1572962.
JD407296 - Sequence 388320 from Patent EP1572962.
JD462649 - Sequence 443673 from Patent EP1572962.
JD430851 - Sequence 411875 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9NVW2 (Reactome details) participates in the following event(s):

R-HSA-983157 Interaction of E3 with substrate and E2-Ub complex
R-HSA-983147 Release of E3 from polyubiquitinated substrate
R-HSA-983140 Transfer of Ub from E2 to substrate and release of E2
R-HSA-983168 Antigen processing: Ubiquitination & Proteasome degradation
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-1280218 Adaptive Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: B2RBQ1, D3DTE0, ENST00000332687.1, ENST00000332687.10, ENST00000332687.2, ENST00000332687.3, ENST00000332687.4, ENST00000332687.5, ENST00000332687.6, ENST00000332687.7, ENST00000332687.8, ENST00000332687.9, NM_016120, Q96D38, Q9NVW2, Q9Y598, RNF12, RNF12_HUMAN, uc317tmp.1, uc317tmp.2
UCSC ID: ENST00000332687.11_7
RefSeq Accession: NM_016120.4
Protein: Q9NVW2 (aka RNF12_HUMAN or RN12_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene RLIM:
cdh-ov (Congenital Diaphragmatic Hernia Overview)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.