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puf60a poly-U binding splicing factor a [ Danio rerio (zebrafish) ]

Gene ID: 562370, updated on 27-Mar-2024

Summary

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Official Symbol
puf60aprovided by ZNC
Official Full Name
poly-U binding splicing factor aprovided by ZNC
Primary source
ZFIN:ZDB-GENE-030131-2891
See related
Ensembl:ENSDARG00000032175 AllianceGenome:ZFIN:ZDB-GENE-030131-2891
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
fc21a05; wu:fc21a05; wu:fi43a08
Summary
Predicted to enable RNA binding activity. Predicted to be involved in alternative mRNA splicing, via spliceosome; mRNA splice site selection; and regulation of alternative mRNA splicing, via spliceosome. Predicted to act upstream of or within RNA splicing and mRNA processing. Predicted to be located in nucleus. Is expressed in central nervous system and pharynx. Orthologous to human PUF60 (poly(U) binding splicing factor 60). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
all
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Genomic context

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See puf60a in Genome Data Viewer
Location:
chromosome: 2
Exon count:
17
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 2 NC_007113.7 (32653970..32671849, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 2 NC_007113.6 (32670752..32688631, complement)

Chromosome 2 - NC_007113.7Genomic Context describing neighboring genes Neighboring gene si:dkeyp-73d8.9 Neighboring gene uncharacterized LOC101887108 Neighboring gene uncharacterized LOC101887030 Neighboring gene nuclear receptor binding protein 2a Neighboring gene uncharacterized LOC101887149 Neighboring gene kelch-like family member 18

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
  • 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. SCRIB and PUF60 are primary drivers of the multisystemic phenotypes of the 8q24.3 copy-number variant. Dauber A, et al. Am J Hum Genet, 2013 Nov 7. PMID 24140112, Free PMC Article
  2. Differential recruitment of co-regulatory proteins to the human estrogen receptor 1 in response to xenoestrogens. Smith LC, et al. Comp Biochem Physiol Part D Genomics Proteomics, 2016 Sep. PMID 27156127, Free PMC Article
  3. RNA-Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation. Rösel TD, et al. EMBO J, 2011 May 18. PMID 21468032, Free PMC Article
  4. Many genes in fish have species-specific asymmetric rates of molecular evolution. Steinke D, et al. BMC Genomics, 2006 Feb 8. PMID 16466575, Free PMC Article
  5. Evolution of complexity in the zebrafish synapse proteome. Bayés À, et al. Nat Commun, 2017 Mar 2. PMID 28252024, Free PMC Article

See all (9) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Suppression of scrib and puf60 in zebrafish leads to reduction in body length, small head size, and craniofacial defects.
    Title: SCRIB and PUF60 are primary drivers of the multisystemic phenotypes of the 8q24.3 copy-number variant.
Submit: New GeneRIF Correction

General gene information

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Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables nucleic acid binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within RNA splicing IEA
Inferred from Electronic Annotation
more info
  
involved_in alternative mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA splice site recognition IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of alternative mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within regulation of alternative mRNA splicing, via spliceosome IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
poly(U)-binding-splicing factor PUF60; poly(U)-binding-splicing factor PUF60a

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_001105588.1 → NP_001099058.1  poly(U)-binding-splicing factor PUF60a

    See identical proteins and their annotated locations for NP_001099058.1

    Status: PROVISIONAL

    Source sequence(s)
    BC153301
    UniProtKB/TrEMBL
    A8E4R7
    Related
    ENSDARP00000121317.1, ENSDART00000144613.3
    Conserved Domains (5) summary
    TIGR01645
    Location:1 → 518
    half-pint; poly-U binding splicing factor, half-pint family
    cd12370
    Location:92 → 167
    RRM1_PUF60; RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins
    cd12371
    Location:189 → 265
    RRM2_PUF60; RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins
    cd12648
    Location:420 → 517
    RRM3_UHM_PUF60; RNA recognition motif 3 in UHM domain of poly(U)-binding-splicing factor PUF60 and similar proteins
    cl21455
    Location:19 → 116
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007113.7 Reference GRCz11 Primary Assembly

    Range
    32653970..32671849 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005163503.3 → XP_005163560.1  poly(U)-binding-splicing factor PUF60 isoform X3

    See identical proteins and their annotated locations for XP_005163560.1

    UniProtKB/TrEMBL
    A0A2R8QFM1, A0A8M2BB09
    Conserved Domains (5) summary
    TIGR01645
    Location:2 → 538
    half-pint; poly-U binding splicing factor, half-pint family
    cd12370
    Location:93 → 168
    RRM1_PUF60; RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins
    cd12371
    Location:190 → 266
    RRM2_PUF60; RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins
    cd12648
    Location:440 → 537
    RRM3_UHM_PUF60; RNA recognition motif 3 in UHM domain of poly(U)-binding-splicing factor PUF60 and similar proteins
    cl21455
    Location:20 → 117
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  2. XM_005163500.4 → XP_005163557.1  poly(U)-binding-splicing factor PUF60 isoform X1

