SYTL4 synaptotagmin like 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SYTL4provided by HGNC
Official Full Name: synaptotagmin like 4provided by HGNC
Primary source: HGNC:HGNC:15588
See related: Ensembl:ENSG00000102362 MIM:300723; AllianceGenome:HGNC:15588
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: SLP4
Summary: This gene encodes a member of the synaptotagmin like protein family. Members of this family are characterized by an N-terminal Rab27 binding domain and C-terminal tandem C2 domains. The encoded protein binds specific small Rab GTPases and is involved in intracellular membrane trafficking. This protein binds Rab27 and may be involved in inhibiting dense core vesicle exocytosis. Alternate splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Mar 2010]
Expression: Broad expression in ovary (RPKM 19.6), endometrium (RPKM 12.8) and 19 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: Xq22.1

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (100674491..100732121, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	X	NC_060947.1 (99116950..99174573, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (99929488..99987108, complement)

Chromosome X - NC_000023.11 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: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Multivalent lipid targeting by the calcium-independent C2A domain of synaptotagmin-like protein 4/granuphilin.
Title: Multivalent lipid targeting by the calcium-independent C2A domain of synaptotagmin-like protein 4/granuphilin.
SYTL4 downregulates microtubule stability and confers paclitaxel resistance in triple-negative breast cancer.
Title: SYTL4 downregulates microtubule stability and confers paclitaxel resistance in triple-negative breast cancer.
LMP1 upregulates SDC2 and SYTL4.
Title: Epstein-Barr virus-encoded latent membrane protein 1 promotes extracellular vesicle secretion through syndecan-2 and synaptotagmin-like-4 in nasopharyngeal carcinoma cells.
Determined the solution structure of human synaptotagmin-like protein 4 (Slp4). Through modification of cysteine residues, found Slp4 binding of two zinc atoms is required for correct folding.
Title: The unique N-terminal zinc finger of synaptotagmin-like protein 4 reveals FYVE structure.
Granuphilin makes granules immobile and fusion-reluctant beneath the plasma membrane. Those granuphilin-positive, docked granules release a portion of granuphilin upon fusion, and fuse at a frequency and time course similar to those of granuphilin-negative undocked granules. Granuphilin forms a 180-nm cluster at the site of each docked granule, along with granuphilin-interacting Rab27a and Munc18-1 clusters.
Title: Granuphilin exclusively mediates functional granule docking to the plasma membrane.
GLUT5 required an interaction cascade of Rab11, Myo5B, Slp4a, Munc18-2, and Vamp7 with Stx3.
Title: Cargo-selective apical exocytosis in epithelial cells is conducted by Myo5B, Slp4a, Vamp7, and Syntaxin 3.
Phosphatidylinositol 4,5-bisphosphate binds to the concave surface of granuphilin-C2A domain. The key residues involved in the binding were validated by mutation analysis.
Title: Insights into the molecular recognition of the granuphilin C2A domain with PI(4,5)P2.
the mechanisms of granuphilin plasma membrane targeting and release
Title: The C2 domains of granuphilin are high-affinity sensors for plasma membrane lipids.
Recruitment of STXBP1 by the Rab27A effector SYTL4 promotes Weibel-Palade body exocytosis.
Title: STXBP1 promotes Weibel-Palade body exocytosis through its interaction with the Rab27A effector Slp4-a.
Slp4 and Rab8 are expressed and interact in human platelets, and might be involved in dense granule release.
Title: Synaptotagmin-like protein 4 and Rab8 interact and increase dense granule release in platelets.

Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

DXS9763 (e-PCR)
- UniSTS:16705

Sytl4 (e-PCR), detects polymorphism
- UniSTS:525516

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables neurexin family protein binding	IBA Inferred from Biological aspect of Ancestor more info
enables neurexin family protein binding	ISS Inferred from Sequence or Structural Similarity more info
enables phospholipid binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables small GTPase binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in exocytosis	IBA Inferred from Biological aspect of Ancestor more info
involved_in insulin secretion	IEA Inferred from Electronic Annotation more info
involved_in intracellular protein transport	IEA Inferred from Electronic Annotation more info
involved_in lysosome localization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in multivesicular body sorting pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of insulin secretion	IEA Inferred from Electronic Annotation more info
involved_in plasma membrane repair	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of exocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein secretion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of plasma membrane repair	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in endosome	IDA Inferred from Direct Assay more info	PubMed
is_active_in exocytic vesicle	IBA Inferred from Biological aspect of Ancestor more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	TAS Traceable Author Statement more info
located_in platelet alpha granule membrane	TAS Traceable Author Statement more info
located_in transport vesicle membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: synaptotagmin-like protein 4

Names: exophilin-2; granuphilin-a

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.

