U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

shank3b SH3 and multiple ankyrin repeat domains 3b [ Danio rerio (zebrafish) ]

Gene ID: 566152, updated on 4-Jan-2025

Summary

Go to the top of the page Help
Official Symbol
shank3bprovided by ZNC
Official Full Name
SH3 and multiple ankyrin repeat domains 3bprovided by ZNC
Primary source
ZFIN:ZDB-GENE-041210-74
See related
Ensembl:ENSDARG00000063054 AllianceGenome:ZFIN:ZDB-GENE-041210-74
Gene type
protein coding
RefSeq status
MODEL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
shank3; si:dkey-153k10.1
Summary
Acts upstream of or within intestinal motility. Predicted to be located in synapse. Is expressed in brain; forebrain; and midbrain. Used to study autism spectrum disorder. Human ortholog(s) of this gene implicated in Phelan-McDermid syndrome and schizophrenia 15. Orthologous to human SHANK3 (SH3 and multiple ankyrin repeat domains 3). [provided by Alliance of Genome Resources, Jan 2025]
Orthologs
all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See shank3b in Genome Data Viewer
Location:
chromosome: 4
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 4 NC_007115.7 (9553280..9586622, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 4 NC_007115.6 (9552327..9585628, complement)

Chromosome 4 - NC_007115.7Genomic Context describing neighboring genes Neighboring gene LSM8 homolog, U6 small nuclear RNA associated Neighboring gene thymidine phosphorylase Neighboring gene cerebral dopamine neurotrophic factor Neighboring gene heat shock protein 14

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. Restoring Shank3 in the rostral brainstem of shank3ab-/- zebrafish autism models rescues sensory deficits. Kozol RA, et al. Commun Biol, 2021 Dec 17. PMID 34921227, Free PMC Article
  2. Developmental profiling of ASD-related shank3 transcripts and their differential regulation by valproic acid in zebrafish. Liu CX, et al. Dev Genes Evol, 2016 Nov. PMID 27562614, Free PMC Article
  3. Oxytocin protective effects on zebrafish larvae models of autism-like spectrum disorder. Rahmati-Holasoo H, et al. Iran J Basic Med Sci, 2023 Mar. PMID 36865037, Free PMC Article
  4. De novo mutations in the gene encoding the synaptic scaffolding protein SHANK3 in patients ascertained for schizophrenia. Gauthier J, et al. Proc Natl Acad Sci U S A, 2010 Apr 27. PMID 20385823, Free PMC Article
  5. Drugs prescribed for Phelan-McDermid syndrome differentially impact sensory behaviors in shank3 zebrafish models. Kozol RA, et al. F1000Res, 2023. PMID 37868296, Free PMC Article

See all (21) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Autism-associated gene shank3 is necessary for social contagion in zebrafish.
    Title: Autism-associated gene shank3 is necessary for social contagion in zebrafish.
  2. Restoring Shank3 in the rostral brainstem of shank3ab-/- zebrafish autism models rescues sensory deficits.
    Title: Restoring Shank3 in the rostral brainstem of shank3ab-/- zebrafish autism models rescues sensory deficits.
  3. Shank3 mutations cause intestinal dysmotility in a zebrafish mutant model of autism.
    Title: Intestinal dysmotility in a zebrafish (Danio rerio) shank3a;shank3b mutant model of autism.
  4. shank3b-/- zebrafish displayed robust autism-like behaviors and altered levels of the synaptic proteins homer1 and synaptophysin.
    Title: CRISPR/Cas9-induced shank3b mutant zebrafish display autism-like behaviors.
  5. Both syngap1b and shank3a play novel roles in morphogenesis resulting in common brain and behavioral phenotypes.
    Title: Two knockdown models of the autism genes SYNGAP1 and SHANK3 in zebrafish produce similar behavioral phenotypes associated with embryonic disruptions of brain morphogenesis.
  6. Study examined shank3a and shank3b, and their different variants; both shank3a and shank3b were barely expressed at very early ages (before 24 h post-fertilization (hpf)), whereas their expression levels were increased and enriched in the nervous system. Findings support the molecular diversity of shank3 in zebrafish and provide a molecular framework to understand the isoform-specific function of shank3 in zebrafish.
    Title: Developmental profiling of ASD-related shank3 transcripts and their differential regulation by valproic acid in zebrafish.
Submit: New GeneRIF Correction

General gene information

Go to the top of the page Help

Markers

Homology

Gene Ontology Provided by ZFIN

Process Evidence Code Pubs
acts_upstream_of_or_within intestinal motility IGI
Inferred from Genetic Interaction
more info
 PubMed 
Component Evidence Code Pubs
located_in synapse IEA
Inferred from Electronic Annotation
more info
  

