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

Summary

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, Dec 2024]
Orthologs: all
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Genomic context

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_007115.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Autism-associated gene shank3 is necessary for social contagion in zebrafish.
Title: Autism-associated gene shank3 is necessary for social contagion in zebrafish.
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.
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.
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.
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.
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.

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General gene information

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Markers

fj56b07.y1 (e-PCR)
- UniSTS:199579

Homology

NCBI Orthologs

Orthologs from OrthoDB

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

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Preferred Names: SH3 and multiple ankyrin repeat domains 3b; SH3 and multiple ankyrin repeat domains protein 3

Names: zs3.1

NCBI Reference Sequences (RefSeq)

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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_007115.7 Reference GRCz11 Primary Assembly

Range

9553280..9586622 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A8M6Z5I4, A0A8M9P8N6
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
XM_068220740.1 → XP_068076841.1 SH3 and multiple ankyrin repeat domains protein 3 isoform X4

UniProtKB/TrEMBL

A0A8M6YZQ6, A0A8M6Z644
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
XM_068220741.1 → XP_068076842.1 SH3 and multiple ankyrin repeat domains protein 3 isoform X5

UniProtKB/TrEMBL

A0A8M6YX80, A0A8M6Z644
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

NW_018394550.1 Reference GRCz11 ALT_DRER_TU_1

Range

104451..137953 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A8M9P8N6, A0A8M9PJP8
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
XM_068218170.1 → XP_068074271.1 SH3 and multiple ankyrin repeat domains protein 3 isoform X6

UniProtKB/TrEMBL

A0A8M9P8N6, A0A8M9Q1C6
XM_068218171.1 → XP_068074272.1 SH3 and multiple ankyrin repeat domains protein 3 isoform X7

UniProtKB/TrEMBL

A0A8M9P8N6, A0A8M9PY09
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
XM_068218172.1 → XP_068074273.1 SH3 and multiple ankyrin repeat domains protein 3 isoform X8

UniProtKB/TrEMBL

A0A8M9P8N6, A0A8M9PQP9
XM_068218173.1 → XP_068074274.1 SH3 and multiple ankyrin repeat domains protein 3 isoform X8

UniProtKB/TrEMBL

A0A8M9P8N6, A0A8M9PQP9