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

    Gene ID: 149041, updated on 3-Dec-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See RC3H1 in Genome Data Viewer
    Location:
    1q25.1
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (173931084..174022357, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (173289302..173380330, complement)
    RS_2024_09 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 uncharacterized LOC124904457 Neighboring gene RNA, 5S ribosomal pseudogene 67 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:173915901-173917100 Neighboring gene RNA, 5S ribosomal pseudogene 68 Neighboring gene MPRA-validated peak465 silencer Neighboring gene MPRA-validated peak466 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2119 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:173990305-173990844 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1558 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1559 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

    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
     
    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
     
    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
     
    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
     
    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
     
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of non-canonical NF-kappaB signal transduction IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in post-transcriptional 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
     
    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
     
    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
     
    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_047303045.1
    XP_047303046.1
    XP_047303047.1
    XP_047303048.1
    XP_047303049.1
    XP_047303050.1
    XP_047303051.1
    XP_047303052.1
    XP_047303053.1
    XP_047303057.1
    XP_047303058.1
    XP_047303059.1
    XP_047303060.1
    XP_047303061.1
    XP_047303062.1
    XP_054190589.1
    XP_054190590.1
    XP_054190591.1
    XP_054190592.1
    XP_054190593.1
    XP_054190594.1
    XP_054190595.1
    XP_054190596.1
    XP_054190597.1
    XP_054190598.1
    XP_054190599.1
    XP_054190600.1
    XP_054190601.1
    XP_054190602.1
    XP_054190603.1
    XP_054190604.1

    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/TrEMBL
      B7ZMB3, 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/TrEMBL
      B7ZMB3
      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/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
      B3KVK1, Q5TC82, Q5W180, Q5W181, Q8IVE6, Q8N9V1
      UniProtKB/TrEMBL
      B7ZMB3
      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: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

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

    mRNA and Protein(s)

    1. XM_047447096.1XP_047303052.1  roquin-1 isoform X5

      UniProtKB/TrEMBL
      B7ZMB3
    2. XM_047447104.1XP_047303060.1  roquin-1 isoform X9

      UniProtKB/TrEMBL
      B7ZMB3
    3. XM_047447095.1XP_047303051.1  roquin-1 isoform X4

      UniProtKB/TrEMBL
      B7ZMB3
    4. XM_047447093.1XP_047303049.1  roquin-1 isoform X3

      UniProtKB/TrEMBL
      B7ZMB3
    5. XM_047447091.1XP_047303047.1  roquin-1 isoform X2

      UniProtKB/Swiss-Prot
      B3KVK1, Q5TC82, Q5W180, Q5W181, Q8IVE6, Q8N9V1
      UniProtKB/TrEMBL
      B7ZMB3
    6. XM_047447090.1XP_047303046.1  roquin-1 isoform X1

      UniProtKB/TrEMBL
      B7ZMB3, B9EGU6
    7. XM_047447106.1XP_047303062.1  roquin-1 isoform X11

      UniProtKB/TrEMBL
      B7ZMB3
    8. XM_047447102.1XP_047303058.1  roquin-1 isoform X8

      UniProtKB/TrEMBL
      B7ZMB3
    9. XM_047447101.1XP_047303057.1  roquin-1 isoform X7

      UniProtKB/TrEMBL
      B7ZMB3
    10. XM_047447097.1XP_047303053.1  roquin-1 isoform X6

      UniProtKB/TrEMBL
      B7ZMB3
    11. XM_005244921.4XP_005244978.1  roquin-1 isoform X5

      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)
    12. XM_047447105.1XP_047303061.1  roquin-1 isoform X10

      UniProtKB/TrEMBL
      B7ZMB3
    13. XM_047447103.1XP_047303059.1  roquin-1 isoform X9

      UniProtKB/TrEMBL
      B7ZMB3
    14. XM_047447094.1XP_047303050.1  roquin-1 isoform X4

      UniProtKB/TrEMBL
      B7ZMB3
    15. XM_047447092.1XP_047303048.1  roquin-1 isoform X3

      UniProtKB/TrEMBL
      B7ZMB3
    16. XM_047447089.1XP_047303045.1  roquin-1 isoform X1

      UniProtKB/TrEMBL
      B7ZMB3, B9EGU6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      173289302..173380330 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054334615.1XP_054190590.1  roquin-1 isoform X1

      UniProtKB/TrEMBL
      B7ZMB3, B9EGU6
    2. XM_054334622.1XP_054190597.1  roquin-1 isoform X5

      UniProtKB/TrEMBL
      B7ZMB3
    3. XM_054334627.1XP_054190602.1  roquin-1 isoform X9

      UniProtKB/TrEMBL
      B7ZMB3
    4. XM_054334620.1XP_054190595.1  roquin-1 isoform X4

      UniProtKB/TrEMBL
      B7ZMB3
    5. XM_054334618.1XP_054190593.1  roquin-1 isoform X3

      UniProtKB/TrEMBL
      B7ZMB3
    6. XM_054334616.1XP_054190591.1  roquin-1 isoform X2

      UniProtKB/Swiss-Prot
      B3KVK1, Q5TC82, Q5W180, Q5W181, Q8IVE6, Q8N9V1
      UniProtKB/TrEMBL
      B7ZMB3
    7. XM_054334629.1XP_054190604.1  roquin-1 isoform X11

      UniProtKB/TrEMBL
      B7ZMB3
    8. XM_054334625.1XP_054190600.1  roquin-1 isoform X8

      UniProtKB/TrEMBL
      B7ZMB3
    9. XM_054334624.1XP_054190599.1  roquin-1 isoform X7

      UniProtKB/TrEMBL
      B7ZMB3
    10. XM_054334623.1XP_054190598.1  roquin-1 isoform X6

      UniProtKB/TrEMBL
      B7ZMB3
    11. XM_054334621.1XP_054190596.1  roquin-1 isoform X5

      UniProtKB/TrEMBL
      B7ZMB3
    12. XM_054334628.1XP_054190603.1  roquin-1 isoform X10

      UniProtKB/TrEMBL
      B7ZMB3
    13. XM_054334626.1XP_054190601.1  roquin-1 isoform X9

      UniProtKB/TrEMBL
      B7ZMB3
    14. XM_054334619.1XP_054190594.1  roquin-1 isoform X4

      UniProtKB/TrEMBL
      B7ZMB3
    15. XM_054334617.1XP_054190592.1  roquin-1 isoform X3

      UniProtKB/TrEMBL
      B7ZMB3
    16. XM_054334614.1XP_054190589.1  roquin-1 isoform X1

      UniProtKB/TrEMBL
      B7ZMB3, B9EGU6