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Rnf138 ring finger protein 138 [ Mus musculus (house mouse) ]

Gene ID: 56515, updated on 5-Mar-2024

Summary

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Official Symbol
Rnf138provided by MGI
Official Full Name
ring finger protein 138provided by MGI
Primary source
MGI:MGI:1929211
See related
Ensembl:ENSMUSG00000024317 AllianceGenome:MGI:1929211
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
Trif; STRIN; Trif-d; 2410015A17Rik; 2810480D20Rik
Summary
Predicted to enable protein kinase binding activity; single-stranded DNA binding activity; and ubiquitin protein ligase activity. Acts upstream of or within cellular response to leukemia inhibitory factor. Predicted to be located in chromosome. Predicted to be active in site of double-strand break. Is expressed in several structures, including genitourinary system; lung; nervous system; sensory organ; and tooth. Orthologous to human RNF138 (ring finger protein 138). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in testis adult (RPKM 61.8), CNS E18 (RPKM 6.3) and 6 other tissues See more
Orthologs
human all
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Genomic context

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Location:
18 A2; 18 11.73 cM
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 18 NC_000084.7 (21134202..21161281)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 18 NC_000084.6 (21001245..21028224)

Chromosome 18 - NC_000084.7Genomic Context describing neighboring genes Neighboring gene trafficking protein particle complex 8 Neighboring gene STARR-positive B cell enhancer ABC_E11655 Neighboring gene STARR-seq mESC enhancer starr_43995 Neighboring gene STARR-seq mESC enhancer starr_43996 Neighboring gene CapStarr-seq enhancer MGSCv37_chr18:21115655-21115838 Neighboring gene STARR-seq mESC enhancer starr_43997 Neighboring gene ring finger protein 125 Neighboring gene STARR-positive B cell enhancer ABC_E3224 Neighboring gene STARR-seq mESC enhancer starr_43999 Neighboring gene STARR-seq mESC enhancer starr_44001 Neighboring gene STARR-seq mESC enhancer starr_44006 Neighboring gene STARR-seq mESC enhancer starr_44007 Neighboring gene ribosomal protein L27A pseudogene Neighboring gene meprin 1 beta Neighboring gene GRB2 associated regulator of MAPK1 subtype 1 Neighboring gene STARR-seq mESC enhancer starr_44011

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. RNF138 inhibits late inflammatory gene transcription through degradation of SMARCC1 of the SWI/SNF complex. Liu W, et al. Cell Rep, 2023 Feb 28. PMID 36800290
  2. Rnf138 deficiency promotes apoptosis of spermatogonia in juvenile male mice. Xu L, et al. Cell Death Dis, 2017 May 18. PMID 28518149, Free PMC Article
  3. RING finger 138 deregulation distorts NF-кB signaling and facilities colitis switch to aggressive malignancy. Lu Y, et al. Signal Transduct Target Ther, 2022 Jun 13. PMID 35697692, Free PMC Article
  4. RNF138 interacts with RAD51D and is required for DNA interstrand crosslink repair and maintaining chromosome integrity. Yard BD, et al. DNA Repair (Amst), 2016 Jun. PMID 27161866, Free PMC Article
  5. TBX1 is required for normal stria vascularis and semicircular canal development. Tian C, et al. Dev Biol, 2020 Jan 1. PMID 31550482, Free PMC Article

See all (30) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. E3 ubiquitin-ligase RNF138 may regulate p53 protein expression to regulate the self-renewal and tumorigenicity of glioma stem cells.
    Title: E3 ubiquitin-ligase RNF138 may regulate p53 protein expression to regulate the self-renewal and tumorigenicity of glioma stem cells.
  2. RING finger 138 deregulation distorts NF-small ka, CyrillicB signaling and facilities colitis switch to aggressive malignancy.
    Title: RING finger 138 deregulation distorts NF-кB signaling and facilities colitis switch to aggressive malignancy.
  3. Rnf138 deficiency promotes the apoptosis of spermatogenic cells.
    Title: Rnf138 deficiency promotes apoptosis of spermatogonia in juvenile male mice.
Submit: New GeneRIF Correction

Variation

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Alleles

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein kinase binding ISO
Inferred from Sequence Orthology
more info
  
enables single-stranded DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables single-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
  
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 ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within DNA damage response IEA
Inferred from Electronic Annotation
more info
  
involved_in DNA double-strand break processing involved in repair via single-strand annealing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in DNA double-strand break processing involved in repair via single-strand annealing ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within DNA repair IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within cellular response to leukemia inhibitory factor IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in double-strand break repair via homologous recombination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in double-strand break repair via homologous recombination ISO
Inferred from Sequence Orthology
more info
  
involved_in protein ubiquitination ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in chromosome IEA
Inferred from Electronic Annotation
more info
  
is_active_in site of double-strand break IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in site of double-strand break ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
E3 ubiquitin-protein ligase RNF138
Names
RING-type E3 ubiquitin transferase RNF138
NP_001289934.1
NP_001289940.1
NP_062680.2
NP_997506.1
XP_006526180.1
XP_006526181.1
XP_006526182.1
XP_011245277.1

