Format

Send to:

Choose Destination

SYTL3 synaptotagmin like 3 [ Homo sapiens (human) ]

Gene ID: 94120, updated on 17-Jun-2019

Summary

Official Symbol
SYTL3provided by HGNC
Official Full Name
synaptotagmin like 3provided by HGNC
Primary source
HGNC:HGNC:15587
See related
Ensembl:ENSG00000164674
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

Genomic context

See SYTL3 in Genome Data Viewer
Location:
6q25.3
Exon count:
22
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (158644867..158766298)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (159065931..159185908)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene transmembrane protein 181 Neighboring gene TatD DNase domain containing 2 pseudogene 2 Neighboring gene microRNA 7161 Neighboring gene dynein light chain Tctex-type 1 Neighboring gene archaelysin family metallopeptidase 2 pseudogene 2 Neighboring gene microRNA 3918 Neighboring gene ezrin Neighboring gene EZR antisense RNA 1 Neighboring gene oligosaccharyltransferase complex subunit pseudogene 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

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

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC105130, MGC118883, MGC118884, MGC118885

Gene Ontology Provided by GOA

Function Evidence Code Pubs
Rab GTPase binding IEA
Inferred from Electronic Annotation
more info
 
calcium-dependent phospholipid binding IEA
Inferred from Electronic Annotation
more info
 
neurexin family protein binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
exocytosis IEA
Inferred from Electronic Annotation
more info
 
intracellular protein transport IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
exocytic vesicle IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extrinsic component of plasma membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
synaptotagmin-like protein 3
Names
exophilin-6

NCBI Reference Sequences (RefSeq)

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

  1. NG_029794.1 RefSeqGene

    Range
    5001..119863
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001009991.3NP_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/Swiss-Prot
    Q4VX76
    UniProtKB/TrEMBL
    B4E2A9
    Conserved Domains (3) summary
    cd04020
    Location:380542
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:239366
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
    cl22851
    Location:60108
    PHD_SF; PHD finger superfamily
  2. NM_001242384.1NP_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
    Q4VX76
    UniProtKB/TrEMBL
    B4E2A9
    Related
    ENSP00000353631.4, ENST00000360448.7
    Conserved Domains (4) summary
    cd04020
    Location:448610
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:307434
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
    cd15765
    Location:60108
    FYVE_Slp3; FYVE-related domain found in synaptotagmin-like protein 3 (Slp3) and similar proteins
    cl22851
    Location:8123
    PHD_SF; PHD finger superfamily
  3. NM_001242394.1NP_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
    Q4VX76
    UniProtKB/TrEMBL
    B4E2A9
    Related
    ENSP00000483936.1, ENST00000611299.4
    Conserved Domains (4) summary
    cd04020
    Location:448610
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:307434
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
    cd15765
    Location:60108
    FYVE_Slp3; FYVE-related domain found in synaptotagmin-like protein 3 (Slp3) and similar proteins
    cl22851
    Location:8123
    PHD_SF; PHD finger superfamily
  4. NM_001242395.1NP_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
    B4E2A9
    Related
    ENSP00000356048.4, ENST00000367081.7
    Conserved Domains (3) summary
    cd04020
    Location:380542
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:239366
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
    cl22851
    Location:60108
    PHD_SF; PHD finger superfamily
  5. NM_001318745.1NP_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, BC085612
    UniProtKB/Swiss-Prot
    Q4VX76
    UniProtKB/TrEMBL
    B4E2A9
    Conserved Domains (2) summary
    cd04020
    Location:242404
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:101228
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    158644867..158766298
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017011498.2XP_016866987.1  synaptotagmin-like protein 3 isoform X5

  2. XM_017011496.1XP_016866985.1  synaptotagmin-like protein 3 isoform X4

    Conserved Domains (2) summary
    cd04020
    Location:242404
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:101228
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
  3. XM_006715605.3XP_006715668.1  synaptotagmin-like protein 3 isoform X1

