Rlim ring finger protein, LIM domain interacting [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Rlimprovided by MGI
Official Full Name: ring finger protein, LIM domain interactingprovided by MGI
Primary source: MGI:MGI:1342291
See related: Ensembl:ENSMUSG00000056537 AllianceGenome:MGI:1342291
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Ha1r; Rlim1; Rnf12
Summary: Enables ubiquitin protein ligase activity. Involved in protein ubiquitination; random inactivation of X chromosome; and ubiquitin-dependent protein catabolic process. Acts upstream of or within negative regulation of DNA-binding transcription factor activity; negative regulation of transcription by RNA polymerase II; and regulation of dosage compensation by inactivation of X chromosome. Located in nucleus. Is expressed in several structures, including extraembryonic component; limb; liver; male reproductive system; and urinary system. Human ortholog(s) of this gene implicated in Tonne-Kalscheuer syndrome. Orthologous to human RLIM (ring finger protein, LIM domain interacting). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in placenta adult (RPKM 25.8), CNS E11.5 (RPKM 7.6) and 20 other tissues See more
Orthologs: human all
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Genomic context

Location:: X 46.42 cM; X D

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	X	NC_000086.8 (103000770..103024886, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	X	NC_000086.7 (103957163..103981296, complement)

Chromosome X - NC_000086.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Roles of the Rlim-Rex1 axis during X chromosome inactivation in mice.
Title: Roles of the Rlim-Rex1 axis during X chromosome inactivation in mice.
An RNF12-USP26 amplification loop drives germ cell specification and is disrupted by disease-associated mutations.
Title: An RNF12-USP26 amplification loop drives germ cell specification and is disrupted by disease-associated mutations.
These data uncover a key function for RNF12 E3 ubiquitin ligase activity in stem cell and neural development.
Title: RNF12 X-Linked Intellectual Disability Mutations Disrupt E3 Ligase Activity and Neural Differentiation.
RNF12 targets pluripotency protein REX1 for degradation to initiate random X chromosome inactivation in embryonic stem cells.
Title: REX1 is the critical target of RNF12 in imprinted X chromosome inactivation in mice.
the existence of Rlim-dependent and Rlim-independent pathways for random X chromosome inactivation in differentiating female embryonic stem cells.
Title: Rlim-Dependent and -Independent Pathways for X Chromosome Inactivation in Female ESCs.
These findings show that control of Lhx2 function by Ldb1 and Rnf12 underpins the coordinated differentiation of neurons and Muller glia in postnatal retina.
Title: Ldb1- and Rnf12-dependent regulation of Lhx2 controls the relative balance between neurogenesis and gliogenesis in the retina.
These results reveal crucial roles of Rlim for the maintenance of high Xist RNA levels, Xist clouds and X-silencing in female embryos at blastocyst stages, while initial Xist expression appears Rlim-independent.
Title: Regulation of X-linked gene expression during early mouse development by Rlim.
In late preimplantation, Oct4 served as a chromatin opener to create transcriptional permissive states at Xm-Xist/Tsix genomic loci. In parthenogenetic embryos, Rnf12 overdose caused Xm-Xist derepression via Xm-Tsix repression; physiological Rnf12 levels were essential for Xm-Xist silencing maintenance in fertilized embryos.
Title: Maintenance of Xist Imprinting Depends on Chromatin Condensation State and Rnf12 Dosage in Mice.
high RNF12 levels may contribute to the specific activation of maternal Xist in XpDeltaXist female ROSI embryos, but upregulation of additional Xp derived factors and/or the specific epigenetic constitution of the round spermatid-derived Xp are expected to be more critical
Title: Round Spermatid Injection Rescues Female Lethality of a Paternally Inherited Xist Deletion in Mouse.
results provide evidence that RLIM is dispensable for rXCI, indicating that in mice an RLIM-independent mechanism activates Xist in the embryo proper
Title: RLIM is dispensable for X-chromosome inactivation in the mouse embryonic epiblast.

Submit: New GeneRIF Correction See all GeneRIFs (17)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Gene trapped (1)
Targeted (2) 1 citation
Endonuclease-mediated (5)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transferase activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin protein ligase activity	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin-protein transferase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within negative regulation of DNA-binding transcription factor activity	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
involved_in protein ubiquitination	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in random inactivation of X chromosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in random inactivation of X chromosome	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within random inactivation of X chromosome	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within random inactivation of X chromosome	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in random inactivation of X chromosome	ISO Inferred from Sequence Orthology more info
involved_in ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in ubiquitin-dependent protein catabolic process	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: E3 ubiquitin-protein ligase RLIM

Names: Hoxa1 regulated; LIM domain-interacting RING finger protein; RING finger LIM domain-binding protein; RING-type E3 ubiquitin transferase RLIM; ring finger protein 12

