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pax2a paired box 2a [ Danio rerio (zebrafish) ]

Gene ID: 30425, updated on 21-Apr-2024

Summary

Official Symbol
pax2aprovided by ZNC
Official Full Name
paired box 2aprovided by ZNC
Primary source
ZFIN:ZDB-GENE-990415-8
See related
Ensembl:ENSDARG00000028148 AllianceGenome:ZFIN:ZDB-GENE-990415-8
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
noi; paxb; Pax-2; cb378; pax-b; pax2.1; pax2a1; PAXZF-B; pax[zf-b]
Summary
Enables sequence-specific DNA binding activity. Involved in nervous system development. Acts upstream of or within several processes, including animal organ development; cilium assembly; and nervous system development. Located in nucleus. Is expressed in several structures, including immature eye; mesoderm; nervous system; neural keel; and pronephros. Used to study coloboma. Human ortholog(s) of this gene implicated in focal segmental glomerulosclerosis 7 and renal coloboma syndrome. Orthologous to human PAX2 (paired box 2). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
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Genomic context

Location:
chromosome: 13
Exon count:
13
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 13 NC_007124.7 (29769732..29804925)
105 previous assembly GRCz10 (GCF_000002035.5) 13 NC_007124.6 (29640165..29673809)

Chromosome 13 - NC_007124.7Genomic Context describing neighboring genes Neighboring gene carbohydrate (chondroitin 6) sulfotransferase 3a Neighboring gene uncharacterized LOC101883680 Neighboring gene CUE domain containing 2 Neighboring gene hypoxia inducible factor 1 subunit alpha inhibitor

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

General gene information

Markers

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables DNA binding IDA
Inferred from Direct Assay
more info
 
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in anatomical structure development IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within anterior/posterior pattern specification IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within anterior/posterior pattern specification IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within anterior/posterior pattern specification involved in pronephros development IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within cell differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within cell fate specification IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within cell fate specification IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cerebellum development IMP
Inferred from Mutant Phenotype
more info
 
acts_upstream_of_or_within cerebellum formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cilium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within closure of optic fissure IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within embryonic camera-type eye morphogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within embryonic pattern specification IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within glial cell development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within hindbrain development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within inner ear receptor cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within kidney development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within locus ceruleus development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within midbrain development IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within midbrain development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within midbrain-hindbrain boundary development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within nervous system development IEA
Inferred from Electronic Annotation
more info
 
involved_in nervous system development IMP
Inferred from Mutant Phenotype
more info
 
acts_upstream_of_or_within otic placode formation IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within otic placode formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within peripheral nervous system development IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within peripheral nervous system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within pronephric glomerulus morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within pronephros development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within pronephros morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within retina development in camera-type eye IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within thyroid gland development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within vestibular receptor cell development IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
paired box protein Pax-2a
Names
no isthmus protein
paired box gene 2.1
paired box gene 2a
paired box homeotic gene 2a

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_131184.2NP_571259.1  paired box protein Pax-2a

    See identical proteins and their annotated locations for NP_571259.1

    Status: PROVISIONAL

    Source sequence(s)
    BC066690
    UniProtKB/Swiss-Prot
    Q90268, Q9PWK8, Q9PWK9, Q9PWL0, Q9PWL1, Q9YGU5, Q9YGU6, Q9YGU7, Q9YGU8, Q9YGU9, Q9YGV0
    Related
    ENSDARP00000071466.4, ENSDART00000076998.6
    Conserved Domains (2) summary
    smart00351
    Location:15139
    PAX; Paired Box domain
    pfam12403
    Location:284389
    Pax2_C; Paired-box protein 2 C terminal

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_007124.7 Reference GRCz11 Primary Assembly

    Range
    29769732..29804925
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_021480493.1XP_021336168.1  paired box protein Pax-2a isoform X1

    UniProtKB/TrEMBL
    A0A8M9Q9G5
    Conserved Domains (2) summary
    smart00351
    Location:19150
    PAX; Paired Box domain
    pfam12403
    Location:391500
    Pax2_C; Paired-box protein 2 C terminal
  2. XM_017358679.2XP_017214168.1  paired box protein Pax-2a isoform X2

    UniProtKB/TrEMBL
    A0A8M6Z270
  3. XM_021480496.1XP_021336171.1  paired box protein Pax-2a isoform X6

