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Zcchc2 zinc finger CCHC-type containing 2 [ Rattus norvegicus (Norway rat) ]

Gene ID: 304695, updated on 7-Sep-2023

Summary

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Official Symbol
Zcchc2provided by RGD
Official Full Name
zinc finger CCHC-type containing 2provided by RGD
Primary source
RGD:1310626
See related
Ensembl:ENSRNOG00000002882 AllianceGenome:RGD:1310626
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
Tnfrsf11a
Summary
Predicted to enable nucleic acid binding activity; phosphatidylinositol binding activity; and zinc ion binding activity. Predicted to be located in cytoplasm. Orthologous to human ZCCHC2 (zinc finger CCHC-type containing 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Thymus (RPKM 136.1), Lung (RPKM 99.4) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Zcchc2 in Genome Data Viewer
Location:
13p11
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_06 current mRatBN7.2 (GCF_015227675.2) 13 NC_051348.1 (22118677..22193626)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 13 NC_005112.4 (25961762..26052472)

Chromosome 13 - NC_051348.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102550337 Neighboring gene uncharacterized LOC102550524 Neighboring gene PH domain and leucine rich repeat protein phosphatase 1 Neighboring gene uncharacterized LOC108352518

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Clone Names

  • MGC112793

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables nucleic acid binding IEA
Inferred from Electronic Annotation
more info
  
enables phosphatidylinositol binding IEA
Inferred from Electronic Annotation
more info
  
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
zinc finger CCHC domain-containing protein 2
Names
tumor necrosis factor receptor superfamily, member 11a

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_001122677.4 → NP_001116149.2  zinc finger CCHC domain-containing protein 2 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    JACYVU010000242
    UniProtKB/TrEMBL
    A0A0H2UHB2
    Related
    ENSRNOP00000003870.6, ENSRNOT00000003870.9
    Conserved Domains (2) summary
    pfam00098
    Location:1124 → 1139
    zf-CCHC; Zinc knuckle
    cl02563
    Location:356 → 456
    PX_domain; The Phox Homology domain, a phosphoinositide binding module

  2. NM_001271042.1 → NP_001257971.1  zinc finger CCHC domain-containing protein 2 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains multiple differences in the coding region and its transcription extends past a splice site that is used in variant 1, resulting in a novel 3' coding region and 3' UTR compared to variant 1. It encodes isoform 2 which is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    BC100090, JACYVU010000242
    UniProtKB/Swiss-Prot
    Q498S6
    Conserved Domains (1) summary
    cl02563
    Location:356 → 456
    PX_domain; The Phox Homology domain, a phosphoinositide binding module

RefSeqs of Annotated Genomes: GCF_015227675.2-RS_2023_06

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

Reference mRatBN7.2 Primary Assembly

Genomic

  1. NC_051348.1 Reference mRatBN7.2 Primary Assembly

    Range
    22118677..22193626
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039090658.1 → XP_038946586.1  zinc finger CCHC domain-containing protein 2 isoform X2

    Conserved Domains (3) summary
    PTZ00368
    Location:1113 → 1136
    PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional
    pfam05109
    Location:682 → 1013
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    cl02563
    Location:356 → 456
    PX_domain; The Phox Homology domain, a phosphoinositide binding module

  2. XM_006249626.4 → XP_006249688.1  zinc finger CCHC domain-containing protein 2 isoform X1

    See identical proteins and their annotated locations for XP_006249688.1

    UniProtKB/Swiss-Prot
    Q498S6
    Conserved Domains (2) summary
    pfam00098
    Location:1123 → 1138
    zf-CCHC; Zinc knuckle
    cl02563
    Location:356 → 456
    PX_domain; The Phox Homology domain, a phosphoinositide binding module

  3. XM_039090661.1 → XP_038946589.1  zinc finger CCHC domain-containing protein 2 isoform X5

    Conserved Domains (3) summary
    PTZ00368
    Location:1070 → 1093
    PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional
    pfam05109
    Location:639 → 970
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    cl02563
    Location:356 → 456
    PX_domain; The Phox Homology domain, a phosphoinositide binding module

  4. XM_039090660.1 → XP_038946588.1  zinc finger CCHC domain-containing protein 2 isoform X4

    UniProtKB/TrEMBL
    A0A8L2R9Z0
    Related
    ENSRNOP00000075165.2, ENSRNOT00000086167.2
    Conserved Domains (3) summary
    smart00343
    Location:1095 → 1110
    ZnF_C2HC; zinc finger
    pfam05109
    Location:654 → 985
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    cl02563
    Location:356 → 456
    PX_domain; The Phox Homology domain, a phosphoinositide binding module

  5. XM_039090659.1 → XP_038946587.1  zinc finger CCHC domain-containing protein 2 isoform X3

    Conserved Domains (2) summary
    smart00343
    Location:1099 → 1114
    ZnF_C2HC; zinc finger
    pfam05109
    Location:658 → 989
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)

  6. XM_039090665.1 → XP_038946593.1  zinc finger CCHC domain-containing protein 2 isoform X8

  7. XM_039090667.1 → XP_038946595.1  zinc finger CCHC domain-containing protein 2 isoform X10

    Conserved Domains (1) summary
    cl02563
    Location:356 → 456
    PX_domain; The Phox Homology domain, a phosphoinositide binding module

  8. XM_039090666.1 → XP_038946594.1  zinc finger CCHC domain-containing protein 2 isoform X9

    Conserved Domains (1) summary
    cl02563
    Location:356 → 456
    PX_domain; The Phox Homology domain, a phosphoinositide binding module

  9. XM_039090663.1 → XP_038946591.1  zinc finger CCHC domain-containing protein 2 isoform X6

    Conserved Domains (3) summary
    smart00343
    Location:609 → 624
    ZnF_C2HC; zinc finger
    PHA03247
    Location:255 → 490
    PHA03247; large tegument protein UL36; Provisional
    pfam15967
    Location:385 → 478
    Nucleoporin_FG2; Nucleoporin FG repeated region

  10. XM_039090662.1 → XP_038946590.1  zinc finger CCHC domain-containing protein 2 isoform X6

    Conserved Domains (3) summary
    smart00343
    Location:609 → 624
    ZnF_C2HC; zinc finger
    PHA03247
    Location:255 → 490
    PHA03247; large tegument protein UL36; Provisional
    pfam15967
    Location:385 → 478
    Nucleoporin_FG2; Nucleoporin FG repeated region

  11. XM_039090664.1 → XP_038946592.1  zinc finger CCHC domain-containing protein 2 isoform X7

    Conserved Domains (3) summary
    smart00343
    Location:599 → 614
    ZnF_C2HC; zinc finger
    PHA03247
    Location:245 → 480
    PHA03247; large tegument protein UL36; Provisional
    pfam15967
    Location:375 → 468
    Nucleoporin_FG2; Nucleoporin FG repeated region

RNA

  1. XR_001840776.2 RNA Sequence

  2. XR_005492235.1 RNA Sequence

  3. XR_005492237.1 RNA Sequence

  4. XR_005492236.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001034142.1: Suppressed sequence

    Description
    NM_001034142.1: This RefSeq was permanently suppressed because the CDS is partial.
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q498S6.2 GenPept UniProtKB/Swiss-Prot:Q498S6

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