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SYNJ1 synaptojanin 1 [ Homo sapiens (human) ]

Gene ID: 8867, updated on 3-Apr-2024

Summary

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Official Symbol
SYNJ1provided by HGNC
Official Full Name
synaptojanin 1provided by HGNC
Primary source
HGNC:HGNC:11503
See related
Ensembl:ENSG00000159082 MIM:604297; AllianceGenome:HGNC:11503
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
DEE53; EIEE53; INPP5G; PARK20
Summary
This gene encodes a phosphoinositide phosphatase that regulates levels of membrane phosphatidylinositol-4,5-bisphosphate. As such, expression of this enzyme may affect synaptic transmission and membrane trafficking. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
Expression
Broad expression in brain (RPKM 21.4), bone marrow (RPKM 6.6) and 22 other tissues See more
Orthologs
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Genomic context

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Location:
21q22.11
Exon count:
34
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (32628759..32728394, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (30994760..31094413, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (34001069..34100351, complement)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene CFAP298-TCP10L readthrough Neighboring gene Sharpr-MPRA regulatory region 410 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18365 Neighboring gene cilia and flagella associated protein 298 Neighboring gene olfactory receptor family 7 subfamily E member 23 pseudogene Neighboring gene uncharacterized LOC124905011 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:34033532-34033721 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:34099530-34100030 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:34100031-34100531 Neighboring gene PAXBP1 antisense RNA 1 Neighboring gene uncharacterized LOC124905010 Neighboring gene PAX3 and PAX7 binding protein 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:34143733-34144722 Neighboring gene EPCIP antisense RNA 1 Neighboring gene exosomal polycystin 1 interacting protein

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. A structure of substrate-bound Synaptojanin1 provides new insights in its mechanism and the effect of disease mutations. Paesmans J, et al. Elife, 2020 Dec 22. PMID 33349335, Free PMC Article
  2. The lipid phosphatase Synaptojanin 1 undergoes a significant alteration in expression and solubility and is associated with brain lesions in Alzheimer's disease. Ando K, et al. Acta Neuropathol Commun, 2020 Jun 3. PMID 32493451, Free PMC Article
  3. A novel homozygous SYNJ1 mutation in two siblings with typical Parkinson's disease. Xie F, et al. Parkinsonism Relat Disord, 2019 Dec. PMID 31751865
  4. A Novel SYNJ1 Mutation in a Tunisian Family with Juvenile Parkinson's Disease Associated with Epilepsy. Ben Romdhan S, et al. J Mol Neurosci, 2018 Oct. PMID 30187305
  5. Alteration of endosomal trafficking is associated with early-onset parkinsonism caused by SYNJ1 mutations. Fasano D, et al. Cell Death Dis, 2018 Mar 7. PMID 29515184, Free PMC Article

See all (91) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. alpha-Synuclein induces deficiency in clathrin-mediated endocytosis through inhibiting synaptojanin1 expression.
    Title: α-Synuclein induces deficiency in clathrin-mediated endocytosis through inhibiting synaptojanin1 expression.
  2. Asparagine endopeptidase cleaves synaptojanin 1 and triggers synaptic dysfunction in Parkinson's disease.
    Title: Asparagine endopeptidase cleaves synaptojanin 1 and triggers synaptic dysfunction in Parkinson's disease.
  3. The lipid phosphatase Synaptojanin 1 undergoes a significant alteration in expression and solubility and is associated with brain lesions in Alzheimer's disease.
    Title: The lipid phosphatase Synaptojanin 1 undergoes a significant alteration in expression and solubility and is associated with brain lesions in Alzheimer's disease.
  4. A structure of substrate-bound Synaptojanin1 provides new insights in its mechanism and the effect of disease mutations.
    Title: A structure of substrate-bound Synaptojanin1 provides new insights in its mechanism and the effect of disease mutations.
  5. TGFbeta receptor endocytosis and Smad signaling require synaptojanin1, PI3K-C2alpha-, and INPP4B-mediated phosphoinositide conversions.
    Title: TGFβ receptor endocytosis and Smad signaling require synaptojanin1, PI3K-C2α-, and INPP4B-mediated phosphoinositide conversions.
  6. A novel homozygous SYNJ1 mutation in two siblings with typical Parkinson's disease.
    Title: A novel homozygous SYNJ1 mutation in two siblings with typical Parkinson's disease.
  7. SYNJ1 contributes to memory deficits in the aging hippocampus in all forms of Alzheimer's disease.
    Title: Excess Synaptojanin 1 Contributes to Place Cell Dysfunction and Memory Deficits in the Aging Hippocampus in Three Types of Alzheimer's Disease.
  8. Data indicate that Synj1 plays a crucial role in regulating the homeostasis and functions of early endosomal compartments in different cell types, and highlight defective cellular pathways in PARK20. In addition, they strengthen the link between endosomal trafficking and Parkinson's disease.
    Title: Alteration of endosomal trafficking is associated with early-onset parkinsonism caused by SYNJ1 mutations.
  9. A novel mutation in the C-terminal domain identified in family members with juvenile PD and epilepsy.
    Title: A Novel SYNJ1 Mutation in a Tunisian Family with Juvenile Parkinson's Disease Associated with Epilepsy.
  10. Excess of rare putative functional variants at SYNJ1 in schizophrenia.
    Title: Identification of putative second genetic hits in schizophrenia carriers of high-risk copy number variants and resequencing in additional samples.
Submit: New GeneRIF Correction See all GeneRIFs (29)

