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    SYTL3 synaptotagmin like 3 [ Homo sapiens (human) ]

    Gene ID: 94120, updated on 3-Apr-2024

    Summary

    Official Symbol
    SYTL3provided by HGNC
    Official Full Name
    synaptotagmin like 3provided by HGNC
    Primary source
    HGNC:HGNC:15587
    See related
    Ensembl:ENSG00000164674 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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Location:
    6q25.3
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (158644936..158764871)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (159886606..160010070)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (159071086..159185903)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene transmembrane protein 181 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:159030351-159030852 Neighboring gene TatD DNase domain containing 2 pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:159051575-159052076 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:159052077-159052576 Neighboring gene microRNA 7161 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:159053255-159053416 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159065146-159066089 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17742 Neighboring gene dynein light chain Tctex-type 1 Neighboring gene MPRA-validated peak6273 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25359 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159128779-159129410 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159129411-159130042 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25360 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:159141094-159142293 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:159151193-159152392 Neighboring gene AMZ2 pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:159176343-159176927 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:159180075-159180750 Neighboring gene Sharpr-MPRA regulatory region 4567 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:159192487-159192693 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:159193631-159194830 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:159205226-159206425 Neighboring gene microRNA 3918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25363 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25364 Neighboring gene ezrin Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25365 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17743 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25366 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25367 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25368 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17744 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17745 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17746 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25369 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159245802-159246776 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25370 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159256297-159256987 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159256988-159257678 Neighboring gene EZR antisense RNA 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159273679-159274204 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159274205-159274730 Neighboring gene uncharacterized LOC124901448 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159274731-159275254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25373 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159275781-159276305 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159276306-159276830 Neighboring gene oligosaccharyltransferase complex subunit pseudogene 1

    Genomic regions, transcripts, and products

    Bibliography

    GeneRIFs: Gene References Into Functions

    What'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 PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    Preferred Names
    synaptotagmin-like protein 3
    Names
    exophilin-6

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_029794.2 RefSeqGene

      Range
      10120..124937
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001009991.4NP_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: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_001242384.2NP_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: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_001242394.2NP_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: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_001242395.2NP_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: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_001318745.2NP_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: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: 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

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      158644936..158764871
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006715606.4XP_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: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
    2. XM_047419556.1XP_047275512.1  synaptotagmin-like protein 3 isoform X2

    3. XM_011536254.3XP_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: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_006715611.4XP_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: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
    5. XM_047419560.1XP_047275516.1  synaptotagmin-like protein 3 isoform X4

    6. XM_047419552.1XP_047275508.1  synaptotagmin-like protein 3 isoform X1

      UniProtKB/Swiss-Prot
      Q496J4, Q496J6, Q4VX76, Q5U3B9
    7. XM_047419557.1XP_047275513.1  synaptotagmin-like protein 3 isoform X2

    8. XM_047419553.1XP_047275509.1  synaptotagmin-like protein 3 isoform X1

      UniProtKB/Swiss-Prot
      Q496J4, Q496J6, Q4VX76, Q5U3B9
    9. XM_047419550.1XP_047275506.1  synaptotagmin-like protein 3 isoform X1

      UniProtKB/Swiss-Prot
      Q496J4, Q496J6, Q4VX76, Q5U3B9
    10. XM_047419554.1XP_047275510.1  synaptotagmin-like protein 3 isoform X2

    11. XM_047419549.1XP_047275505.1  synaptotagmin-like protein 3 isoform X1

      UniProtKB/Swiss-Prot
      Q496J4, Q496J6, Q4VX76, Q5U3B9
    12. XM_047419555.1XP_047275511.1  synaptotagmin-like protein 3 isoform X2

    13. XM_047419558.1XP_047275514.1  synaptotagmin-like protein 3 isoform X2

    14. XM_047419551.1XP_047275507.1  synaptotagmin-like protein 3 isoform X1

      UniProtKB/Swiss-Prot
      Q496J4, Q496J6, Q4VX76, Q5U3B9
    15. XM_047419561.1XP_047275517.1  synaptotagmin-like protein 3 isoform X4

    16. XM_017011499.2XP_016866988.1  synaptotagmin-like protein 3 isoform X6

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

      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
    18. XM_047419562.1XP_047275518.1  synaptotagmin-like protein 3 isoform X5

    19. XM_047419559.1XP_047275515.1  synaptotagmin-like protein 3 isoform X4

    20. XM_005267222.5XP_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: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
    21. XM_011536255.3XP_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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      159886606..160010070
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356804.1XP_054212779.1  synaptotagmin-like protein 3 isoform X1

    2. XM_054356801.1XP_054212776.1  synaptotagmin-like protein 3 isoform X1

    3. XM_054356814.1XP_054212789.1  synaptotagmin-like protein 3 isoform X2

    4. XM_054356824.1XP_054212799.1  synaptotagmin-like protein 3 isoform X6

    5. XM_054356806.1XP_054212781.1  synaptotagmin-like protein 3 isoform X2

    6. XM_054356793.1XP_054212768.1  synaptotagmin-like protein 3 isoform X1

    7. XM_054356794.1XP_054212769.1  synaptotagmin-like protein 3 isoform X1

    8. XM_054356811.1XP_054212786.1  synaptotagmin-like protein 3 isoform X2

    9. XM_054356798.1XP_054212773.1  synaptotagmin-like protein 3 isoform X1

    10. XM_054356797.1XP_054212772.1  synaptotagmin-like protein 3 isoform X1

    11. XM_054356809.1XP_054212784.1  synaptotagmin-like protein 3 isoform X2

    12. XM_054356803.1XP_054212778.1  synaptotagmin-like protein 3 isoform X1

    13. XM_054356807.1XP_054212782.1  synaptotagmin-like protein 3 isoform X2

    14. XM_054356800.1XP_054212775.1  synaptotagmin-like protein 3 isoform X1

    15. XM_054356812.1XP_054212787.1  synaptotagmin-like protein 3 isoform X2

    16. XM_054356819.1XP_054212794.1  synaptotagmin-like protein 3 isoform X4

    17. XM_054356818.1XP_054212793.1  synaptotagmin-like protein 3 isoform X4

    18. XM_054356802.1XP_054212777.1  synaptotagmin-like protein 3 isoform X1

    19. XM_054356796.1XP_054212771.1  synaptotagmin-like protein 3 isoform X1

    20. XM_054356808.1XP_054212783.1  synaptotagmin-like protein 3 isoform X2

    21. XM_054356795.1XP_054212770.1  synaptotagmin-like protein 3 isoform X1

    22. XM_054356810.1XP_054212785.1  synaptotagmin-like protein 3 isoform X2

    23. XM_054356813.1XP_054212788.1  synaptotagmin-like protein 3 isoform X2

    24. XM_054356799.1XP_054212774.1  synaptotagmin-like protein 3 isoform X1

    25. XM_054356805.1XP_054212780.1  synaptotagmin-like protein 3 isoform X1

    26. XM_054356822.1XP_054212797.1  synaptotagmin-like protein 3 isoform X4

    27. XM_054356821.1XP_054212796.1  synaptotagmin-like protein 3 isoform X4

    28. XM_054356820.1XP_054212795.1  synaptotagmin-like protein 3 isoform X4

    29. XM_054356823.1XP_054212798.1  synaptotagmin-like protein 3 isoform X4

    30. XM_054356816.1XP_054212791.1  synaptotagmin-like protein 3 isoform X4

    31. XM_054356817.1XP_054212792.1  synaptotagmin-like protein 3 isoform X4

    32. XM_054356815.1XP_054212790.1  synaptotagmin-like protein 3 isoform X3