General protein information

Go to the top of the page Help
Preferred Names
SH3 and multiple ankyrin repeat domains 3b; SH3 and multiple ankyrin repeat domains protein 3
Names
zs3.1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_007115.7 Reference GRCz11 Primary Assembly

    Range
    9553280..9586622 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_009300184.4 → XP_009298459.1  SH3 and multiple ankyrin repeat domains protein 3 isoform X2

    See identical proteins and their annotated locations for XP_009298459.1

    UniProtKB/TrEMBL
    A0A8M3ARK3, A0A8M6Z644
    Related
    ENSDARP00000116758.2, ENSDART00000145613.3
    Conserved Domains (9) summary
    cd09506
    Location:1576 → 1641
    SAM_Shank1,2,3; SAM domain of Shank1,2,3 family proteins
    smart00454
    Location:1580 → 1643
    SAM; Sterile alpha motif
    cd00204
    Location:222 → 348
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cd00992
    Location:601 → 690
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    pfam12796
    Location:299 → 388
    Ank_2; Ankyrin repeats (3 copies)
    pfam13637
    Location:228 → 282
    Ank_4; Ankyrin repeats (many copies)
    pfam16511
    Location:55 → 126
    FERM_f0; N-terminal or F0 domain of Talin-head FERM
    sd00045
    Location:227 → 258
    ANK; ANK repeat [structural motif]
    cl17036
    Location:502 → 553
    SH3; Src Homology 3 domain superfamily

  2. XM_005164598.5 → XP_005164655.1  SH3 and multiple ankyrin repeat domains protein 3 isoform X2

    See identical proteins and their annotated locations for XP_005164655.1

    UniProtKB/TrEMBL
    A0A8M3ARK3, A0A8M6Z644
    Conserved Domains (9) summary
    cd09506
    Location:1576 → 1641
    SAM_Shank1,2,3; SAM domain of Shank1,2,3 family proteins
    smart00454
    Location:1580 → 1643
    SAM; Sterile alpha motif
    cd00204
    Location:222 → 348
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cd00992
    Location:601 → 690
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    pfam12796
    Location:299 → 388
    Ank_2; Ankyrin repeats (3 copies)
    pfam13637
    Location:228 → 282
    Ank_4; Ankyrin repeats (many copies)
    pfam16511
    Location:55 → 126
    FERM_f0; N-terminal or F0 domain of Talin-head FERM
    sd00045
    Location:227 → 258
    ANK; ANK repeat [structural motif]
    cl17036
    Location:502 → 553
    SH3; Src Homology 3 domain superfamily

  3. XM_068220738.1 → XP_068076839.1  SH3 and multiple ankyrin repeat domains protein 3 isoform X1

    UniProtKB/TrEMBL
    A0A8M6Z5I4, A0A8M9P8N6

  4. XM_068220739.1 → XP_068076840.1  SH3 and multiple ankyrin repeat domains protein 3 isoform X3

    UniProtKB/TrEMBL
    A0A8M6YY75, A0A8M6Z644
    Related
    ENSDARP00000086242.5, ENSDART00000091809.5

  5. XM_068220740.1 → XP_068076841.1  SH3 and multiple ankyrin repeat domains protein 3 isoform X4

    UniProtKB/TrEMBL
    A0A8M6YZQ6, A0A8M6Z644

  6. XM_009300183.4 → XP_009298458.1  SH3 and multiple ankyrin repeat domains protein 3 isoform X2

    See identical proteins and their annotated locations for XP_009298458.1

    UniProtKB/TrEMBL
    A0A8M3ARK3, A0A8M6Z644
    Conserved Domains (9) summary
    cd09506
    Location:1576 → 1641
    SAM_Shank1,2,3; SAM domain of Shank1,2,3 family proteins
    smart00454
    Location:1580 → 1643
    SAM; Sterile alpha motif
    cd00204
    Location:222 → 348
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cd00992
    Location:601 → 690
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    pfam12796
    Location:299 → 388
    Ank_2; Ankyrin repeats (3 copies)
    pfam13637
    Location:228 → 282
    Ank_4; Ankyrin repeats (many copies)
    pfam16511
    Location:55 → 126
    FERM_f0; N-terminal or F0 domain of Talin-head FERM
    sd00045
    Location:227 → 258
    ANK; ANK repeat [structural motif]
    cl17036
    Location:502 → 553
    SH3; Src Homology 3 domain superfamily