    UniProtKB/TrEMBL
    A0A8M9QJH4
    Conserved Domains (2) summary
    smart00351
    Location:19150
    PAX; Paired Box domain
    pfam12403
    Location:376485
    Pax2_C; Paired-box protein 2 C terminal
  4. XM_021480495.1XP_021336170.1  paired box protein Pax-2a isoform X5

    UniProtKB/Swiss-Prot
    Q90268, Q9PWK8, Q9PWK9, Q9PWL0, Q9PWL1, Q9YGU5, Q9YGU6, Q9YGU7, Q9YGU8, Q9YGU9, Q9YGV0
    UniProtKB/TrEMBL
    A0A8M9QN86
    Conserved Domains (2) summary
    smart00351
    Location:19150
    PAX; Paired Box domain
    pfam12403
    Location:391502
    Pax2_C; Paired-box protein 2 C terminal
  5. XM_021480510.1XP_021336185.1  paired box protein Pax-2a isoform X25

    UniProtKB/TrEMBL
    A0A8M9QN98
    Conserved Domains (2) summary
    smart00351
    Location:19150
    PAX; Paired Box domain
    pfam12403
    Location:233316
    Pax2_C; Paired-box protein 2 C terminal
  6. XM_021480497.1XP_021336172.1  paired box protein Pax-2a isoform X7

    UniProtKB/TrEMBL
    A0A8M9PXK5
    Conserved Domains (2) summary
    smart00351
    Location:19150
    PAX; Paired Box domain
    pfam12403
    Location:374483
    Pax2_C; Paired-box protein 2 C terminal
  7. XM_021480499.1XP_021336174.1  paired box protein Pax-2a isoform X10

    UniProtKB/TrEMBL
    A0A8M9QF63
    Conserved Domains (2) summary
    smart00351
    Location:19150
    PAX; Paired Box domain
    pfam12403
    Location:359468
    Pax2_C; Paired-box protein 2 C terminal
  8. XM_021480494.1XP_021336169.1  paired box protein Pax-2a isoform X3

    UniProtKB/TrEMBL
    A0A8M9QF58
    Conserved Domains (2) summary
    smart00351
    Location:19143
    PAX; Paired Box domain
    pfam12403
    Location:384493
    Pax2_C; Paired-box protein 2 C terminal
  9. XM_005156735.4XP_005156792.1  paired box protein Pax-2a isoform X4

    UniProtKB/TrEMBL
    A0A8M2B324
    Conserved Domains (2) summary
    smart00351
    Location:15139
    PAX; Paired Box domain
    pfam12403
    Location:380489
    Pax2_C; Paired-box protein 2 C terminal
  10. XM_021480502.1XP_021336177.1  paired box protein Pax-2a isoform X14

    UniProtKB/Swiss-Prot
    Q90268, Q9PWK8, Q9PWK9, Q9PWL0, Q9PWL1, Q9YGU5, Q9YGU6, Q9YGU7, Q9YGU8, Q9YGU9, Q9YGV0
    UniProtKB/TrEMBL
    A0A8M9PXL0
    Conserved Domains (2) summary
    smart00351
    Location:19150
    PAX; Paired Box domain
    pfam12403
    Location:327430
    Pax2_C; Paired-box protein 2 C terminal
  11. XM_021480511.1XP_021336186.1  paired box protein Pax-2a isoform X26

    UniProtKB/TrEMBL
    A0A8M9QJI6
    Conserved Domains (2) summary
    smart00351
    Location:19150
    PAX; Paired Box domain
    pfam12403
    Location:216299
    Pax2_C; Paired-box protein 2 C terminal
  12. XM_021480503.1XP_021336178.1  paired box protein Pax-2a isoform X15

    UniProtKB/Swiss-Prot
    Q90268, Q9PWK8, Q9PWK9, Q9PWL0, Q9PWL1, Q9YGU5, Q9YGU6, Q9YGU7, Q9YGU8, Q9YGU9, Q9YGV0
    UniProtKB/TrEMBL
    A0A8M9Q9H5
    Conserved Domains (2) summary
    smart00351
    Location:19150
    PAX; Paired Box domain
    pfam12403
    Location:327432
    Pax2_C; Paired-box protein 2 C terminal
  13. XM_021480498.1XP_021336173.1  paired box protein Pax-2a isoform X8