Genomic

NG_016858.2 RefSeqGene

Range

5026..62656

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001129896.3 → NP_001123368.1 synaptotagmin-like protein 4 isoform 1

See identical proteins and their annotated locations for NP_001123368.1

Status: REVIEWED

Source sequence(s)

AL390040

Consensus CDS

CCDS14472.1

UniProtKB/Swiss-Prot

Q5H9J3, Q5JPG8, Q8N9P4, Q96C24, Q9H4R0, Q9H4R1

UniProtKB/TrEMBL

A8K973, B2R7R4

Conserved Domains (4) summary

cd04020
Location:496 → 661

C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4

cd04029
Location:357 → 481

C2A_SLP-4_5; C2 domain first repeat present in Synaptotagmin-like proteins 4 and 5

cd15764
Location:58 → 107

FYVE_Slp4; FYVE-related domain found in synaptotagmin-like protein 4 (Slp4) and similar proteins

cl22851
Location:8 → 121

PHD_SF; PHD finger superfamily
NM_001174068.2 → NP_001167539.1 synaptotagmin-like protein 4 isoform 1

See identical proteins and their annotated locations for NP_001167539.1

Status: REVIEWED

Source sequence(s)

AL390040

Consensus CDS

CCDS14472.1

UniProtKB/Swiss-Prot

Q5H9J3, Q5JPG8, Q8N9P4, Q96C24, Q9H4R0, Q9H4R1

UniProtKB/TrEMBL

A8K973, B2R7R4

Related

ENSP00000276141.6, ENST00000276141.10

Conserved Domains (4) summary

cd04020
Location:496 → 661

C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4

cd04029
Location:357 → 481

C2A_SLP-4_5; C2 domain first repeat present in Synaptotagmin-like proteins 4 and 5

cd15764
Location:58 → 107

FYVE_Slp4; FYVE-related domain found in synaptotagmin-like protein 4 (Slp4) and similar proteins

cl22851
Location:8 → 121

PHD_SF; PHD finger superfamily
NM_001370160.1 → NP_001357089.1 synaptotagmin-like protein 4 isoform 1

Status: REVIEWED

Source sequence(s)

AL390040

Consensus CDS

CCDS14472.1

UniProtKB/Swiss-Prot

Q5H9J3, Q5JPG8, Q8N9P4, Q96C24, Q9H4R0, Q9H4R1

UniProtKB/TrEMBL

A8K973, B2R7R4

Conserved Domains (4) summary

cd04020
Location:496 → 661

C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4

cd04029
Location:357 → 481

C2A_SLP-4_5; C2 domain first repeat present in Synaptotagmin-like proteins 4 and 5

cd15764
Location:58 → 107

FYVE_Slp4; FYVE-related domain found in synaptotagmin-like protein 4 (Slp4) and similar proteins

cl22851
Location:8 → 121

PHD_SF; PHD finger superfamily
NM_001370161.1 → NP_001357090.1 synaptotagmin-like protein 4 isoform 1

Status: REVIEWED

Source sequence(s)

AL390040

Consensus CDS

CCDS14472.1

UniProtKB/Swiss-Prot

Q5H9J3, Q5JPG8, Q8N9P4, Q96C24, Q9H4R0, Q9H4R1

UniProtKB/TrEMBL

A8K973, B2R7R4

Related

ENSP00000263033.5, ENST00000263033.9

Conserved Domains (4) summary

cd04020
Location:496 → 661

C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4

cd04029
Location:357 → 481

C2A_SLP-4_5; C2 domain first repeat present in Synaptotagmin-like proteins 4 and 5

cd15764
Location:58 → 107

FYVE_Slp4; FYVE-related domain found in synaptotagmin-like protein 4 (Slp4) and similar proteins

cl22851
Location:8 → 121

PHD_SF; PHD finger superfamily
NM_001370162.1 → NP_001357091.1 synaptotagmin-like protein 4 isoform 2

Status: REVIEWED

Source sequence(s)

AL390040

UniProtKB/TrEMBL

A8K973, B2R7R4

Conserved Domains (4) summary

cd04020
Location:496 → 622

C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4

cd04029
Location:357 → 481

C2A_SLP-4_5; C2 domain first repeat present in Synaptotagmin-like proteins 4 and 5

cd15764
Location:58 → 107

FYVE_Slp4; FYVE-related domain found in synaptotagmin-like protein 4 (Slp4) and similar proteins

pfam02318
Location:8 → 121

FYVE_2; FYVE-type zinc finger
NM_001370163.1 → NP_001357092.1 synaptotagmin-like protein 4 isoform 1

Status: REVIEWED

Source sequence(s)