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

Associated conditions

Description Tests
Developmental and epileptic encephalopathy, 53
MedGen: C4479313 OMIM: 617389 GeneReviews: Not available
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Early-onset Parkinson disease 20
MedGen: C3809824 OMIM: 615530 GeneReviews: Not available
Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables SH3 domain binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables inositol-1,4,5-trisphosphate 5-phosphatase activity TAS
Traceable Author Statement
more info
  
enables phosphatidylinositol phosphate 4-phosphatase activity TAS
Traceable Author Statement
more info
  
enables phosphatidylinositol phosphate 5-phosphatase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity TAS
Traceable Author Statement
more info
  
enables phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity TAS
Traceable Author Statement
more info
  
enables phosphatidylinositol-3-phosphate phosphatase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables phosphatidylinositol-3-phosphate phosphatase activity TAS
Traceable Author Statement
more info
  
enables phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity TAS
Traceable Author Statement
more info
  
enables phosphatidylinositol-4-phosphate phosphatase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in inositol phosphate metabolic process TAS
Traceable Author Statement
more info
  
involved_in learning IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in membrane organization TAS
Traceable Author Statement
more info
  
involved_in neurotransmitter transport ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in phosphatidylinositol biosynthetic process TAS
Traceable Author Statement
more info
  
involved_in phosphatidylinositol dephosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in phosphatidylinositol dephosphorylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in phosphatidylinositol dephosphorylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in phosphatidylinositol dephosphorylation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in phosphatidylinositol metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in phosphatidylinositol-3-phosphate biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of endosome organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in synaptic vesicle endocytosis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in synaptic vesicle endocytosis IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in synaptic vesicle endocytosis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in synaptic vesicle priming ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in synaptic vesicle transport ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in synaptic vesicle uncoating ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
part_of clathrin coat of coated pit ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
part_of membrane coat ISS
Inferred from Sequence or Structural Similarity
more info
  
colocalizes_with microtubule ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
is_active_in perinuclear region of cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in perinuclear region of cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in presynapse IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in presynapse IDA
Inferred from Direct Assay
more info
 PubMed 
located_in synaptic membrane ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
located_in terminal bouton ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in vesicle membrane ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
synaptojanin-1
Names
inositol 5'-phosphatase (synaptojanin 1)
inositol polyphosphate-5-phosphatase G
phosphoinositide 5-phosphatase
synaptic inositol 1,4,5-trisphosphate 5-phosphatase 1
synaptojanin-1, polyphosphoinositide phosphatase
NP_001153774.1
NP_001153778.1
NP_003886.3
NP_982271.3
XP_016883984.1
XP_016883986.1
XP_016883988.1
XP_047296990.1
XP_047296991.1
XP_047296992.1
XP_047296993.1
XP_047296994.1
XP_047296995.1
XP_047296996.1
XP_047296997.1
XP_047296998.1
XP_047296999.1
XP_047297000.1
XP_047297001.1
XP_047297002.1
XP_047297003.1
XP_047297004.1
XP_047297005.1
XP_047297006.1
XP_054180906.1
XP_054180907.1
XP_054180908.1
XP_054180909.1
XP_054180910.1
XP_054180911.1
XP_054180912.1
XP_054180913.1
XP_054180914.1
XP_054180915.1
XP_054180916.1
XP_054180917.1
XP_054180918.1
XP_054180919.1
XP_054180920.1
XP_054180921.1
XP_054180922.1
XP_054180923.1
XP_054180924.1
XP_054180925.1