    UniProtKB/TrEMBL
    A0A8M9Q9H0
    Conserved Domains (2) summary
    smart00351
    Location:19143
    PAX; Paired Box domain
    pfam12403
    Location:367476
    Pax2_C; Paired-box protein 2 C terminal
  14. XM_017358683.2XP_017214172.1  paired box protein Pax-2a isoform X9

    UniProtKB/TrEMBL
    A0A8M6Z3Q2
  15. XM_021480500.1XP_021336175.1  paired box protein Pax-2a isoform X11

    UniProtKB/TrEMBL
    A0A8M9QN89
    Conserved Domains (2) summary
    smart00351
    Location:19143
    PAX; Paired Box domain
    pfam12403
    Location:352461
    Pax2_C; Paired-box protein 2 C terminal
  16. XM_017358684.2XP_017214173.1  paired box protein Pax-2a isoform X12

    UniProtKB/TrEMBL
    A0A8M6Z9H7
  17. XM_021480504.1XP_021336179.1  paired box protein Pax-2a isoform X16

    UniProtKB/Swiss-Prot
    Q90268, Q9PWK8, Q9PWK9, Q9PWL0, Q9PWL1, Q9YGU5, Q9YGU6, Q9YGU7, Q9YGU8, Q9YGU9, Q9YGV0
    UniProtKB/TrEMBL
    A0A8M9QF68
    Related
    ENSDARP00000131368.2, ENSDART00000160921.2
    Conserved Domains (2) summary
    smart00351
    Location:19150
    PAX; Paired Box domain
    pfam12403
    Location:310413
    Pax2_C; Paired-box protein 2 C terminal
  18. XM_021480501.1XP_021336176.1  paired box protein Pax-2a isoform X13

    UniProtKB/Swiss-Prot
    Q90268, Q9PWK8, Q9PWK9, Q9PWL0, Q9PWL1, Q9YGU5, Q9YGU6, Q9YGU7, Q9YGU8, Q9YGU9, Q9YGV0
    UniProtKB/TrEMBL
    A0A8M9QJH9
    Conserved Domains (2) summary
    smart00351
    Location:19143
    PAX; Paired Box domain
    pfam12403
    Location:352463
    Pax2_C; Paired-box protein 2 C terminal
  19. XM_017358685.2XP_017214174.1  paired box protein Pax-2a isoform X29

    UniProtKB/Swiss-Prot
    Q90268, Q9PWK8, Q9PWK9, Q9PWL0, Q9PWL1, Q9YGU5, Q9YGU6, Q9YGU7, Q9YGU8, Q9YGU9, Q9YGV0
    UniProtKB/TrEMBL
    A0A8M6Z1K8
  20. XM_021480506.1XP_021336181.1  paired box protein Pax-2a isoform X19

    UniProtKB/Swiss-Prot
    Q90268, Q9PWK8, Q9PWK9, Q9PWL0, Q9PWL1, Q9YGU5, Q9YGU6, Q9YGU7, Q9YGU8, Q9YGU9, Q9YGV0
    UniProtKB/TrEMBL
    A0A8M9QJI2
    Conserved Domains (2) summary
    smart00351
    Location:19150
    PAX; Paired Box domain
    pfam12403
    Location:295398
    Pax2_C; Paired-box protein 2 C terminal
  21. XM_021480505.1XP_021336180.1  paired box protein Pax-2a isoform X17

    UniProtKB/Swiss-Prot
    Q90268, Q9PWK8, Q9PWK9, Q9PWL0, Q9PWL1, Q9YGU5, Q9YGU6, Q9YGU7, Q9YGU8, Q9YGU9, Q9YGV0
    UniProtKB/TrEMBL
    A0A8M9QN93
    Related
    ENSDARP00000119623.1, ENSDART00000141310.3
    Conserved Domains (2) summary
    smart00351
    Location:19143
    PAX; Paired Box domain
    pfam12403
    Location:303406
    Pax2_C; Paired-box protein 2 C terminal
  22. XM_005156744.4XP_005156801.1  paired box protein Pax-2a isoform X18

    UniProtKB/Swiss-Prot
    Q90268, Q9PWK8, Q9PWK9, Q9PWL0, Q9PWL1, Q9YGU5, Q9YGU6, Q9YGU7, Q9YGU8, Q9YGU9, Q9YGV0
    UniProtKB/TrEMBL
    A0A8M2B3N2
    Related
    ENSDARP00000112529.1, ENSDART00000138332.3
    Conserved Domains (2) summary
    smart00351
    Location:15139
    PAX; Paired Box domain
    pfam12403
    Location:299402
    Pax2_C; Paired-box protein 2 C terminal
  23. XM_021480508.1XP_021336183.1  paired box protein Pax-2a isoform X21

