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pdcd11 programmed cell death 11 [ Danio rerio (zebrafish) ]

Gene ID: 794079, updated on 12-Sep-2024

Summary

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Official Symbol
pdcd11provided by ZNC
Official Full Name
programmed cell death 11provided by ZNC
Primary source
ZFIN:ZDB-GENE-030131-4076
See related
Ensembl:ENSDARG00000052480 AllianceGenome:ZFIN:ZDB-GENE-030131-4076
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
cb680; sb:cb680; im:7148359; wu:fc68c10
Summary
Predicted to enable RNA binding activity. Predicted to act upstream of or within mRNA processing and rRNA processing. Predicted to be located in nucleus. Predicted to be part of small-subunit processome. Predicted to be active in nucleolus. Is expressed in several structures, including alar plate midbrain region; head; midbrain; musculature system; and segmental plate. Orthologous to human PDCD11 (programmed cell death 11). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
human mouse all
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Genomic context

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See pdcd11 in Genome Data Viewer
Location:
chromosome: 1
Exon count:
36
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 1 NC_007112.7 (49435038..49481167)
105 previous assembly GRCz10 (GCF_000002035.5) 1 NC_007112.6 (48790602..48836747)

Chromosome 1 - NC_007112.7Genomic Context describing neighboring genes Neighboring gene TAF5 RNA polymerase II, TATA box binding protein (TBP)-associated factor Neighboring gene ATP synthase membrane subunit k Neighboring gene zgc:175214 Neighboring gene calcium homeostasis modulator 1b

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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Related articles in PubMed

  1. Zebrafish let-7b acts downstream of hypoxia-inducible factor-1α to assist in hypoxia-mediated cell proliferation and cell cycle regulation. Huang CX, et al. Life Sci, 2017 Feb 15. PMID 28077310
  2. Yolk sac-derived Pdcd11-positive cells modulate zebrafish microglia differentiation through the NF-κB-Tgfβ1 pathway. Yang R, et al. Cell Death Differ, 2021 Jan. PMID 32709934, Free PMC Article
  3. Zebrafish midbrain slow-amplifying progenitors exhibit high levels of transcripts for nucleotide and ribosome biogenesis. Recher G, et al. Development, 2013 Dec. PMID 24198278
  4. Hematopoietic gene expression profile in zebrafish kidney marrow. Song HD, et al. Proc Natl Acad Sci U S A, 2004 Nov 16. PMID 15520368, Free PMC Article
  5. The zebrafish gene map defines ancestral vertebrate chromosomes. Woods IG, et al. Genome Res, 2005 Sep. PMID 16109975, Free PMC Article

See all (8) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Yolk sac-derived Pdcd11-positive cells modulate zebrafish microglia differentiation through the NF-kappaB-Tgfbeta1 pathway.
    Title: Yolk sac-derived Pdcd11-positive cells modulate zebrafish microglia differentiation through the NF-κB-Tgfβ1 pathway.
Submit: New GeneRIF Correction

General gene information

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Markers

Homology

Clone Names

  • MGC162501

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables nucleic acid binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within RNA processing IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within rRNA processing IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
part_of small-subunit processome IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
protein RRP5 homolog

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_001089368.2 → NP_001082837.2  protein RRP5 homolog

    Status: PROVISIONAL

    Source sequence(s)
    BC095720, BC117594
    UniProtKB/TrEMBL
    A0A8M1NCQ8
    Related
    ENSDARP00000112333.2, ENSDART00000124833.4
    Conserved Domains (20) summary
    COG0539
    Location:168 → 779
    RpsA; Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
    cd04461
    Location:703 → 783
    S1_Rrp5_repeat_hs8_sc7; S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct ...
    cd05693
    Location:78 → 174
    S1_Rrp5_repeat_hs1_sc1; S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats ...
    cd05694
    Location:181 → 254
    S1_Rrp5_repeat_hs2_sc2; S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats ...
    cd05695
    Location:272 → 335
    S1_Rrp5_repeat_hs3; S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in ...
    cd05696
    Location:357 → 427
    S1_Rrp5_repeat_hs4; S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in ...
    cd05697
    Location:445 → 513
    S1_Rrp5_repeat_hs5; S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in ...
    cd05698
    Location:534 → 603
    S1_Rrp5_repeat_hs6_sc5; S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats ...
    cd05699
    Location:623 → 695
    S1_Rrp5_repeat_hs7; S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in ...
    cd05700
    Location:833 → 897
    S1_Rrp5_repeat_hs9; S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in ...
    cd05702
    Location:998 → 1067
    S1_Rrp5_repeat_hs11_sc8; S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats ...
    cd05703
    Location:1102 → 1177
    S1_Rrp5_repeat_hs12_sc9; S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats ...
    cd05704
    Location:1181 → 1252
    S1_Rrp5_repeat_hs13; S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in ...
    cd05705
    Location:1275 → 1348
    S1_Rrp5_repeat_hs14; S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in ...
    TIGR00717
    Location:527 → 1056
    rpsA; ribosomal protein S1
    sd00006
    Location:1608 → 1637
    TPR; TPR repeat [structural motif]
    pfam13414
    Location:1637 → 1698
    TPR_11; TPR repeat
    pfam14559
    Location:1680 → 1745
    TPR_19; Tetratricopeptide repeat
    pfam16228
    Location:1371 → 1534
    DUF4887; Domain of unknown function (DUF4887)
    cl09927
    Location:911 → 979
    S1_like; S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. ...

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007112.7 Reference GRCz11 Primary Assembly

    Range
    49435038..49481167
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005160117.5 → XP_005160174.1  protein RRP5 homolog isoform X2

    UniProtKB/TrEMBL
    A0A8M2B6U9
    Conserved Domains (18) summary
    COG0539
    Location:168 → 783
    RpsA; Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
    cd04461
    Location:703 → 783
    S1_Rrp5_repeat_hs8_sc7; S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct ...
    cd05693
    Location:78 → 174
    S1_Rrp5_repeat_hs1_sc1; S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats ...
    cd05694
    Location:181 → 254
    S1_Rrp5_repeat_hs2_sc2; S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats ...
    cd05695
    Location:272 → 335
    S1_Rrp5_repeat_hs3; S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in ...
    cd05696
    Location:357 → 427
    S1_Rrp5_repeat_hs4; S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in ...
    cd05697
    Location:445 → 513
    S1_Rrp5_repeat_hs5; S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in ...
    cd05698
    Location:534 → 603
    S1_Rrp5_repeat_hs6_sc5; S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats ...
    cd05700
    Location:833 → 897
    S1_Rrp5_repeat_hs9; S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in ...
    cd05702
    Location:998 → 1067
    S1_Rrp5_repeat_hs11_sc8; S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats ...
    cd05703
    Location:1102 → 1177
    S1_Rrp5_repeat_hs12_sc9; S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats ...
    cd05704
    Location:1181 → 1252
    S1_Rrp5_repeat_hs13; S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in ...
    cd05705
    Location:1275 → 1348
    S1_Rrp5_repeat_hs14; S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in ...
    TIGR00717
    Location:527 → 1056
    rpsA; ribosomal protein S1
    sd00006
    Location:1607 → 1636
    TPR; TPR repeat [structural motif]
    pfam13414
    Location:1636 → 1697
    TPR_11; TPR repeat
    pfam14559
    Location:1679 → 1744
    TPR_19; Tetratricopeptide repeat
    cl09927
    Location:623 → 695
    S1_like; S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. ...

  2. XM_068220860.1 → XP_068076961.1  protein RRP5 homolog isoform X1

Nucleotide Protein Strain
Heading Accession and Version

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