Itsn1 intersectin 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Itsn1provided by RGD
Full Name: intersectin 1provided by RGD
Primary source: RGD:2935
See related: EnsemblRapid:ENSRNOG00000002001 AllianceGenome:RGD:2935
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Itsn; EHSH1
Summary: Predicted to enable kinase activator activity; molecular adaptor activity; and proline-rich region binding activity. Involved in positive regulation of dendritic spine development; positive regulation of transport; and regulation of synapse organization. Located in several cellular components, including clathrin-coated pit; dendrite; and neuronal cell body. Is active in glutamatergic synapse; postsynaptic actin cytoskeleton; and postsynaptic endocytic zone. Orthologous to human ITSN1 (intersectin 1). [provided by Alliance of Genome Resources, Jan 2025]
Expression: Biased expression in Brain (RPKM 143.3), Spleen (RPKM 120.7) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 11q11

Exon count:: 45

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	11	NC_086029.1 (44464515..44646598)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	11	NC_051346.1 (30978590..31160645)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	11	NC_005110.4 (31943119..32069249)

Chromosome 11 - NC_086029.1 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?

Expression levels of NPPB, ITGB6, CPNE4, EML5, and ITSN1 in fresh exudates swabbed from critically colonised and infected full-thickness wounds in rats.
Title: Expression levels of NPPB, ITGB6, CPNE4, EML5, and ITSN1 in fresh exudates swabbed from critically colonised and infected full-thickness wounds in rats.
The intersectin1-L protein was primarily expressed in neurons in brain tissue. Its expression was remarkably increased in patients with refractory epilepsy and in epilepsy model rats.
Title: Altered Expression of Intersectin1-L in Patients with Refractory Epilepsy and in Experimental Epileptic Rats.
intersectin is an endocytic scaffold with a role in fast neurotransmitter release, which may be of prime importance for information processing in the brain
Title: Fast neurotransmitter release regulated by the endocytic scaffold intersectin.
Intersectin-1L and beta-Pix, play essential roles in neuroendocrine exocytosis by controlling the activity of Cdc42 and Rac1, respectively.
Title: The Rho guanine nucleotide exchange factors Intersectin 1L and β-Pix control calcium-regulated exocytosis in neuroendocrine PC12 cells.
intersectin-l is indeed an important regulator of constitutive endocytosis and neuronal development but that it is not a prominent player in the regulated endocytosis of SVs.
Title: Intersectin regulates dendritic spine development and somatodendritic endocytosis but not synaptic vesicle recycling in hippocampal neurons.
These results highlight a role of Numb for dendritic spine development and synaptic functions with intersectin and EphB2.
Title: Role of numb in dendritic spine development with a Cdc42 GEF intersectin and EphB2.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH135361 (e-PCR)
- UniSTS:218638