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

  1. NG_030017.2 RefSeqGene

    Range
    5027..104277
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001160302.2 → NP_001153774.1  synaptojanin-1 isoform c

    See identical proteins and their annotated locations for NP_001153774.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in its 5' UTR, 5' coding region and 3' coding region, and uses a downstream translational start codon, compared to variant 1. The encoded isoform (c) has a shorter N-terminus, a distinct C-terminus, and is shorter than isoform a.
    Source sequence(s)
    AP000275, AP000276, AP000277, AP000278, AP000279
    Consensus CDS
    CCDS54483.1
    UniProtKB/TrEMBL
    J3KPK1
    Related
    ENSP00000349903.3, ENST00000357345.7
    Conserved Domains (5) summary
    cd09098
    Location:533 → 868
    INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
    PRK05641
    Location:1017 → 1097
    PRK05641; putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
    pfam02383
    Location:60 → 340
    Syja_N; SacI homology domain
    pfam08952
    Location:867 → 1008
    DUF1866; Domain of unknown function (DUF1866)
    pfam11235
    Location:1078 → 1262
    Med25_SD1; Mediator complex subunit 25 synapsin 1

  2. NM_001160306.2 → NP_001153778.1  synaptojanin-1 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, uses a downstream translational start codon, and has multiple differences in the coding region, compared to variant 1. The encoded isoform (d) has a shorter N-terminus, a distinct C-terminus, and is shorter than isoform a.
    Source sequence(s)
    AB020717, BC098395, BC136603, BP350252, CA944966
    Consensus CDS
    CCDS54484.1
    UniProtKB/Swiss-Prot
    O43425, O43426, O94984, Q4KMR1
    UniProtKB/TrEMBL
    A0A0D9SGJ6
    Related
    ENSP00000487560.1, ENST00000630077.3
    Conserved Domains (4) summary
    cd09098
    Location:528 → 863
    INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
    pfam02383
    Location:60 → 340
    Syja_N; SacI homology domain
    pfam08952
    Location:862 → 1003
    DUF1866; Domain of unknown function (DUF1866)
    pfam11235
    Location:1054 → 1231
    Med25_SD1; Mediator complex subunit 25 synapsin 1

  3. NM_003895.4 → NP_003886.3  synaptojanin-1 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AP000275, AP000276, AP000277, AP000278, AP000279
    Consensus CDS
    CCDS33539.2
    UniProtKB/Swiss-Prot
    O43425, O43426, O94984, Q4KMR1
    UniProtKB/TrEMBL
    J3KQV8
    Related
    ENSP00000409667.2, ENST00000433931.7
    Conserved Domains (3) summary
    cd09098
    Location:572 → 907
    INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
    pfam02383
    Location:99 → 379
    Syja_N; SacI homology domain
    pfam08952
    Location:906 → 1047
    DUF1866; Domain of unknown function (DUF1866)

  4. NM_203446.3 → NP_982271.3  synaptojanin-1 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) includes an alternate exon in the 3' coding region that causes a frameshift, compared to variant 1. The encoded isoform (b) has a distinct and shorter C-terminus, compared to isoform a.
    Source sequence(s)
    AB020717, AF009039, AF009040, AP000275, AP000279, BC019630
    Consensus CDS
    CCDS33540.3
    UniProtKB/TrEMBL
    J3KPK1
    Related
    ENSP00000501530.1, ENST00000674351.1
    Conserved Domains (4) summary
    cd09098
    Location:533 → 868
    INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
    PHA03247
    Location:1054 → 1278
    PHA03247; large tegument protein UL36; Provisional
    COG5329
    Location:34 → 480
    COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
    pfam08952
    Location:867 → 1008
    DUF1866; Domain of unknown function (DUF1866)

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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    32628759..32728394 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047441038.1 → XP_047296994.1  synaptojanin-1 isoform X8

