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Synj1 synaptojanin 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 85238, updated on 13-Apr-2024

Summary

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Official Symbol
Synj1provided by RGD
Official Full Name
synaptojanin 1provided by RGD
Primary source
RGD:69434
See related
Ensembl:ENSRNOG00000002051 AllianceGenome:RGD:69434
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Enables phosphatase activity; protein C-terminus binding activity; and protein domain specific binding activity. Involved in several processes, including nervous system development; positive regulation of receptor-mediated endocytosis; and response to retinoic acid. Located in cytoplasm; neuron projection; and synaptic membrane. Part of clathrin coat of coated pit. Is active in parallel fiber to Purkinje cell synapse and presynapse. Colocalizes with microtubule. Human ortholog(s) of this gene implicated in Parkinson's disease; Parkinson's disease 20; and developmental and epileptic encephalopathy 53. Orthologous to human SYNJ1 (synaptojanin 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Brain (RPKM 382.5), Spleen (RPKM 139.7) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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Location:
11q11
Exon count:
36
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 11 NC_086029.1 (43678709..43755526, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 11 NC_051346.1 (30192629..30269447, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 11 NC_005110.4 (31105784..31181573, complement)

Chromosome 11 - NC_086029.1Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA2/SNORA34 family Neighboring gene cilia and flagella associated protein 298 Neighboring gene PAX3 and PAX7 binding protein 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. MNB/DYRK1A phosphorylation regulates the interactions of synaptojanin 1 with endocytic accessory proteins. Adayev T, et al. Biochem Biophys Res Commun, 2006 Dec 29. PMID 17097615, Free PMC Article
  2. Characterization and purification of phosphatidylinositol trisphosphate 5-phosphatase from rat brain tissues. Woscholski R. Methods Enzymol, 2002. PMID 11665617
  3. Identification and characterisation of a novel splice variant of synaptojanin1. Woscholski R, et al. FEBS Lett, 1998 Jul 31. PMID 9710239
  4. Tissue-specific alternative splicing generates two synaptojanin isoforms with differential membrane binding properties. Ramjaun AR, et al. J Biol Chem, 1996 Oct 4. PMID 8798761
  5. A presynaptic inositol-5-phosphatase. McPherson PS, et al. Nature, 1996 Jan 25. PMID 8552192

See all (43) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. concentrated in presynaptic nerve terminals, where it dephosphorylates a pool of phosphatidylinositol
    Title: Regulation of synaptojanin 1 by cyclin-dependent kinase 5 at synapses.
  2. EphrinB-EphB signalling regulates clathrin-mediated endocytosis in various cellular contexts by influencing protein interactions and phosphoinositide turnover through tyrosine phosphorylation of synaptojanin 1.
    Title: EphrinB-EphB signalling regulates clathrin-mediated endocytosis through tyrosine phosphorylation of synaptojanin 1.
  3. characterization and purification from rat brain
    Title: Characterization and purification of phosphatidylinositol trisphosphate 5-phosphatase from rat brain tissues.
  4. Two proteins with prominent functions in endocytosis, synaptojanin-1 and dynamin, bind to the SH3 domain of human Myo1E.
    Title: Myosin 1E interacts with synaptojanin-1 and dynamin and is involved in endocytosis.
Submit: New GeneRIF Correction

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 RGD

Function Evidence Code Pubs
enables EH domain binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables SH3 domain binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables SH3 domain binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables SH3 domain binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables inositol phosphate phosphatase activity IEA
Inferred from Electronic Annotation
more info
  
enables inositol-1,4,5-trisphosphate 5-phosphatase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables phosphatidylinositol phosphate 5-phosphatase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables phosphatidylinositol phosphate 5-phosphatase activity ISO
Inferred from Sequence Orthology
more info
  
enables phosphatidylinositol-3-phosphate phosphatase activity IEA
Inferred from Electronic Annotation
more info
  
enables phosphatidylinositol-3-phosphate phosphatase activity ISO
Inferred from Sequence Orthology
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 IEA
Inferred from Electronic Annotation
more info
  
enables phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity ISO
Inferred from Sequence Orthology
more info
  
enables phosphatidylinositol-4-phosphate phosphatase activity IEA
Inferred from Electronic Annotation
more info
  
enables phosphatidylinositol-4-phosphate phosphatase activity ISO
Inferred from Sequence Orthology
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-containing complex binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in learning IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within learning ISO
Inferred from Sequence Orthology
more info
  
involved_in learning ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within neurotransmitter transport ISO
Inferred from Sequence Orthology
more info
  
involved_in phosphatidylinositol dephosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in phosphatidylinositol dephosphorylation IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within phosphatidylinositol dephosphorylation ISO
Inferred from Sequence Orthology
more info
  