REN86881 (e-PCR)
- UniSTS:411679

D11Got26 (e-PCR)
- UniSTS:112733

BI283741 (e-PCR)
- UniSTS:243623

RH140585 (e-PCR)
- UniSTS:222654

D11Rat13 (e-PCR), detects polymorphism
- UniSTS:118229

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables guanyl-nucleotide exchange factor activity	IEA Inferred from Electronic Annotation more info
enables kinase activator activity	ISO Inferred from Sequence Orthology more info
enables molecular adaptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables molecular adaptor activity	IEA Inferred from Electronic Annotation more info
enables molecular adaptor activity	ISO Inferred from Sequence Orthology more info
enables proline-rich region binding	IEA Inferred from Electronic Annotation more info
enables proline-rich region binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in clathrin-dependent synaptic vesicle endocytosis	IBA Inferred from Biological aspect of Ancestor more info
involved_in endocytosis	IEA Inferred from Electronic Annotation more info
involved_in endosomal transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in exocytosis	IEA Inferred from Electronic Annotation more info
involved_in intracellular signal transduction	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of neuron apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of neuron apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of caveolin-mediated endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of dendritic spine development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of growth hormone secretion	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	ISO Inferred from Sequence Orthology more info
involved_in protein localization	IEA Inferred from Electronic Annotation more info
involved_in protein localization	ISO Inferred from Sequence Orthology more info
involved_in protein transport	IEA Inferred from Electronic Annotation more info
involved_in regulation of modification of postsynaptic actin cytoskeleton	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of modification of postsynaptic actin cytoskeleton	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of postsynapse organization	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of postsynapse organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within small GTPase-mediated signal transduction	ISO Inferred from Sequence Orthology more info
involved_in synaptic vesicle endocytosis	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in apical dendrite	IDA Inferred from Direct Assay more info	PubMed
is_active_in calyx of Held	ISO Inferred from Sequence Orthology more info
located_in cell projection	IEA Inferred from Electronic Annotation more info
located_in clathrin-coated pit	IDA Inferred from Direct Assay more info	PubMed
located_in clathrin-coated pit	IEA Inferred from Electronic Annotation more info
located_in clathrin-coated pit	ISO Inferred from Sequence Orthology more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IEA Inferred from Electronic Annotation 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 dendritic spine	IDA Inferred from Direct Assay more info	PubMed
located_in endocytic vesicle	ISO Inferred from Sequence Orthology more info
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	IMP Inferred from Mutant Phenotype more info	PubMed
is_active_in intracellular vesicle	IBA Inferred from Biological aspect of Ancestor more info
located_in intracellular vesicle	IDA Inferred from Direct Assay more info	PubMed
located_in lamellipodium	ISO Inferred from Sequence Orthology more info
located_in neuronal cell body	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear envelope	IEA Inferred from Electronic Annotation more info
located_in nuclear envelope	ISO Inferred from Sequence Orthology more info
located_in nuclear envelope	ISS Inferred from Sequence or Structural Similarity more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
is_active_in postsynaptic actin cytoskeleton	IDA Inferred from Direct Assay more info	PubMed
is_active_in postsynaptic endocytic zone	IDA Inferred from Direct Assay more info	PubMed
is_active_in postsynaptic endocytic zone	IMP Inferred from Mutant Phenotype more info	PubMed
is_active_in presynaptic endocytic zone	ISO Inferred from Sequence Orthology more info
is_active_in presynaptic membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in recycling endosome	IEA Inferred from Electronic Annotation more info
located_in synapse	IEA Inferred from Electronic Annotation more info
located_in terminal bouton	HDA more info	PubMed

General protein information

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Preferred Names: intersectin-1

Names: EH domain and SH3 domain regulator of endocytosis 1; intersectin 1 (SH3 domain protein 1A); intersectin 1 (SH3 domain protein); intersectin-1-like

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_001136096.4 → NP_001129568.1 intersectin-1 isoform a

See identical proteins and their annotated locations for NP_001129568.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer isoform (a).

Source sequence(s)

JAXUCZ010000011

UniProtKB/Swiss-Prot

D3ZV52, F1M823, Q9WVE1, Q9WVE9

UniProtKB/TrEMBL

A0A8I5Y9J0

Related

ENSRNOP00000095645.2, ENSRNOT00000096792.2

Conserved Domains (16) summary

cd08375
Location:1574 → 1708

C2_Intersectin; C2 domain present in Intersectin

smart00027
Location:217 → 309

EH; Eps15 homology domain

cd11987
Location:741 → 795

SH3_Intersectin1_1; First Src homology 3 domain (or SH3A) of Intersectin-1

cd11989
Location:909 → 960

SH3_Intersectin1_2; Second Src homology 3 domain (or SH3B) of Intersectin-1

cd11993
Location:1066 → 1130

SH3_Intersectin1_4; Fourth Src homology 3 domain (or SH3D) of Intersectin-1

cd11995
Location:1150 → 1203

SH3_Intersectin1_5; Fifth Src homology 3 domain (or SH3E) of Intersectin-1

COG1340
Location:371 → 694

COG1340; Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]

cd00052
Location:225 → 291

EH; Eps15 homology domain; found in proteins implicated in endocytosis, vesicle transport, and signal transduction. The alignment contains a pair of EF-hand motifs, typically one of them is canonical and binds to Ca2+, while the other may not bind to Ca2+. A ...