    UniProtKB/Swiss-Prot
    Q90268, Q9PWK8, Q9PWK9, Q9PWL0, Q9PWL1, Q9YGU5, Q9YGU6, Q9YGU7, Q9YGU8, Q9YGU9, Q9YGV0
    UniProtKB/TrEMBL
    A0A8M9Q9I1
    Related
    ENSDARP00000123397.1, ENSDART00000133796.3
    Conserved Domains (2) summary
    smart00351
    Location:19143
    PAX; Paired Box domain
    pfam12403
    Location:288391
    Pax2_C; Paired-box protein 2 C terminal
  24. XM_021480507.1XP_021336182.1  paired box protein Pax-2a isoform X20

    UniProtKB/Swiss-Prot
    Q90268, Q9PWK8, Q9PWK9, Q9PWL0, Q9PWL1, Q9YGU5, Q9YGU6, Q9YGU7, Q9YGU8, Q9YGU9, Q9YGV0
    UniProtKB/TrEMBL
    A0A8M9PXL5
    Related
    ENSDARP00000134011.2, ENSDART00000160944.2
    Conserved Domains (2) summary
    smart00351
    Location:19143
    PAX; Paired Box domain
    pfam12403
    Location:303408
    Pax2_C; Paired-box protein 2 C terminal
  25. XM_021480512.1XP_021336187.1  paired box protein Pax-2a isoform X27

    UniProtKB/TrEMBL
    A0A8M9PXM3
    Conserved Domains (2) summary
    smart00351
    Location:19143
    PAX; Paired Box domain
    pfam12403
    Location:209294
    Pax2_C; Paired-box protein 2 C terminal
  26. XM_005156748.4XP_005156805.1  paired box protein Pax-2a isoform X23

    UniProtKB/Swiss-Prot
    Q90268, Q9PWK8, Q9PWK9, Q9PWL0, Q9PWL1, Q9YGU5, Q9YGU6, Q9YGU7, Q9YGU8, Q9YGU9, Q9YGV0
    UniProtKB/TrEMBL
    A0A8M2B2T3
    Conserved Domains (2) summary
    smart00351
    Location:15139
    PAX; Paired Box domain
    pfam12403
    Location:284387
    Pax2_C; Paired-box protein 2 C terminal
  27. XM_005156747.4XP_005156804.1  paired box protein Pax-2a isoform X22

    UniProtKB/Swiss-Prot
    Q90268, Q9PWK8, Q9PWK9, Q9PWL0, Q9PWL1, Q9YGU5, Q9YGU6, Q9YGU7, Q9YGU8, Q9YGU9, Q9YGV0
    UniProtKB/TrEMBL
    A0A8M2B3H8, B8JJS4
    Related
    ENSDARP00000113404.1, ENSDART00000134330.3
    Conserved Domains (2) summary
    smart00351
    Location:15139
    PAX; Paired Box domain
    pfam12403
    Location:299404
    Pax2_C; Paired-box protein 2 C terminal
  28. XM_021480513.1XP_021336188.1  paired box protein Pax-2a isoform X28

    UniProtKB/TrEMBL
    A0A8M9Q9I5
    Related
    ENSDARP00000121417.1, ENSDART00000134424.3
    Conserved Domains (2) summary
    smart00351
    Location:15139
    PAX; Paired Box domain
    pfam12403
    Location:205290
    Pax2_C; Paired-box protein 2 C terminal
  29. XM_021480509.1XP_021336184.1  paired box protein Pax-2a isoform X24

    UniProtKB/Swiss-Prot
    Q90268, Q9PWK8, Q9PWK9, Q9PWL0, Q9PWL1, Q9YGU5, Q9YGU6, Q9YGU7, Q9YGU8, Q9YGU9, Q9YGV0
    UniProtKB/TrEMBL
    A0A8M9QF73
    Related
    ENSDARP00000071460.5, ENSDART00000076992.6
    Conserved Domains (2) summary
    smart00351
    Location:19143
    PAX; Paired Box domain
    pfam12403
    Location:288393
    Pax2_C; Paired-box protein 2 C terminal