  7. XM_068220741.1 → XP_068076842.1  SH3 and multiple ankyrin repeat domains protein 3 isoform X5

    UniProtKB/TrEMBL
    A0A8M6YX80, A0A8M6Z644

  8. XM_068220742.1 → XP_068076843.1  SH3 and multiple ankyrin repeat domains protein 3 isoform X5

    UniProtKB/TrEMBL
    A0A8M6YX80, A0A8M6Z644

Reference GRCz11 ALT_DRER_TU_1

Genomic

  1. NW_018394550.1 Reference GRCz11 ALT_DRER_TU_1

    Range
    104451..137953 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_021471517.2 → XP_021327192.1  SH3 and multiple ankyrin repeat domains protein 3 isoform X1

    UniProtKB/TrEMBL
    A0A8M9P8N6, A0A8M9PJP8
    Conserved Domains (8) summary
    cd09506
    Location:1569 → 1634
    SAM_Shank1,2,3; SAM domain of Shank1,2,3 family proteins
    cd00204
    Location:222 → 348
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cd00992
    Location:601 → 690
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    sd00045
    Location:227 → 258
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:164 → 258
    Ank_2; Ankyrin repeats (3 copies)
    pfam16511
    Location:55 → 126
    FERM_f0; N-terminal or F0 domain of Talin-head FERM
    cl17036
    Location:502 → 553
    SH3; Src Homology 3 domain superfamily
    cl26464
    Location:919 → 1209
    Atrophin-1; Atrophin-1 family

  2. XM_068218169.1 → XP_068074270.1  SH3 and multiple ankyrin repeat domains protein 3 isoform X1

    UniProtKB/TrEMBL
    A0A8M9P8N6, A0A8M9PJP8

  3. XM_021471519.2 → XP_021327194.1  SH3 and multiple ankyrin repeat domains protein 3 isoform X1

    UniProtKB/TrEMBL
    A0A8M9P8N6, A0A8M9PJP8
    Conserved Domains (8) summary
    cd09506
    Location:1569 → 1634
    SAM_Shank1,2,3; SAM domain of Shank1,2,3 family proteins
    cd00204
    Location:222 → 348
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cd00992
    Location:601 → 690
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    sd00045
    Location:227 → 258
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:164 → 258
    Ank_2; Ankyrin repeats (3 copies)
    pfam16511
    Location:55 → 126
    FERM_f0; N-terminal or F0 domain of Talin-head FERM
    cl17036
    Location:502 → 553
    SH3; Src Homology 3 domain superfamily
    cl26464
    Location:919 → 1209
    Atrophin-1; Atrophin-1 family

  4. XM_068218170.1 → XP_068074271.1  SH3 and multiple ankyrin repeat domains protein 3 isoform X6

    UniProtKB/TrEMBL
    A0A8M9P8N6, A0A8M9Q1C6

  5. XM_068218171.1 → XP_068074272.1  SH3 and multiple ankyrin repeat domains protein 3 isoform X7

    UniProtKB/TrEMBL
    A0A8M9P8N6, A0A8M9PY09

  6. XM_021471518.2 → XP_021327193.1  SH3 and multiple ankyrin repeat domains protein 3 isoform X1

    UniProtKB/TrEMBL
    A0A8M9P8N6, A0A8M9PJP8
    Conserved Domains (8) summary
    cd09506
    Location:1569 → 1634
    SAM_Shank1,2,3; SAM domain of Shank1,2,3 family proteins
    cd00204
    Location:222 → 348
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cd00992
    Location:601 → 690
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    sd00045
    Location:227 → 258
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:164 → 258
    Ank_2; Ankyrin repeats (3 copies)
    pfam16511
    Location:55 → 126
    FERM_f0; N-terminal or F0 domain of Talin-head FERM
    cl17036
    Location:502 → 553
    SH3; Src Homology 3 domain superfamily
    cl26464
    Location:919 → 1209
    Atrophin-1; Atrophin-1 family

  7. XM_068218172.1 → XP_068074273.1  SH3 and multiple ankyrin repeat domains protein 3 isoform X8

    UniProtKB/TrEMBL
    A0A8M9P8N6, A0A8M9PQP9

  8. XM_068218173.1 → XP_068074274.1  SH3 and multiple ankyrin repeat domains protein 3 isoform X8

    UniProtKB/TrEMBL
    A0A8M9P8N6, A0A8M9PQP9

Reference GRCz11 ALT_DRER_TU_2

Genomic

  1. NW_018395230.1 Reference GRCz11 ALT_DRER_TU_2

    Range
    232..10584 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_068219179.1 → XP_068075280.1  SH3 and multiple ankyrin repeat domains protein 3 isoform X9

    UniProtKB/TrEMBL
    A0A8M9Q4D9
Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.