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)

  1. NM_001303005.1 → NP_001289934.1  E3 ubiquitin-protein ligase RNF138 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the 5' coding region and lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. These differences cause translation initiation at an alternate downstream start codon and result in an isoform (3) that is shorter and has a distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AC138611, AK013419, AK020748, AK136138, BB673818
    UniProtKB/Swiss-Prot
    Q9CQE0
    UniProtKB/TrEMBL
    Q9CSA3

  2. NM_001303011.1 → NP_001289940.1  E3 ubiquitin-protein ligase RNF138 isoform 4

    See identical proteins and their annotated locations for NP_001289940.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks two alternate in-frame exons in the 3' coding region, compared to variant 1. The resulting protein (isoform 4) is shorter than isoform 1.
    Source sequence(s)
    AC138611, AK004238, AK013419, AK020748, AK136138, BB673818
    UniProtKB/TrEMBL
    A0A3Q4EHU1
    Related
    ENSMUSP00000157123.2, ENSMUST00000234545.2
    Conserved Domains (2) summary
    pfam18574
    Location:80 → 112
    zf_C2HC_14; C2HC Zing finger domain
    cl17238
    Location:14 → 59
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

  3. NM_019706.3 → NP_062680.2  E3 ubiquitin-protein ligase RNF138 isoform 2

    See identical proteins and their annotated locations for NP_062680.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The resulting protein (isoform 2) is shorter than isoform 1.
    Source sequence(s)
    AC138611, AK013419, AK020748, AK136138, BB673818
    Consensus CDS
    CCDS29089.1
    UniProtKB/TrEMBL
    A0A3Q4EHU1
    Related
    ENSMUSP00000072626.6, ENSMUST00000072847.12
    Conserved Domains (2) summary
    pfam18574
    Location:80 → 112
    zf_C2HC_14; C2HC Zing finger domain
    cl17238
    Location:14 → 59
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

  4. NM_207623.2 → NP_997506.1  E3 ubiquitin-protein ligase RNF138 isoform 1

    See identical proteins and their annotated locations for NP_997506.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC138611, AK004238, AK013419, AK020748, AK136138, BB673818
    Consensus CDS
    CCDS29090.1
    UniProtKB/Swiss-Prot
    Q9CQE0, Q9WTR9, Q9WTS0
    Related
    ENSMUSP00000157047.2, ENSMUST00000234536.2
    Conserved Domains (3) summary
    cd16544
    Location:14 → 59
    RING-HC_RNF138; RING finger, HC subclass, found in RING finger protein 138 (RNF138) and similar proteins
    pfam05605
    Location:156 → 215
    zf-Di19; Drought induced 19 protein (Di19), zinc-binding
    pfam18574
    Location:80 → 112
    zf_C2HC_14; C2HC Zing finger 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

  1. NC_000084.7 Reference GRCm39 C57BL/6J

    Range
    21134202..21161281
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011246975.4 → XP_011245277.1  E3 ubiquitin-protein ligase RNF138 isoform X1

    See identical proteins and their annotated locations for XP_011245277.1

    UniProtKB/Swiss-Prot
    Q9CQE0, Q9WTR9, Q9WTS0
    Related
    ENSMUSP00000157102.2, ENSMUST00000234107.2
    Conserved Domains (3) summary
    cd16544
    Location:14 → 59
    RING-HC_RNF138; RING finger, HC subclass, found in RING finger protein 138 (RNF138) and similar proteins
    pfam05605
    Location:156 → 215
    zf-Di19; Drought induced 19 protein (Di19), zinc-binding
    pfam18574
    Location:80 → 112
    zf_C2HC_14; C2HC Zing finger domain

  2. XM_006526117.5 → XP_006526180.1  E3 ubiquitin-protein ligase RNF138 isoform X2

    Conserved Domains (4) summary
    cd00162
    Location:18 → 57
    RING_Ubox; RING-HC finger (C3HC4-type) [structural motif]
    pfam05605
    Location:137 → 196
    zf-Di19; Drought induced 19 protein (Di19), zinc-binding
    pfam18574
    Location:80 → 112
    zf_C2HC_14; C2HC Zing finger domain
    cl17238
    Location:14 → 59
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

  3. XM_006526118.5 → XP_006526181.1  E3 ubiquitin-protein ligase RNF138 isoform X3

    See identical proteins and their annotated locations for XP_006526181.1

    UniProtKB/TrEMBL
    A0A3Q4EHU1
    Conserved Domains (2) summary
    pfam18574
    Location:80 → 112
    zf_C2HC_14; C2HC Zing finger domain
    cl17238
    Location:14 → 59
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

  4. XM_006526119.5 → XP_006526182.1  E3 ubiquitin-protein ligase RNF138 isoform X4

    Conserved Domains (2) summary
    pfam05605
    Location:43 → 102
    zf-Di19; Drought induced 19 protein (Di19), zinc-binding
    cl17238
    Location:14 → 37
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

RNA

  1. XR_004939875.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9CQE0.1 GenPept UniProtKB/Swiss-Prot:Q9CQE0

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