cd13264
Location:1440 → 1571

PH_ITSN; Intersectin Pleckstrin homology (PH) domain

pfam00169
Location:1457 → 1563

PH; PH domain

pfam00621
Location:1234 → 1414

RhoGEF; RhoGEF domain

pfam16617
Location:795 → 909

INTAP; Intersectin and clathrin adaptor AP2 binding region

cd16269
Location:382 → 393

GBP_C; coiled coil [structural motif]

cl17036
Location:998 → 1049

SH3; Src Homology 3 domain superfamily

cl20817
Location:338 → 413

GBP_C; Guanylate-binding protein, C-terminal domain

cl23720
Location:546 → 646

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
NM_019227.2 → NP_062100.2 intersectin-1 isoform b

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks alternate exons in the 3' coding region and 3' UTR, compared to variant 1, resulting in a novel 3' coding region and 3' UTR. It encodes the shorter isoform (b), compared to isoform a.

Source sequence(s)

JAXUCZ010000011

UniProtKB/TrEMBL

A0A8L2QLK0

Conserved Domains (6) summary

smart00027
Location:217 → 309

EH; Eps15 homology domain

cd11995
Location:1155 → 1208

SH3_Intersectin1_5; Fifth Src homology 3 domain (or SH3E) of Intersectin-1

TIGR02168
Location:347 → 657

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam16617
Location:800 → 914

INTAP; Intersectin and clathrin adaptor AP2 binding region

NF033761
Location:93 → 184

gliding_GltJ; adventurous gliding motility protein GltJ

cl17036
Location:1071 → 1135

SH3; Src Homology 3 domain superfamily

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_086029.1 Reference GRCr8

Range

44464515..44646598

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063270445.1 → XP_063126515.1 intersectin-1 isoform X4

UniProtKB/TrEMBL

A0A8L2QLK0

Related

ENSRNOP00000044773.6, ENSRNOT00000042750.7
XM_039088249.2 → XP_038944177.1 intersectin-1 isoform X7

Conserved Domains (5) summary

smart00027
Location:217 → 309

EH; Eps15 homology domain

cd11987
Location:741 → 795

SH3_Intersectin1_1; First Src homology 3 domain (or SH3A) of Intersectin-1

TIGR02168
Location:347 → 657

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam16617
Location:795 → 901

INTAP; Intersectin and clathrin adaptor AP2 binding region

NF033761
Location:93 → 184

gliding_GltJ; adventurous gliding motility protein GltJ
XM_039088246.2 → XP_038944174.1 intersectin-1 isoform X1

UniProtKB/TrEMBL

A0A8I5Y9J0, A0A8I6ARZ8

Related

ENSRNOP00000097531.1, ENSRNOT00000096706.2

Conserved Domains (12) summary

cd08375
Location:1579 → 1713

C2_Intersectin; C2 domain present in Intersectin

smart00027
Location:217 → 309

EH; Eps15 homology domain

cd11989
Location:914 → 965

SH3_Intersectin1_2; Second Src homology 3 domain (or SH3B) of Intersectin-1

cd11993
Location:1071 → 1135

SH3_Intersectin1_4; Fourth Src homology 3 domain (or SH3D) of Intersectin-1

cd11995
Location:1155 → 1208

SH3_Intersectin1_5; Fifth Src homology 3 domain (or SH3E) of Intersectin-1

PRK09510
Location:615 → 719

tolA; cell envelope integrity inner membrane protein TolA; Provisional

cd00160
Location:1235 → 1418

RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.