AL390040

Consensus CDS

CCDS14472.1

UniProtKB/Swiss-Prot

Q5H9J3, Q5JPG8, Q8N9P4, Q96C24, Q9H4R0, Q9H4R1

UniProtKB/TrEMBL

A8K973, B2R7R4

Conserved Domains (4) summary

cd04020
Location:496 → 661

C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4

cd04029
Location:357 → 481

C2A_SLP-4_5; C2 domain first repeat present in Synaptotagmin-like proteins 4 and 5

cd15764
Location:58 → 107

FYVE_Slp4; FYVE-related domain found in synaptotagmin-like protein 4 (Slp4) and similar proteins

cl22851
Location:8 → 121

PHD_SF; PHD finger superfamily
NM_001370164.1 → NP_001357093.1 synaptotagmin-like protein 4 isoform 1

Status: REVIEWED

Source sequence(s)

AL390040

Consensus CDS

CCDS14472.1

UniProtKB/Swiss-Prot

Q5H9J3, Q5JPG8, Q8N9P4, Q96C24, Q9H4R0, Q9H4R1

UniProtKB/TrEMBL

A8K973, B2R7R4

Conserved Domains (4) summary

cd04020
Location:496 → 661

C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4

cd04029
Location:357 → 481

C2A_SLP-4_5; C2 domain first repeat present in Synaptotagmin-like proteins 4 and 5

cd15764
Location:58 → 107

FYVE_Slp4; FYVE-related domain found in synaptotagmin-like protein 4 (Slp4) and similar proteins

cl22851
Location:8 → 121

PHD_SF; PHD finger superfamily
NM_001370165.1 → NP_001357094.1 synaptotagmin-like protein 4 isoform 1

Status: REVIEWED

Source sequence(s)

AL390040

Consensus CDS

CCDS14472.1

UniProtKB/Swiss-Prot

Q5H9J3, Q5JPG8, Q8N9P4, Q96C24, Q9H4R0, Q9H4R1

UniProtKB/TrEMBL

A8K973, B2R7R4

Related

ENSP00000362080.1, ENST00000372989.6

Conserved Domains (4) summary

cd04020
Location:496 → 661

C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4

cd04029
Location:357 → 481

C2A_SLP-4_5; C2 domain first repeat present in Synaptotagmin-like proteins 4 and 5

cd15764
Location:58 → 107

FYVE_Slp4; FYVE-related domain found in synaptotagmin-like protein 4 (Slp4) and similar proteins

cl22851
Location:8 → 121

PHD_SF; PHD finger superfamily
NM_001370166.1 → NP_001357095.1 synaptotagmin-like protein 4 isoform 1

Status: REVIEWED

Source sequence(s)

AL390040

Consensus CDS

CCDS14472.1

UniProtKB/Swiss-Prot

Q5H9J3, Q5JPG8, Q8N9P4, Q96C24, Q9H4R0, Q9H4R1

UniProtKB/TrEMBL

A8K973, B2R7R4

Conserved Domains (4) summary

cd04020
Location:496 → 661

C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4

cd04029
Location:357 → 481

C2A_SLP-4_5; C2 domain first repeat present in Synaptotagmin-like proteins 4 and 5

cd15764
Location:58 → 107

FYVE_Slp4; FYVE-related domain found in synaptotagmin-like protein 4 (Slp4) and similar proteins

cl22851
Location:8 → 121

PHD_SF; PHD finger superfamily
NM_001370167.1 → NP_001357096.1 synaptotagmin-like protein 4 isoform 1

Status: REVIEWED

Source sequence(s)

AL390040

Consensus CDS

CCDS14472.1

UniProtKB/Swiss-Prot

Q5H9J3, Q5JPG8, Q8N9P4, Q96C24, Q9H4R0, Q9H4R1

UniProtKB/TrEMBL

A8K973, B2R7R4

Related

ENSP00000509693.1, ENST00000685623.1

Conserved Domains (4) summary

cd04020
Location:496 → 661

C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4

cd04029
Location:357 → 481

C2A_SLP-4_5; C2 domain first repeat present in Synaptotagmin-like proteins 4 and 5

cd15764
Location:58 → 107

FYVE_Slp4; FYVE-related domain found in synaptotagmin-like protein 4 (Slp4) and similar proteins

cl22851
Location:8 → 121

PHD_SF; PHD finger superfamily
NM_001370168.1 → NP_001357097.1 synaptotagmin-like protein 4 isoform 1

Status: REVIEWED

Source sequence(s)

