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

Summary

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: VALIDATED
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 recognition; 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, Dec 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 2

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	2	NC_007113.7 (32653970..32671777, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	2	NC_007113.6 (32670752..32688631, complement)

Chromosome 2 - NC_007113.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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

fc21a05.x1 (e-PCR)
- UniSTS:193027

fi43a08.x1 (e-PCR)
- UniSTS:197518

AI658283 (e-PCR)
- UniSTS:206077

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 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)

NM_001105588.2 → NP_001099058.1 poly(U)-binding-splicing factor PUF60a

See identical proteins and their annotated locations for NP_001099058.1

Status: VALIDATED

Source sequence(s)

BX323559

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: 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

NC_007113.7 Reference GRCz11 Primary Assembly

Range

32653970..32671777 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_068224477.1 → XP_068080578.1 poly(U)-binding-splicing factor PUF60a isoform X5
XM_005163501.5 → XP_005163558.1 poly(U)-binding-splicing factor PUF60a 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
XM_068224479.1 → XP_068080580.1 poly(U)-binding-splicing factor PUF60a isoform X6
XM_005163503.4 → XP_005163560.1 poly(U)-binding-splicing factor PUF60a isoform X3

See identical proteins and their annotated locations for XP_005163560.1

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
XM_068224481.1 → XP_068080582.1 poly(U)-binding-splicing factor PUF60a isoform X6
XM_005163508.5 → XP_005163565.1 poly(U)-binding-splicing factor PUF60a 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
XM_068224484.1 → XP_068080585.1 poly(U)-binding-splicing factor PUF60a isoform X6

Related

ENSDARP00000152687.1, ENSDART00000190450.1
XM_009298620.4 → XP_009296895.1 poly(U)-binding-splicing factor PUF60a 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
XM_005163507.5 → XP_005163564.1 poly(U)-binding-splicing factor PUF60a 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
XM_068224474.1 → XP_068080575.1 poly(U)-binding-splicing factor PUF60a isoform X3

UniProtKB/TrEMBL

A0A2R8QFM1, A0A8M2BB09
XM_005163509.5 → XP_005163566.1 poly(U)-binding-splicing factor PUF60a 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
XM_005163500.5 → XP_005163557.1 poly(U)-binding-splicing factor PUF60a 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
XM_005163502.5 → XP_005163559.1 poly(U)-binding-splicing factor PUF60a isoform X3

See identical proteins and their annotated locations for XP_005163559.1

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
XM_068224483.1 → XP_068080584.1 poly(U)-binding-splicing factor PUF60a isoform X6
XM_009298622.4 → XP_009296897.1 poly(U)-binding-splicing factor PUF60a 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
XM_005163505.4 → XP_005163562.1 poly(U)-binding-splicing factor PUF60a 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
XM_005163506.4 → XP_005163563.1 poly(U)-binding-splicing factor PUF60a 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