Sh3kbp1 SH3 domain-containing kinase-binding protein 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Sh3kbp1provided by RGD
Official Full Name: SH3 domain-containing kinase-binding protein 1provided by RGD
Primary source: RGD:620904
See related: Ensembl:ENSRNOG00000004322 AllianceGenome:RGD:620904
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Seta; CIN85
Summary: Enables ubiquitin protein ligase binding activity. Predicted to be involved in several processes, including actin filament organization; positive regulation of B cell activation; and regulation of cell shape. Predicted to be located in cell-cell junction and endocytic vesicle. Human ortholog(s) of this gene implicated in immunodeficiency 61. Orthologous to human SH3KBP1 (SH3 domain containing kinase binding protein 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Heart (RPKM 509.1), Thymus (RPKM 268.2) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: Xq14

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	X	NC_086039.1 (38686530..39031658, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	X	NC_051356.1 (34877862..35223013, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	X	NC_005120.4 (37790004..38196365, complement)

Chromosome X - NC_086039.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Seta/Sh3kbp1/CIN85 directs a more rapid receptor sorting in early endosomes and delivery to a lysosomal compartment and may contribute to dampening mast-cell functional response
Title: CIN85 regulates the ligand-dependent endocytosis of the IgE receptor: a new molecular mechanism to dampen mast cell function.
All 3 isoforms of Ruk are ubiquitinated. Specific interaction between the E3 ubiquitin ligase Cbl and all three Ruk isoforms was demonstrated.The interaction of Ruk M and S isoforms with Cbl was found to be mediated via heterodimerization with Ruk L.
Title: Ruk is ubiquitinated but not degraded by the proteasome.
Data characterize 5 monoclonal antibodies against SETA/CIN85/Ruk and conclude that additional splice variants remain to be described.
Title: Studying protein isoforms of the adaptor SETA/CIN85/Ruk with monoclonal antibodies.
adaptor protein SETA (CIN85) and its binding partner AIP1 are involved with the cytoskeleton and in the regulation of cell adhesion
Title: SETA/CIN85/Ruk and its binding partner AIP1 associate with diverse cytoskeletal elements, including FAKs, and modulate cell adhesion.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH18201 (e-PCR)
- UniSTS:41536

AW530792 (e-PCR)
- UniSTS:244559

AU048313 (e-PCR)
- UniSTS:109659

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables SH3 domain binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin protein ligase binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in actin filament organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell migration	IEA Inferred from Electronic Annotation more info
involved_in cell migration	ISO Inferred from Sequence Orthology more info
involved_in cell migration	ISS Inferred from Sequence or Structural Similarity more info
involved_in cytoskeleton organization	IEA Inferred from Electronic Annotation more info
involved_in cytoskeleton organization	ISO Inferred from Sequence Orthology more info
involved_in cytoskeleton organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in endocytosis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of B cell activation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of B cell activation	ISO Inferred from Sequence Orthology more info
involved_in regulation of apoptotic process	TAS Traceable Author Statement more info	PubMed
involved_in regulation of cell shape	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell shape	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell shape	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in GABA-ergic synapse	IDA Inferred from Direct Assay more info	PubMed
located_in cell-cell junction	IEA Inferred from Electronic Annotation more info
located_in cell-cell junction	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasmic vesicle membrane	IEA Inferred from Electronic Annotation more info
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info
located_in endocytic vesicle	IEA Inferred from Electronic Annotation more info
located_in endocytic vesicle	ISO Inferred from Sequence Orthology more info
located_in endocytic vesicle	ISS Inferred from Sequence or Structural Similarity more info
located_in focal adhesion	IEA Inferred from Electronic Annotation more info
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
located_in neuron projection	IEA Inferred from Electronic Annotation more info
is_active_in postsynaptic density	IDA Inferred from Direct Assay more info	PubMed
is_active_in synapse	IDA Inferred from Direct Assay more info	PubMed
located_in synapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: SH3 domain-containing kinase-binding protein 1