AL390040

Consensus CDS

CCDS14472.1

UniProtKB/Swiss-Prot

Q5H9J3, Q5JPG8, Q8N9P4, Q96C24, Q9H4R0, Q9H4R1

UniProtKB/TrEMBL

A8K973, B2R7R4

Conserved Domains (4) summary

cd04020
Location:496 → 661

C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4

cd04029
Location:357 → 481

C2A_SLP-4_5; C2 domain first repeat present in Synaptotagmin-like proteins 4 and 5

cd15764
Location:58 → 107

FYVE_Slp4; FYVE-related domain found in synaptotagmin-like protein 4 (Slp4) and similar proteins

cl22851
Location:8 → 121

PHD_SF; PHD finger superfamily
NM_001370169.1 → NP_001357098.1 synaptotagmin-like protein 4 isoform 1

Status: REVIEWED

Source sequence(s)

AL390040

Consensus CDS

CCDS14472.1

UniProtKB/Swiss-Prot

Q5H9J3, Q5JPG8, Q8N9P4, Q96C24, Q9H4R0, Q9H4R1

UniProtKB/TrEMBL

A8K973, B2R7R4

Conserved Domains (4) summary

cd04020
Location:496 → 661

C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4

cd04029
Location:357 → 481

C2A_SLP-4_5; C2 domain first repeat present in Synaptotagmin-like proteins 4 and 5

cd15764
Location:58 → 107

FYVE_Slp4; FYVE-related domain found in synaptotagmin-like protein 4 (Slp4) and similar proteins

cl22851
Location:8 → 121

PHD_SF; PHD finger superfamily
NM_080737.3 → NP_542775.2 synaptotagmin-like protein 4 isoform 1

See identical proteins and their annotated locations for NP_542775.2

Status: REVIEWED

Source sequence(s)

AL390040

Consensus CDS

CCDS14472.1

UniProtKB/Swiss-Prot

Q5H9J3, Q5JPG8, Q8N9P4, Q96C24, Q9H4R0, Q9H4R1

UniProtKB/TrEMBL

A8K973, B2R7R4

Conserved Domains (4) summary

cd04020
Location:496 → 661

C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4

cd04029
Location:357 → 481

C2A_SLP-4_5; C2 domain first repeat present in Synaptotagmin-like proteins 4 and 5

cd15764
Location:58 → 107

FYVE_Slp4; FYVE-related domain found in synaptotagmin-like protein 4 (Slp4) and similar proteins

cl22851
Location:8 → 121

PHD_SF; PHD finger superfamily

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000023.11 Reference GRCh38.p14 Primary Assembly

Range

100674491..100732121 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017029968.2 → XP_016885457.1 synaptotagmin-like protein 4 isoform X1

UniProtKB/TrEMBL

A8K973, B2R7R4

Conserved Domains (4) summary

cd04020
Location:496 → 622

C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4

cd04029
Location:357 → 481

C2A_SLP-4_5; C2 domain first repeat present in Synaptotagmin-like proteins 4 and 5

cd15764
Location:58 → 107

FYVE_Slp4; FYVE-related domain found in synaptotagmin-like protein 4 (Slp4) and similar proteins

pfam02318
Location:8 → 121

FYVE_2; FYVE-type zinc finger
XM_017029967.3 → XP_016885456.1 synaptotagmin-like protein 4 isoform X1

UniProtKB/TrEMBL

A8K973, B2R7R4

Conserved Domains (4) summary

cd04020
Location:496 → 622

C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4

cd04029
Location:357 → 481

C2A_SLP-4_5; C2 domain first repeat present in Synaptotagmin-like proteins 4 and 5

cd15764
Location:58 → 107

FYVE_Slp4; FYVE-related domain found in synaptotagmin-like protein 4 (Slp4) and similar proteins

pfam02318
Location:8 → 121

FYVE_2; FYVE-type zinc finger
XM_047442649.1 → XP_047298605.1 synaptotagmin-like protein 4 isoform X1
XM_017029966.2 → XP_016885455.1 synaptotagmin-like protein 4 isoform X1

UniProtKB/TrEMBL

A8K973, B2R7R4

Conserved Domains (4) summary

cd04020
Location:496 → 622

C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4

cd04029
Location:357 → 481

C2A_SLP-4_5; C2 domain first repeat present in Synaptotagmin-like proteins 4 and 5

cd15764
Location:58 → 107

FYVE_Slp4; FYVE-related domain found in synaptotagmin-like protein 4 (Slp4) and similar proteins

pfam02318
Location:8 → 121

FYVE_2; FYVE-type zinc finger
XM_047442651.1 → XP_047298607.1 synaptotagmin-like protein 4 isoform X2

UniProtKB/Swiss-Prot

Q5H9J3, Q5JPG8, Q8N9P4, Q96C24, Q9H4R0, Q9H4R1
XM_047442650.1 → XP_047298606.1 synaptotagmin-like protein 4 isoform X1