TIGR02168
Location:347 → 657

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam16617
Location:800 → 914

INTAP; Intersectin and clathrin adaptor AP2 binding region

pfam16652
Location:1437 → 1579

PH_13; Pleckstrin homology domain

NF033761
Location:93 → 184

gliding_GltJ; adventurous gliding motility protein GltJ

cl17036
Location:741 → 800

SH3; Src Homology 3 domain superfamily
XM_039088248.2 → XP_038944176.1 intersectin-1 isoform X6

Conserved Domains (5) summary

smart00027
Location:217 → 309

EH; Eps15 homology domain

TIGR02168
Location:347 → 657

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam16617
Location:800 → 906

INTAP; Intersectin and clathrin adaptor AP2 binding region

NF033761
Location:93 → 184

gliding_GltJ; adventurous gliding motility protein GltJ

cl17036
Location:741 → 800

SH3; Src Homology 3 domain superfamily
XM_039088251.2 → XP_038944179.1 intersectin-1 isoform X9

Conserved Domains (4) summary

smart00027
Location:217 → 309

EH; Eps15 homology domain

TIGR02168
Location:358 → 657

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

NF033761
Location:93 → 184

gliding_GltJ; adventurous gliding motility protein GltJ

cl17036
Location:741 → 778

SH3; Src Homology 3 domain superfamily
XM_039088250.2 → XP_038944178.1 intersectin-1 isoform X8

UniProtKB/TrEMBL

A0A8L2QM65

Conserved Domains (5) summary

smart00027
Location:217 → 309

EH; Eps15 homology domain

TIGR02168
Location:347 → 657

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam16617
Location:800 → 914

INTAP; Intersectin and clathrin adaptor AP2 binding region

NF033761
Location:93 → 184

gliding_GltJ; adventurous gliding motility protein GltJ

cl17036
Location:741 → 800

SH3; Src Homology 3 domain superfamily
XM_039088247.2 → XP_038944175.1 intersectin-1 isoform X1

UniProtKB/TrEMBL

A0A8I5Y9J0, A0A8I6ARZ8

Conserved Domains (12) summary

cd08375
Location:1579 → 1713

C2_Intersectin; C2 domain present in Intersectin

smart00027
Location:217 → 309

EH; Eps15 homology domain

cd11989
Location:914 → 965

SH3_Intersectin1_2; Second Src homology 3 domain (or SH3B) of Intersectin-1

cd11993
Location:1071 → 1135

SH3_Intersectin1_4; Fourth Src homology 3 domain (or SH3D) of Intersectin-1

cd11995
Location:1155 → 1208

SH3_Intersectin1_5; Fifth Src homology 3 domain (or SH3E) of Intersectin-1

PRK09510
Location:615 → 719

tolA; cell envelope integrity inner membrane protein TolA; Provisional

cd00160
Location:1235 → 1418

RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.

TIGR02168
Location:347 → 657

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam16617
Location:800 → 914

INTAP; Intersectin and clathrin adaptor AP2 binding region

pfam16652
Location:1437 → 1579

PH_13; Pleckstrin homology domain

NF033761
Location:93 → 184

gliding_GltJ; adventurous gliding motility protein GltJ

cl17036
Location:741 → 800

SH3; Src Homology 3 domain superfamily
XM_063270443.1 → XP_063126513.1 intersectin-1 isoform X2

UniProtKB/Swiss-Prot

D3ZV52, F1M823, Q9WVE1, Q9WVE9

UniProtKB/TrEMBL

A0A8I5Y9J0
XM_063270444.1 → XP_063126514.1 intersectin-1 isoform X3

UniProtKB/TrEMBL

A0A8I5Y9J0
XM_063270446.1 → XP_063126516.1 intersectin-1 isoform X5

UniProtKB/TrEMBL

A0A8L2QLK0