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RC3H1 ring finger and CCCH-type domains 1 [ Homo sapiens (human) ]

Gene ID: 149041, updated on 25-Jan-2022

Summary

Official Symbol
RC3H1provided by HGNC
Official Full Name
ring finger and CCCH-type domains 1provided by HGNC
Primary source
HGNC:HGNC:29434
See related
Ensembl:ENSG00000135870 MIM:609424; AllianceGenome:HGNC:29434
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
FHL6; IMDSHY; RNF198; ROQUIN
Summary
This gene encodes a protein containing RING-type and C3H1-type zinc finger motifs. The encoded protein recognizes and binds to a constitutive decay element (CDE) in the 3' UTR of mRNAs, leading to mRNA deadenylation and degradation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
Expression
Ubiquitous expression in bone marrow (RPKM 7.1), skin (RPKM 3.9) and 25 other tissues See more
Orthologs
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Genomic context

See RC3H1 in Genome Data Viewer
Location:
1q25.1
Exon count:
20
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (173931084..174022357, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (173900222..173991495, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene serpin family C member 1 Neighboring gene RNA, 5S ribosomal pseudogene 67 Neighboring gene RNA, 5S ribosomal pseudogene 68 Neighboring gene RC3H1 divergent transcript Neighboring gene ribosomal protein L30 pseudogene 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA2025

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables CCR4-NOT complex binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables RNA binding HDA PubMed 
enables RNA stem-loop binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables RNA stem-loop binding IDA
Inferred from Direct Assay
more info
PubMed 
enables RNA stem-loop binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables double-stranded RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables double-stranded RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables mRNA 3'-UTR binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables miRNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables ubiquitin protein ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables ubiquitin protein ligase activity TAS
Traceable Author Statement
more info
PubMed 
enables ubiquitin-protein transferase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables zinc ion binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
involved_in 3'-UTR-mediated mRNA destabilization ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in B cell homeostasis IEA
Inferred from Electronic Annotation
more info
 
involved_in P-body assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in T cell homeostasis IEA
Inferred from Electronic Annotation
more info
 
involved_in T cell proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in T cell receptor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in T follicular helper cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to interleukin-1 ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in lymph node development IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of B cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of T-helper 17 cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of T-helper cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of activated T cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of germinal center formation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in nuclear-transcribed mRNA catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
involved_in nuclear-transcribed mRNA catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of NIK/NF-kappaB signaling IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of mRNA catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in posttranscriptional regulation of gene expression ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in protein polyubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in protein polyubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of T cell receptor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of germinal center formation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of mRNA stability ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of miRNA metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in spleen development IEA
Inferred from Electronic Annotation
more info
 
involved_in ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
located_in P-body IMP
Inferred from Mutant Phenotype
more info
PubMed 
located_in P-body ISS
Inferred from Sequence or Structural Similarity
more info
 
is_active_in cytoplasmic stress granule IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in cytoplasmic stress granule ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
roquin-1
Names
RING finger and C3H zinc finger protein 1
RING finger and CCCH-type zinc finger domain-containing protein 1
RING finger protein 198
probable E3 ubiquitin-protein ligase Roquin
NP_001287779.1
NP_001287780.1
NP_001287781.1
NP_742068.1
XP_005244978.1
XP_011507533.1

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_001300850.1NP_001287779.1  roquin-1 isoform a

    See identical proteins and their annotated locations for NP_001287779.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AK122948, AL136170, BC136784
    UniProtKB/Swiss-Prot
    Q5TC82
    UniProtKB/TrEMBL
    B9EGU6
    Conserved Domains (2) summary
    smart00184
    Location:1452
    RING; Ring finger
    pfam00642
    Location:414440
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
  2. NM_001300851.1NP_001287780.1  roquin-1 isoform c

    See identical proteins and their annotated locations for NP_001287780.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (c) is shorter than isoform a.
    Source sequence(s)
    AK122948, AL136170
    Consensus CDS
    CCDS72987.1
    UniProtKB/Swiss-Prot
    Q5TC82
    Related
    ENSP00000356667.2, ENST00000367694.2
    Conserved Domains (2) summary
    smart00184
    Location:1452
    RING; Ring finger
    pfam00642
    Location:414440
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
  3. NM_001300852.1NP_001287781.1  roquin-1 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses two alternate in-frame splice sites in the 3' coding region, compared to variant 1. The encoded isoform (d) is shorter than isoform a.
    Source sequence(s)
    AK122948, AL136170, BC144408
    UniProtKB/Swiss-Prot
    Q5TC82
    UniProtKB/TrEMBL
    B7ZMB3
    Conserved Domains (2) summary
    smart00184
    Location:1452
    RING; Ring finger
    pfam00642
    Location:414440
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
  4. NM_172071.4NP_742068.1  roquin-1 isoform b

    See identical proteins and their annotated locations for NP_742068.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (b) is shorter than isoform a.
    Source sequence(s)
    AB095945, AL121983, AL136170
    Consensus CDS
    CCDS30940.1
    UniProtKB/Swiss-Prot
    Q5TC82
    Related
    ENSP00000356669.2, ENST00000367696.7
    Conserved Domains (2) summary
    smart00184
    Location:1452
    RING; Ring finger
    pfam00642
    Location:414440
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    173931084..174022357 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005244921.3XP_005244978.1  roquin-1 isoform X1

    Conserved Domains (2) summary
    smart00184
    Location:1452
    RING; Ring finger
    pfam00642
    Location:414440
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
  2. XM_011509231.2XP_011507533.1  roquin-1 isoform X2

    Conserved Domains (2) summary
    smart00184
    Location:1452
    RING; Ring finger
    pfam00642
    Location:414440
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
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