involved_in phosphatidylinositol dephosphorylation ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within phosphatidylinositol metabolic process ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of endosome organization IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of endosome organization ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of gliogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of receptor-mediated endocytosis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in postsynaptic neurotransmitter receptor internalization ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of postsynaptic neurotransmitter receptor internalization ISO
Inferred from Sequence Orthology
more info
  
involved_in response to cytokine IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in response to retinoic acid 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 IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within synaptic vesicle endocytosis ISO
Inferred from Sequence Orthology
more info
  
involved_in synaptic vesicle endocytosis ISO
Inferred from Sequence Orthology
more info
  
involved_in synaptic vesicle endocytosis ISS
Inferred from Sequence or Structural Similarity
more info
  
acts_upstream_of_or_within synaptic vesicle priming ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within synaptic vesicle transport ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within synaptic vesicle uncoating ISO
Inferred from Sequence Orthology
more info
  
involved_in synaptic vesicle uncoating ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
is_active_in Schaffer collateral - CA1 synapse ISO
Inferred from Sequence Orthology
more info
  
part_of clathrin coat of coated pit IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in glutamatergic synapse ISO
Inferred from Sequence Orthology
more info
  
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 
part_of membrane coat ISO
Inferred from Sequence Orthology
more info
  
located_in microtubule IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in parallel fiber to Purkinje cell synapse IDA
Inferred from Direct Assay
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
  
located_in postsynapse IEA
Inferred from Electronic Annotation
more info
  
is_active_in presynapse IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in presynapse IDA
Inferred from Direct Assay
more info
 PubMed 
located_in presynapse IEA
Inferred from Electronic Annotation
more info
  
located_in presynapse ISO
Inferred from Sequence Orthology
more info
  
part_of protein-containing complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in synaptic membrane IDA
Inferred from Direct Assay
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
synaptic inositol 1,4,5-trisphosphate 5-phosphatase 1
NP_001401979.1
NP_445928.3
XP_038944618.1
XP_038944619.1
XP_038944620.1
XP_038944621.1
XP_038944622.1
XP_038944623.1
XP_038944624.1
XP_038944625.1
XP_038944627.1
XP_038944628.1
XP_038944630.1
XP_038944634.1
XP_063126875.1
XP_063126876.1
XP_063126877.1
XP_063126879.1
XP_063126880.1
XP_063126881.1
XP_063126882.1
XP_063126883.1
XP_063126884.1
XP_063126885.1
XP_063126886.1
XP_063126887.1
XP_063126888.1
XP_063126889.1
XP_063126890.1
XP_063126891.1
XP_063126892.1
XP_063126893.1
XP_063126894.1
XP_063126895.1
XP_063126896.1
XP_063126897.1
XP_063126898.1

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.

mRNA and Protein(s)

  1. NM_001415050.1 → NP_001401979.1  synaptojanin-1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000011
    Related
    ENSRNOP00000045019.6, ENSRNOT00000052033.7

  2. NM_053476.4 → NP_445928.3  synaptojanin-1 isoform 1

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000011

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086029.1 Reference GRCr8

    Range
    43678709..43755526 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_063270813.1 → XP_063126883.1  synaptojanin-1 isoform X16

  2. XM_063270805.1 → XP_063126875.1  synaptojanin-1 isoform X4

  3. XM_063270811.1 → XP_063126881.1  synaptojanin-1 isoform X13

  4. XM_063270806.1 → XP_063126876.1  synaptojanin-1 isoform X6

  5. XM_063270807.1 → XP_063126877.1  synaptojanin-1 isoform X8

  6. XM_039088691.2 → XP_038944619.1  synaptojanin-1 isoform X2

    UniProtKB/Swiss-Prot
    O89092, Q62910, Q62911, Q810Z8
    UniProtKB/TrEMBL
    A0A8L2QTB1
    Related
    ENSRNOP00000060346.4
    Conserved Domains (4) summary
    cd09098
    Location:573 → 908
    INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
    PHA03247
    Location:1094 → 1495
    PHA03247; large tegument protein UL36; Provisional
    COG5329
    Location:100 → 520
    COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
    cl17169
    Location:907 → 1049
    RRM_SF; RNA recognition motif (RRM) superfamily

  7. XM_039088697.2 → XP_038944625.1  synaptojanin-1 isoform X15

    UniProtKB/TrEMBL
    A0A8I6AHP8
    Conserved Domains (4) summary
    cd09098
    Location:568 → 903
    INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
    COG5329
    Location:100 → 523
    COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
    pfam03154
    Location:1023 → 1448
    Atrophin-1; Atrophin-1 family
    cl17169
    Location:902 → 1044
    RRM_SF; RNA recognition motif (RRM) superfamily