  2. XM_017028497.3 → XP_016883986.1  synaptojanin-1 isoform X3

    UniProtKB/Swiss-Prot
    O43425, O43426, O94984, Q4KMR1
    Conserved Domains (4) summary
    cd09098
    Location:572 → 907
    INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
    PHA03247
    Location:1098 → 1491
    PHA03247; large tegument protein UL36; Provisional
    COG5329
    Location:73 → 519
    COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
    pfam08952
    Location:906 → 1047
    DUF1866; Domain of unknown function (DUF1866)

  3. XM_017028499.3 → XP_016883988.1  synaptojanin-1 isoform X7

    UniProtKB/Swiss-Prot
    O43425, O43426, O94984, Q4KMR1

  4. XM_047441036.1 → XP_047296992.1  synaptojanin-1 isoform X5

  5. XM_017028495.3 → XP_016883984.1  synaptojanin-1 isoform X1

    UniProtKB/Swiss-Prot
    O43425, O43426, O94984, Q4KMR1

  6. XM_047441037.1 → XP_047296993.1  synaptojanin-1 isoform X6

  7. XM_047441035.1 → XP_047296991.1  synaptojanin-1 isoform X4

  8. XM_047441034.1 → XP_047296990.1  synaptojanin-1 isoform X2

  9. XM_047441039.1 → XP_047296995.1  synaptojanin-1 isoform X9

  10. XM_047441040.1 → XP_047296996.1  synaptojanin-1 isoform X10

  11. XM_047441041.1 → XP_047296997.1  synaptojanin-1 isoform X11

  12. XM_047441047.1 → XP_047297003.1  synaptojanin-1 isoform X17

    Related
    ENSP00000371931.4, ENST00000382491.7

  13. XM_047441046.1 → XP_047297002.1  synaptojanin-1 isoform X16

  14. XM_047441050.1 → XP_047297006.1  synaptojanin-1 isoform X20

  15. XM_047441045.1 → XP_047297001.1  synaptojanin-1 isoform X15

  16. XM_047441043.1 → XP_047296999.1  synaptojanin-1 isoform X13

    UniProtKB/TrEMBL
    C9JFZ1
    Related
    ENSP00000371939.2, ENST00000382499.7

  17. XM_047441048.1 → XP_047297004.1  synaptojanin-1 isoform X18

  18. XM_047441044.1 → XP_047297000.1  synaptojanin-1 isoform X14

  19. XM_047441042.1 → XP_047296998.1  synaptojanin-1 isoform X12

  20. XM_047441049.1 → XP_047297005.1  synaptojanin-1 isoform X19

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    30994760..31094413 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054324938.1 → XP_054180913.1  synaptojanin-1 isoform X8

  2. XM_054324933.1 → XP_054180908.1  synaptojanin-1 isoform X3

  3. XM_054324937.1 → XP_054180912.1  synaptojanin-1 isoform X7

  4. XM_054324935.1 → XP_054180910.1  synaptojanin-1 isoform X5

  5. XM_054324931.1 → XP_054180906.1  synaptojanin-1 isoform X1

  6. XM_054324936.1 → XP_054180911.1  synaptojanin-1 isoform X6

  7. XM_054324934.1 → XP_054180909.1  synaptojanin-1 isoform X4

  8. XM_054324932.1 → XP_054180907.1  synaptojanin-1 isoform X2

  9. XM_054324939.1 → XP_054180914.1  synaptojanin-1 isoform X9

  10. XM_054324940.1 → XP_054180915.1  synaptojanin-1 isoform X10

  11. XM_054324941.1 → XP_054180916.1  synaptojanin-1 isoform X11

  12. XM_054324947.1 → XP_054180922.1  synaptojanin-1 isoform X17

  13. XM_054324946.1 → XP_054180921.1  synaptojanin-1 isoform X16

  14. XM_054324950.1 → XP_054180925.1  synaptojanin-1 isoform X20

  15. XM_054324945.1 → XP_054180920.1  synaptojanin-1 isoform X15

  16. XM_054324943.1 → XP_054180918.1  synaptojanin-1 isoform X13

    UniProtKB/TrEMBL
    C9JFZ1

  17. XM_054324948.1 → XP_054180923.1  synaptojanin-1 isoform X18

  18. XM_054324944.1 → XP_054180919.1  synaptojanin-1 isoform X14

  19. XM_054324942.1 → XP_054180917.1  synaptojanin-1 isoform X12

  20. XM_054324949.1 → XP_054180924.1  synaptojanin-1 isoform X19

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O43426.2 GenPept UniProtKB/Swiss-Prot:O43426

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