Names: SH3 domain-containing adapter protein; SH3-containing, expressed in tumorigenic astrocytes; SH3-domain kinase binding protein 1; regulator of ubiquitous kinase; ruk

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_053360.3 → NP_445812.1 SH3 domain-containing kinase-binding protein 1

See identical proteins and their annotated locations for NP_445812.1

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000021

UniProtKB/TrEMBL

A6IPM0, Q6IRL5

Conserved Domains (3) summary

cd12052
Location:3 → 55

SH3_CIN85_1; First Src Homology 3 domain (SH3A) of Cbl-interacting protein of 85 kDa

cd12055
Location:102 → 154

SH3_CIN85_2; Second Src Homology 3 domain (SH3B) of Cbl-interacting protein of 85 kDa

cd12057
Location:271 → 326

SH3_CIN85_3; Third Src Homology 3 domain (SH3C) of Cbl-interacting protein of 85 kDa

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086039.1 Reference GRCr8

Range

38686530..39031658 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039100102.2 → XP_038956030.1 SH3 domain-containing kinase-binding protein 1 isoform X5

UniProtKB/TrEMBL

A6IPM1

Conserved Domains (3) summary

cd12052
Location:3 → 55

SH3_CIN85_1; First Src Homology 3 domain (SH3A) of Cbl-interacting protein of 85 kDa

cd12055
Location:102 → 154

SH3_CIN85_2; Second Src Homology 3 domain (SH3B) of Cbl-interacting protein of 85 kDa

cd12057
Location:315 → 370

SH3_CIN85_3; Third Src Homology 3 domain (SH3C) of Cbl-interacting protein of 85 kDa
XM_039100103.2 → XP_038956031.1 SH3 domain-containing kinase-binding protein 1 isoform X7

UniProtKB/TrEMBL

A6IPM1

Conserved Domains (3) summary

cd12052
Location:3 → 55

SH3_CIN85_1; First Src Homology 3 domain (SH3A) of Cbl-interacting protein of 85 kDa

cd12055
Location:102 → 154

SH3_CIN85_2; Second Src Homology 3 domain (SH3B) of Cbl-interacting protein of 85 kDa

cd12057
Location:296 → 351

SH3_CIN85_3; Third Src Homology 3 domain (SH3C) of Cbl-interacting protein of 85 kDa
XM_006256931.3 → XP_006256993.1 SH3 domain-containing kinase-binding protein 1 isoform X1

See identical proteins and their annotated locations for XP_006256993.1

UniProtKB/Swiss-Prot

Q925Q9, Q925R0, Q925R1, Q925R2, Q925R3, Q9JKQ0, Q9JKQ1, Q9JLU9

UniProtKB/TrEMBL

A6IPL9, A6IPM1

Related

ENSRNOP00000006741.7

Conserved Domains (3) summary

cd12052
Location:3 → 55

SH3_CIN85_1; First Src Homology 3 domain (SH3A) of Cbl-interacting protein of 85 kDa

cd12055
Location:102 → 154

SH3_CIN85_2; Second Src Homology 3 domain (SH3B) of Cbl-interacting protein of 85 kDa

cd12057
Location:315 → 370

SH3_CIN85_3; Third Src Homology 3 domain (SH3C) of Cbl-interacting protein of 85 kDa
XM_039100100.2 → XP_038956028.1 SH3 domain-containing kinase-binding protein 1 isoform X2

UniProtKB/TrEMBL

A6IPM1, M0RBZ7

Related

ENSRNOP00000067100.3

Conserved Domains (3) summary

cd12052
Location:3 → 55

SH3_CIN85_1; First Src Homology 3 domain (SH3A) of Cbl-interacting protein of 85 kDa

cd12055
Location:102 → 154

SH3_CIN85_2; Second Src Homology 3 domain (SH3B) of Cbl-interacting protein of 85 kDa

cd12057
Location:296 → 351

SH3_CIN85_3; Third Src Homology 3 domain (SH3C) of Cbl-interacting protein of 85 kDa
XM_039100101.2 → XP_038956029.1 SH3 domain-containing kinase-binding protein 1 isoform X3