    See identical proteins and their annotated locations for XP_006715668.1

    UniProtKB/Swiss-Prot
    Q4VX76
    Conserved Domains (4) summary
    cd04020
    Location:448610
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:307434
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
    cd15765
    Location:60108
    FYVE_Slp3; FYVE-related domain found in synaptotagmin-like protein 3 (Slp3) and similar proteins
    cl22851
    Location:8123
    PHD_SF; PHD finger superfamily
  4. XM_006715606.3XP_006715669.1  synaptotagmin-like protein 3 isoform X1

    See identical proteins and their annotated locations for XP_006715669.1

    UniProtKB/Swiss-Prot
    Q4VX76
    Conserved Domains (4) summary
    cd04020
    Location:448610
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:307434
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
    cd15765
    Location:60108
    FYVE_Slp3; FYVE-related domain found in synaptotagmin-like protein 3 (Slp3) and similar proteins
    cl22851
    Location:8123
    PHD_SF; PHD finger superfamily
  5. XM_011536254.2XP_011534556.1  synaptotagmin-like protein 3 isoform X1

    See identical proteins and their annotated locations for XP_011534556.1

    UniProtKB/Swiss-Prot
    Q4VX76
    Conserved Domains (4) summary
    cd04020
    Location:448610
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:307434
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
    cd15765
    Location:60108
    FYVE_Slp3; FYVE-related domain found in synaptotagmin-like protein 3 (Slp3) and similar proteins
    cl22851
    Location:8123
    PHD_SF; PHD finger superfamily
  6. XM_006715611.3XP_006715674.1  synaptotagmin-like protein 3 isoform X4

    See identical proteins and their annotated locations for XP_006715674.1

    Conserved Domains (2) summary
    cd04020
    Location:242404
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:101228
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
  7. XM_017011495.1XP_016866984.1  synaptotagmin-like protein 3 isoform X2

    Conserved Domains (3) summary
    cd08392
    Location:239366
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
    cl14603
    Location:380438
    C2; C2 domain
    cl22851
    Location:60108
    PHD_SF; PHD finger superfamily
  8. XM_017011499.1XP_016866988.1  synaptotagmin-like protein 3 isoform X6

  9. XM_005267215.4XP_005267272.1  synaptotagmin-like protein 3 isoform X1

    See identical proteins and their annotated locations for XP_005267272.1

    UniProtKB/Swiss-Prot
    Q4VX76
    Conserved Domains (4) summary
    cd04020
    Location:448610
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:307434
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
    cd15765
    Location:60108
    FYVE_Slp3; FYVE-related domain found in synaptotagmin-like protein 3 (Slp3) and similar proteins
    cl22851
    Location:8123
    PHD_SF; PHD finger superfamily
  10. XM_024446588.1XP_024302356.1  synaptotagmin-like protein 3 isoform X1

    Conserved Domains (4) summary
    cd04020
    Location:448610
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:307434
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
    cd15765
    Location:60108
    FYVE_Slp3; FYVE-related domain found in synaptotagmin-like protein 3 (Slp3) and similar proteins
    cl22851
    Location:8123
    PHD_SF; PHD finger superfamily
  11. XM_017011497.1XP_016866986.1  synaptotagmin-like protein 3 isoform X4

    Conserved Domains (2) summary
    cd04020
    Location:242404
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:101228
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
  12. XM_005267218.4XP_005267275.1  synaptotagmin-like protein 3 isoform X4

    See identical proteins and their annotated locations for XP_005267275.1

    Conserved Domains (2) summary
    cd04020
    Location:242404
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:101228
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
  13. XM_005267222.4XP_005267279.1  synaptotagmin-like protein 3 isoform X4

    See identical proteins and their annotated locations for XP_005267279.1

    Conserved Domains (2) summary
    cd04020
    Location:242404
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:101228
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
  14. XM_011536255.2XP_011534557.1  synaptotagmin-like protein 3 isoform X3

    Conserved Domains (2) summary
    cd04020
    Location:247409
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:106233
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
Support Center