    UniProtKB/TrEMBL
    A0A8M2BAM3, F1QZ57
    Related
    ENSDARP00000056644.5, ENSDART00000056645.6
    Conserved Domains (5) summary
    TIGR01645
    Location:16 → 552
    half-pint; poly-U binding splicing factor, half-pint family
    cd12370
    Location:107 → 182
    RRM1_PUF60; RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins
    cd12371
    Location:204 → 280
    RRM2_PUF60; RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins
    cd12648
    Location:454 → 551
    RRM3_UHM_PUF60; RNA recognition motif 3 in UHM domain of poly(U)-binding-splicing factor PUF60 and similar proteins
    cl21455
    Location:34 → 131
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  3. XM_009298620.3 → XP_009296895.1  poly(U)-binding-splicing factor PUF60 isoform X3

    See identical proteins and their annotated locations for XP_009296895.1

    UniProtKB/TrEMBL
    A0A2R8QFM1, A0A8M2BB09
    Related
    ENSDARP00000150823.1, ENSDART00000192586.1
    Conserved Domains (5) summary
    TIGR01645
    Location:2 → 538
    half-pint; poly-U binding splicing factor, half-pint family
    cd12370
    Location:93 → 168
    RRM1_PUF60; RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins
    cd12371
    Location:190 → 266
    RRM2_PUF60; RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins
    cd12648
    Location:440 → 537
    RRM3_UHM_PUF60; RNA recognition motif 3 in UHM domain of poly(U)-binding-splicing factor PUF60 and similar proteins
    cl21455
    Location:20 → 117
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  4. XM_005163507.4 → XP_005163564.1  poly(U)-binding-splicing factor PUF60 isoform X3

    See identical proteins and their annotated locations for XP_005163564.1

    UniProtKB/TrEMBL
    A0A2R8QFM1, A0A8M2BB09
    Conserved Domains (5) summary
    TIGR01645
    Location:2 → 538
    half-pint; poly-U binding splicing factor, half-pint family
    cd12370
    Location:93 → 168
    RRM1_PUF60; RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins
    cd12371
    Location:190 → 266
    RRM2_PUF60; RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins
    cd12648
    Location:440 → 537
    RRM3_UHM_PUF60; RNA recognition motif 3 in UHM domain of poly(U)-binding-splicing factor PUF60 and similar proteins
    cl21455
    Location:20 → 117
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  5. XM_005163508.4 → XP_005163565.1  poly(U)-binding-splicing factor PUF60 isoform X3

    See identical proteins and their annotated locations for XP_005163565.1

    UniProtKB/TrEMBL
    A0A2R8QFM1, A0A8M2BB09
    Conserved Domains (5) summary
    TIGR01645
    Location:2 → 538
    half-pint; poly-U binding splicing factor, half-pint family
    cd12370
    Location:93 → 168
    RRM1_PUF60; RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins
    cd12371
    Location:190 → 266
    RRM2_PUF60; RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins
    cd12648
    Location:440 → 537
    RRM3_UHM_PUF60; RNA recognition motif 3 in UHM domain of poly(U)-binding-splicing factor PUF60 and similar proteins
    cl21455
    Location:20 → 117
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  6. XM_005163502.4 → XP_005163559.1  poly(U)-binding-splicing factor PUF60 isoform X3

    See identical proteins and their annotated locations for XP_005163559.1

    UniProtKB/TrEMBL
    A0A2R8QFM1, A0A8M2BB09
    Related
    ENSDARP00000150778.1, ENSDART00000191410.1
    Conserved Domains (5) summary
    TIGR01645
    Location:2 → 538
    half-pint; poly-U binding splicing factor, half-pint family
    cd12370
    Location:93 → 168
    RRM1_PUF60; RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins
    cd12371
    Location:190 → 266
    RRM2_PUF60; RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins
    cd12648
    Location:440 → 537
    RRM3_UHM_PUF60; RNA recognition motif 3 in UHM domain of poly(U)-binding-splicing factor PUF60 and similar proteins
    cl21455
    Location:20 → 117
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  7. XM_005163501.4 → XP_005163558.1  poly(U)-binding-splicing factor PUF60 isoform X2

    UniProtKB/TrEMBL
    A0A8M2BAZ4
    Conserved Domains (5) summary
    TIGR01645
    Location:14 → 550
    half-pint; poly-U binding splicing factor, half-pint family
    cd12370
    Location:105 → 180
    RRM1_PUF60; RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins
    cd12371
    Location:202 → 278
    RRM2_PUF60; RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins
    cd12648
    Location:452 → 549
    RRM3_UHM_PUF60; RNA recognition motif 3 in UHM domain of poly(U)-binding-splicing factor PUF60 and similar proteins
    cl21455
    Location:32 → 129
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  8. XM_005163509.4 → XP_005163566.1  poly(U)-binding-splicing factor PUF60 isoform X4