UniProtKB/TrEMBL

A0A0H2UHD8, A6IPM0

Related

ENSRNOP00000006438.5

Conserved Domains (3) summary

cd12052
Location:3 → 55

SH3_CIN85_1; First Src Homology 3 domain (SH3A) of Cbl-interacting protein of 85 kDa

cd12055
Location:102 → 154

SH3_CIN85_2; Second Src Homology 3 domain (SH3B) of Cbl-interacting protein of 85 kDa

cd12057
Location:290 → 345

SH3_CIN85_3; Third Src Homology 3 domain (SH3C) of Cbl-interacting protein of 85 kDa
XM_039100104.2 → XP_038956032.1 SH3 domain-containing kinase-binding protein 1 isoform X9

UniProtKB/TrEMBL

A0A8I6AJT1, A6IPM0

Related

ENSRNOP00000093532.1

Conserved Domains (3) summary

cd12052
Location:3 → 55

SH3_CIN85_1; First Src Homology 3 domain (SH3A) of Cbl-interacting protein of 85 kDa

cd12055
Location:102 → 154

SH3_CIN85_2; Second Src Homology 3 domain (SH3B) of Cbl-interacting protein of 85 kDa

cd12057
Location:271 → 326

SH3_CIN85_3; Third Src Homology 3 domain (SH3C) of Cbl-interacting protein of 85 kDa
XM_063280333.1 → XP_063136403.1 SH3 domain-containing kinase-binding protein 1 isoform X10

UniProtKB/TrEMBL

A6IPM2
XM_063280332.1 → XP_063136402.1 SH3 domain-containing kinase-binding protein 1 isoform X6

UniProtKB/TrEMBL

A6IPM2
XM_006256924.5 → XP_006256986.3 SH3 domain-containing kinase-binding protein 1 isoform X4

UniProtKB/TrEMBL

A6IPM1

Conserved Domains (2) summary

cd12055
Location:65 → 117

SH3_CIN85_2; Second Src Homology 3 domain (SH3B) of Cbl-interacting protein of 85 kDa

cd12057
Location:278 → 333

SH3_CIN85_3; Third Src Homology 3 domain (SH3C) of Cbl-interacting protein of 85 kDa
XM_006256929.5 → XP_006256991.3 SH3 domain-containing kinase-binding protein 1 isoform X8

UniProtKB/TrEMBL

A0A8I6A8U3, A6IPM2

Related

ENSRNOP00000089759.1

Conserved Domains (2) summary

cd12055
Location:65 → 117

SH3_CIN85_2; Second Src Homology 3 domain (SH3B) of Cbl-interacting protein of 85 kDa

cd12057
Location:234 → 289

SH3_CIN85_3; Third Src Homology 3 domain (SH3C) of Cbl-interacting protein of 85 kDa
XM_006256930.5 → XP_006256992.1 SH3 domain-containing kinase-binding protein 1 isoform X11

See identical proteins and their annotated locations for XP_006256992.1

UniProtKB/TrEMBL

A6IPM3, A6IPM4

Related

ENSRNOP00000083463.1

Conserved Domains (1) summary

cd12057
Location:33 → 88

SH3_CIN85_3; Third Src Homology 3 domain (SH3C) of Cbl-interacting protein of 85 kDa
XM_063280334.1 → XP_063136404.1 SH3 domain-containing kinase-binding protein 1 isoform X12

UniProtKB/TrEMBL

A6IPM4
XM_063280335.1 → XP_063136405.1 SH3 domain-containing kinase-binding protein 1 isoform X14
XM_008773199.4 → XP_008771421.1 SH3 domain-containing kinase-binding protein 1 isoform X13
XM_063280336.1 → XP_063136406.1 SH3 domain-containing kinase-binding protein 1 isoform X15

UniProtKB/TrEMBL

A6IPM6
XM_008773200.4 → XP_008771422.1 SH3 domain-containing kinase-binding protein 1 isoform X15

See identical proteins and their annotated locations for XP_008771422.1

UniProtKB/TrEMBL

A6IPM6