NP_001345134.1

EC 2.3.2.27

NP_001412889.1

EC 2.3.2.27

NP_001412890.1

EC 2.3.2.27

NP_001412891.1

EC 2.3.2.27

NP_001412892.1

EC 2.3.2.27

NP_001412893.1

EC 2.3.2.27

NP_001412894.1

EC 2.3.2.27

NP_001412895.1

EC 2.3.2.27

NP_035406.3

EC 2.3.2.27

XP_006527981.1

EC 2.3.2.27

XP_006527983.1

EC 2.3.2.27

XP_006527984.1

EC 2.3.2.27

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001358205.2 → NP_001345134.1 E3 ubiquitin-protein ligase RLIM

Status: VALIDATED

Source sequence(s)

AL805911

Consensus CDS

CCDS30331.1

UniProtKB/Swiss-Prot

Q8CE02, Q91X19, Q9CYY2, Q9WTV7

Related

ENSMUSP00000070662.5, ENSMUST00000070705.6

Conserved Domains (1) summary

cl17238
Location:544 → 588

RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
NM_001425960.1 → NP_001412889.1 E3 ubiquitin-protein ligase RLIM

Status: VALIDATED

Source sequence(s)

AL805911

UniProtKB/Swiss-Prot

Q8CE02, Q91X19, Q9CYY2, Q9WTV7
NM_001425961.1 → NP_001412890.1 E3 ubiquitin-protein ligase RLIM

Status: VALIDATED

Source sequence(s)

AL805911

UniProtKB/Swiss-Prot

Q8CE02, Q91X19, Q9CYY2, Q9WTV7
NM_001425962.1 → NP_001412891.1 E3 ubiquitin-protein ligase RLIM

Status: VALIDATED

Source sequence(s)

AL805911

UniProtKB/Swiss-Prot

Q8CE02, Q91X19, Q9CYY2, Q9WTV7
NM_001425963.1 → NP_001412892.1 E3 ubiquitin-protein ligase RLIM

Status: VALIDATED

Source sequence(s)

AL805911

UniProtKB/Swiss-Prot

Q8CE02, Q91X19, Q9CYY2, Q9WTV7
NM_001425964.1 → NP_001412893.1 E3 ubiquitin-protein ligase RLIM

Status: VALIDATED

Source sequence(s)

AL805911

UniProtKB/Swiss-Prot

Q8CE02, Q91X19, Q9CYY2, Q9WTV7
NM_001425965.1 → NP_001412894.1 E3 ubiquitin-protein ligase RLIM

Status: VALIDATED

Source sequence(s)

AL805911

UniProtKB/Swiss-Prot

Q8CE02, Q91X19, Q9CYY2, Q9WTV7
NM_001425966.1 → NP_001412895.1 E3 ubiquitin-protein ligase RLIM

Status: VALIDATED

Source sequence(s)

AL805911

UniProtKB/Swiss-Prot

Q8CE02, Q91X19, Q9CYY2, Q9WTV7
NM_011276.5 → NP_035406.3 E3 ubiquitin-protein ligase RLIM

See identical proteins and their annotated locations for NP_035406.3

Status: VALIDATED

Source sequence(s)

AL805911

Consensus CDS

CCDS30331.1

UniProtKB/Swiss-Prot

Q8CE02, Q91X19, Q9CYY2, Q9WTV7

Related

ENSMUSP00000112820.2, ENSMUST00000121153.8

Conserved Domains (1) summary

cl17238
Location:544 → 588

RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000086.8 Reference GRCm39 C57BL/6J

Range

103000770..103024886 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006527918.5 → XP_006527981.1 E3 ubiquitin-protein ligase RLIM isoform X1

See identical proteins and their annotated locations for XP_006527981.1

UniProtKB/Swiss-Prot

Q8CE02, Q91X19, Q9CYY2, Q9WTV7

Conserved Domains (1) summary

cl17238
Location:544 → 588

RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
XM_006527921.5 → XP_006527984.1 E3 ubiquitin-protein ligase RLIM isoform X1

See identical proteins and their annotated locations for XP_006527984.1

UniProtKB/Swiss-Prot

Q8CE02, Q91X19, Q9CYY2, Q9WTV7

Conserved Domains (1) summary

cl17238
Location:544 → 588

RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
XM_006527920.4 → XP_006527983.1 E3 ubiquitin-protein ligase RLIM isoform X1

See identical proteins and their annotated locations for XP_006527983.1

UniProtKB/Swiss-Prot

Q8CE02, Q91X19, Q9CYY2, Q9WTV7

Conserved Domains (1) summary

cl17238
Location:544 → 588

RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain