SYTL3 synaptotagmin like 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SYTL3provided by HGNC
Official Full Name: synaptotagmin like 3provided by HGNC
Primary source: HGNC:HGNC:15587
See related: Ensembl:ENSG00000164674 MIM:620973; AllianceGenome:HGNC:15587
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: SLP3
Summary: The protein encoded by this gene belongs to a family of peripheral membrane proteins that play a role in vesicular trafficking. This protein binds phospholipids in the presence of calcium ions. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016]
Expression: Ubiquitous expression in thyroid (RPKM 15.0), small intestine (RPKM 10.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6q25.3

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (158644936..158764871)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (159886606..160010070)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (159071086..159185903)

Chromosome 6 - NC_000006.12 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?

Transcriptional networks identify synaptotagmin-like 3 as a regulator of cortical neuronal migration during early neurodevelopment.
Title: Transcriptional networks identify synaptotagmin-like 3 as a regulator of cortical neuronal migration during early neurodevelopment.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
Synaptotagmin-like protein 3-a (Slp3-a) contains an N-terminal Slp homology domain (SHD) (PMID: 11327731). The SHD of Slp3-a specifically and directly binds the GTP-bound form of Rab27A.
Title: The Slp homology domain of synaptotagmin-like proteins 1-4 and Slac2 functions as a novel Rab27A binding domain.

Submit: New GeneRIF Correction

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)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Silencing of SLP3 by shRNA inhibits HIV-1 replication in Jurkat cells	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Pr55(Gag)	gag	Silencing the expression of SLP3 leads to a diffuse intracellular HIV-1 Gag staining pattern accompanied by a dramatic reduction in the association of Gag with the plasma membrane	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-2438 (e-PCR)
- UniSTS:92173

SHGC-132381 (e-PCR)
- UniSTS:170808

D16S325 (e-PCR)
- UniSTS:147089

RH46204 (e-PCR)
- UniSTS:2965

SHGC-147444 (e-PCR)
- UniSTS:175814

D6S1975 (e-PCR)
- UniSTS:74723

RH122273 (e-PCR)
- UniSTS:134899

Clone Names

MGC105130, MGC118883, MGC118884, MGC118885

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium-dependent phospholipid binding	IEA Inferred from Electronic Annotation more info
enables neurexin family protein binding	IBA Inferred from Biological aspect of Ancestor 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 intracellular protein transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
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

General protein information

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Preferred Names: synaptotagmin-like protein 3

Names: exophilin-6

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_029794.2 RefSeqGene

Range

10120..124937

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001009991.4 → NP_001009991.2 synaptotagmin-like protein 3 isoform 2

See identical proteins and their annotated locations for NP_001009991.2

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate splice site in the 5' UTR and lacks two in-frame coding exons compared to variant 1. This results in a shorter isoform (2) compared to isoform 1. Variants 3 and 4 encode the same isoform (2).

Source sequence(s)

AI674404, AK304191, AL567177, BC085612, DC394549

Consensus CDS

CCDS34563.1

UniProtKB/TrEMBL

B4DQA6

Conserved Domains (3) summary

cd04020
Location:380 → 542

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

cd08392
Location:239 → 366

C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3

cl22851
Location:60 → 108

PHD_SF; PHD finger superfamily
NM_001242384.2 → NP_001229313.1 synaptotagmin-like protein 3 isoform 1

See identical proteins and their annotated locations for NP_001229313.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1). Variants 1 and 2 encode the same isoform (1).

Source sequence(s)

AI674404, AK304191, AL567177, BC100830, DC394549

Consensus CDS

CCDS56458.1

UniProtKB/Swiss-Prot

Q496J4, Q496J6, Q4VX76, Q5U3B9

UniProtKB/TrEMBL

B4DQA6

Related

ENSP00000353631.4, ENST00000360448.8

Conserved Domains (4) summary

cd04020
Location:448 → 610

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

cd08392
Location:307 → 434

C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3

cd15765
Location:60 → 108

FYVE_Slp3; FYVE-related domain found in synaptotagmin-like protein 3 (Slp3) and similar proteins

cl22851
Location:8 → 123

PHD_SF; PHD finger superfamily
NM_001242394.2 → NP_001229323.1 synaptotagmin-like protein 3 isoform 1

See identical proteins and their annotated locations for NP_001229323.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains an alternate segment in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (1).

Source sequence(s)

AI674404, AK304191, AL567177, BC100829, DC394549

Consensus CDS

CCDS56458.1

UniProtKB/Swiss-Prot

Q496J4, Q496J6, Q4VX76, Q5U3B9

UniProtKB/TrEMBL

B4DQA6

Related

ENSP00000483936.1, ENST00000611299.5

Conserved Domains (4) summary

cd04020
Location:448 → 610

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

cd08392
Location:307 → 434

C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3

cd15765
Location:60 → 108

FYVE_Slp3; FYVE-related domain found in synaptotagmin-like protein 3 (Slp3) and similar proteins

cl22851
Location:8 → 123

PHD_SF; PHD finger superfamily
NM_001242395.2 → NP_001229324.1 synaptotagmin-like protein 3 isoform 2

See identical proteins and their annotated locations for NP_001229324.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) contains an alternate segment in the 5' UTR and lacks two in-frame coding exons compared to variant 1. This results in a shorter isoform (2) compared to isoform 1. Variants 3 and 4 encode the same isoform (2).

Source sequence(s)

AI674404, AK304191, AL567177, BC100828, DC394549

Consensus CDS

CCDS34563.1

UniProtKB/TrEMBL

B4DQA6

Related

ENSP00000356048.4, ENST00000367081.7

Conserved Domains (3) summary

cd04020
Location:380 → 542

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

cd08392
Location:239 → 366

C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3

cl22851
Location:60 → 108

PHD_SF; PHD finger superfamily
NM_001318745.2 → NP_001305674.1 synaptotagmin-like protein 3 isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon compared to variant 1. The resulting isoform (3) has a shorter N-terminus than isoform 1.

Source sequence(s)

AI674404, AK055750, AK304191, AL589931, BC085612

UniProtKB/TrEMBL

B4E2A9

Conserved Domains (2) summary

cd04020
Location:242 → 404

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

cd08392
Location:101 → 228

C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

158644936..158764871

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006715606.4 → XP_006715669.1 synaptotagmin-like protein 3 isoform X1

See identical proteins and their annotated locations for XP_006715669.1

UniProtKB/Swiss-Prot

Q496J4, Q496J6, Q4VX76, Q5U3B9

UniProtKB/TrEMBL

B4DQA6

Conserved Domains (4) summary

cd04020
Location:448 → 610

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

cd08392
Location:307 → 434

C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3

cd15765
Location:60 → 108

FYVE_Slp3; FYVE-related domain found in synaptotagmin-like protein 3 (Slp3) and similar proteins

cl22851
Location:8 → 123

PHD_SF; PHD finger superfamily
XM_047419556.1 → XP_047275512.1 synaptotagmin-like protein 3 isoform X2
XM_011536254.3 → XP_011534556.1 synaptotagmin-like protein 3 isoform X1

See identical proteins and their annotated locations for XP_011534556.1

UniProtKB/Swiss-Prot

Q496J4, Q496J6, Q4VX76, Q5U3B9

UniProtKB/TrEMBL

B4DQA6

Conserved Domains (4) summary

cd04020
Location:448 → 610

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

cd08392
Location:307 → 434

C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3

cd15765
Location:60 → 108

FYVE_Slp3; FYVE-related domain found in synaptotagmin-like protein 3 (Slp3) and similar proteins

cl22851
Location:8 → 123

PHD_SF; PHD finger superfamily
XM_006715611.4 → XP_006715674.1 synaptotagmin-like protein 3 isoform X4

See identical proteins and their annotated locations for XP_006715674.1

UniProtKB/TrEMBL

B4E2A9

Conserved Domains (2) summary

cd04020
Location:242 → 404

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

cd08392
Location:101 → 228

C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
XM_047419560.1 → XP_047275516.1 synaptotagmin-like protein 3 isoform X4
XM_047419552.1 → XP_047275508.1 synaptotagmin-like protein 3 isoform X1

UniProtKB/Swiss-Prot

Q496J4, Q496J6, Q4VX76, Q5U3B9
XM_047419557.1 → XP_047275513.1 synaptotagmin-like protein 3 isoform X2
XM_047419553.1 → XP_047275509.1 synaptotagmin-like protein 3 isoform X1

UniProtKB/Swiss-Prot

Q496J4, Q496J6, Q4VX76, Q5U3B9
XM_047419550.1 → XP_047275506.1 synaptotagmin-like protein 3 isoform X1

UniProtKB/Swiss-Prot

Q496J4, Q496J6, Q4VX76, Q5U3B9
XM_047419554.1 → XP_047275510.1 synaptotagmin-like protein 3 isoform X2
XM_047419549.1 → XP_047275505.1 synaptotagmin-like protein 3 isoform X1

UniProtKB/Swiss-Prot

Q496J4, Q496J6, Q4VX76, Q5U3B9
XM_047419555.1 → XP_047275511.1 synaptotagmin-like protein 3 isoform X2
XM_047419558.1 → XP_047275514.1 synaptotagmin-like protein 3 isoform X2
XM_047419551.1 → XP_047275507.1 synaptotagmin-like protein 3 isoform X1

UniProtKB/Swiss-Prot

Q496J4, Q496J6, Q4VX76, Q5U3B9
XM_047419561.1 → XP_047275517.1 synaptotagmin-like protein 3 isoform X4
XM_017011499.2 → XP_016866988.1 synaptotagmin-like protein 3 isoform X6
XM_017011496.2 → XP_016866985.1 synaptotagmin-like protein 3 isoform X4

UniProtKB/TrEMBL

B4E2A9

Conserved Domains (2) summary

cd04020
Location:242 → 404

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

cd08392
Location:101 → 228

C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
XM_047419562.1 → XP_047275518.1 synaptotagmin-like protein 3 isoform X5
XM_047419559.1 → XP_047275515.1 synaptotagmin-like protein 3 isoform X4
XM_005267222.5 → XP_005267279.1 synaptotagmin-like protein 3 isoform X4

See identical proteins and their annotated locations for XP_005267279.1

UniProtKB/TrEMBL

B4E2A9

Conserved Domains (2) summary

cd04020
Location:242 → 404

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

cd08392
Location:101 → 228

C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
XM_011536255.3 → XP_011534557.1 synaptotagmin-like protein 3 isoform X3

Conserved Domains (2) summary

cd04020
Location:247 → 409

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

cd08392
Location:106 → 233

C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3