    UniProtKB/TrEMBL
    A0A8M2BAQ4
    Conserved Domains (5) summary
    TIGR01645
    Location:16 → 533
    half-pint; poly-U binding splicing factor, half-pint family
    cd12370
    Location:107 → 182
    RRM1_PUF60; RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins
    cd12371
    Location:204 → 280
    RRM2_PUF60; RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins
    cd12648
    Location:435 → 532
    RRM3_UHM_PUF60; RNA recognition motif 3 in UHM domain of poly(U)-binding-splicing factor PUF60 and similar proteins
    cl21455
    Location:34 → 131
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  9. XM_005163505.3 → XP_005163562.1  poly(U)-binding-splicing factor PUF60 isoform X3

    See identical proteins and their annotated locations for XP_005163562.1

    UniProtKB/TrEMBL
    A0A2R8QFM1, A0A8M2BB09
    Conserved Domains (5) summary
    TIGR01645
    Location:2 → 538
    half-pint; poly-U binding splicing factor, half-pint family
    cd12370
    Location:93 → 168
    RRM1_PUF60; RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins
    cd12371
    Location:190 → 266
    RRM2_PUF60; RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins
    cd12648
    Location:440 → 537
    RRM3_UHM_PUF60; RNA recognition motif 3 in UHM domain of poly(U)-binding-splicing factor PUF60 and similar proteins
    cl21455
    Location:20 → 117
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  10. XM_005163506.3 → XP_005163563.1  poly(U)-binding-splicing factor PUF60 isoform X3

    See identical proteins and their annotated locations for XP_005163563.1

    UniProtKB/TrEMBL
    A0A2R8QFM1, A0A8M2BB09
    Conserved Domains (5) summary
    TIGR01645
    Location:2 → 538
    half-pint; poly-U binding splicing factor, half-pint family
    cd12370
    Location:93 → 168
    RRM1_PUF60; RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins
    cd12371
    Location:190 → 266
    RRM2_PUF60; RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins
    cd12648
    Location:440 → 537
    RRM3_UHM_PUF60; RNA recognition motif 3 in UHM domain of poly(U)-binding-splicing factor PUF60 and similar proteins
    cl21455
    Location:20 → 117
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  11. XM_009298622.3 → XP_009296897.1  poly(U)-binding-splicing factor PUF60 isoform X3

    See identical proteins and their annotated locations for XP_009296897.1

    UniProtKB/TrEMBL
    A0A2R8QFM1, A0A8M2BB09
    Conserved Domains (5) summary
    TIGR01645
    Location:2 → 538
    half-pint; poly-U binding splicing factor, half-pint family
    cd12370
    Location:93 → 168
    RRM1_PUF60; RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins
    cd12371
    Location:190 → 266
    RRM2_PUF60; RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins
    cd12648
    Location:440 → 537
    RRM3_UHM_PUF60; RNA recognition motif 3 in UHM domain of poly(U)-binding-splicing factor PUF60 and similar proteins
    cl21455
    Location:20 → 117
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  12. XM_005163510.1 → XP_005163567.1  poly(U)-binding-splicing factor PUF60 isoform X7

    UniProtKB/TrEMBL
    A0A8M2BAV4
    Conserved Domains (3) summary
    TIGR01645
    Location:1 → 288
    half-pint; poly-U binding splicing factor, half-pint family
    cd12648
    Location:190 → 287
    RRM3_UHM_PUF60; RNA recognition motif 3 in UHM domain of poly(U)-binding-splicing factor PUF60 and similar proteins
    cl17169
    Location:1 → 16
    RRM_SF; RNA recognition motif (RRM) superfamily

  13. XM_017358672.2 → XP_017214161.1  poly(U)-binding-splicing factor PUF60 isoform X7

    UniProtKB/TrEMBL
    A0A8M2BAV4
    Conserved Domains (3) summary
    TIGR01645
    Location:1 → 288
    half-pint; poly-U binding splicing factor, half-pint family
    cd12648
    Location:190 → 287
    RRM3_UHM_PUF60; RNA recognition motif 3 in UHM domain of poly(U)-binding-splicing factor PUF60 and similar proteins
    cl17169
    Location:1 → 16
    RRM_SF; RNA recognition motif (RRM) superfamily

  14. XM_021480690.1 → XP_021336365.1  poly(U)-binding-splicing factor PUF60 isoform X6

    UniProtKB/TrEMBL
    A0A8M9QNK1
    Related
    ENSDARP00000106172.2, ENSDART00000129931.4
    Conserved Domains (1) summary
    cl25887
    Location:16 → 352
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]

  15. XM_021480683.1 → XP_021336358.1  poly(U)-binding-splicing factor PUF60 isoform X5

    UniProtKB/TrEMBL
    A0A8M9Q9Z9
    Conserved Domains (1) summary
    cl25887
    Location:16 → 371
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
Nucleotide Protein
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