  8. XM_063270809.1 → XP_063126879.1  synaptojanin-1 isoform X10

  9. XM_039088692.2 → XP_038944620.1  synaptojanin-1 isoform X3

    UniProtKB/Swiss-Prot
    O89092, Q62910, Q62911, Q810Z8
    Conserved Domains (4) summary
    cd09098
    Location:568 → 903
    INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
    PHA03247
    Location:1089 → 1490
    PHA03247; large tegument protein UL36; Provisional
    COG5329
    Location:100 → 523
    COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
    cl17169
    Location:902 → 1044
    RRM_SF; RNA recognition motif (RRM) superfamily

  10. XM_039088696.2 → XP_038944624.1  synaptojanin-1 isoform X12

    UniProtKB/TrEMBL
    A0A8I6AHP8
    Related
    ENSRNOP00000092530.1
    Conserved Domains (4) summary
    cd09098
    Location:576 → 911
    INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
    COG5329
    Location:100 → 523
    COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
    pfam03154
    Location:1031 → 1456
    Atrophin-1; Atrophin-1 family
    cl17169
    Location:910 → 1052
    RRM_SF; RNA recognition motif (RRM) superfamily

  11. XM_039088695.2 → XP_038944623.1  synaptojanin-1 isoform X9

    UniProtKB/TrEMBL
    A0A8I6AFG5
    Related
    ENSRNOP00000086242.1
    Conserved Domains (4) summary
    cd09098
    Location:576 → 911
    INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
    COG5329
    Location:100 → 523
    COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
    pfam03154
    Location:1031 → 1469
    Atrophin-1; Atrophin-1 family
    cl17169
    Location:910 → 1052
    RRM_SF; RNA recognition motif (RRM) superfamily

  12. XM_039088693.2 → XP_038944621.1  synaptojanin-1 isoform X5

    UniProtKB/TrEMBL
    A0A8I6AFG5
    Conserved Domains (4) summary
    cd09098
    Location:576 → 911
    INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
    PHA03247
    Location:1073 → 1304
    PHA03247; large tegument protein UL36; Provisional
    COG5329
    Location:100 → 523
    COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
    cl17169
    Location:910 → 1052
    RRM_SF; RNA recognition motif (RRM) superfamily

  13. XM_039088694.2 → XP_038944622.1  synaptojanin-1 isoform X7

    UniProtKB/TrEMBL
    A0A8I6AFG5
    Related
    ENSRNOP00000092411.1
    Conserved Domains (4) summary
    cd09098
    Location:576 → 911
    INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
    PHA03247
    Location:1097 → 1494
    PHA03247; large tegument protein UL36; Provisional
    COG5329
    Location:100 → 523
    COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
    cl17169
    Location:910 → 1052
    RRM_SF; RNA recognition motif (RRM) superfamily

  14. XM_039088690.2 → XP_038944618.1  synaptojanin-1 isoform X1

    UniProtKB/Swiss-Prot
    O89092, Q62910, Q62911, Q810Z8
    Conserved Domains (4) summary
    cd09098
    Location:576 → 911
    INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
    PHA03247
    Location:1097 → 1498
    PHA03247; large tegument protein UL36; Provisional
    COG5329
    Location:100 → 523
    COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
    cl17169
    Location:910 → 1052
    RRM_SF; RNA recognition motif (RRM) superfamily

  15. XM_063270816.1 → XP_063126886.1  synaptojanin-1 isoform X19

  16. XM_063270817.1 → XP_063126887.1  synaptojanin-1 isoform X20

  17. XM_063270814.1 → XP_063126884.1  synaptojanin-1 isoform X17

    UniProtKB/TrEMBL
    A0A8I6A4X9

  18. XM_063270815.1 → XP_063126885.1  synaptojanin-1 isoform X18

  19. XM_063270812.1 → XP_063126882.1  synaptojanin-1 isoform X14

  20. XM_063270810.1 → XP_063126880.1  synaptojanin-1 isoform X11

  21. XM_039088706.2 → XP_038944634.1  synaptojanin-1 isoform X33

    UniProtKB/TrEMBL
    A6JLD6
    Conserved Domains (3) summary
    cd09098
    Location:86 → 421
    INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
    PHA03247
    Location:607 → 1008
    PHA03247; large tegument protein UL36; Provisional
    cl17169
    Location:420 → 562
    RRM_SF; RNA recognition motif (RRM) superfamily

  22. XM_063270827.1 → XP_063126897.1  synaptojanin-1 isoform X31

  23. XM_063270821.1 → XP_063126891.1  synaptojanin-1 isoform X25

  24. XM_063270825.1 → XP_063126895.1  synaptojanin-1 isoform X29

  25. XM_063270822.1 → XP_063126892.1  synaptojanin-1 isoform X26

  26. XM_063270823.1 → XP_063126893.1  synaptojanin-1 isoform X27

  27. XM_063270819.1 → XP_063126889.1  synaptojanin-1 isoform X23

  28. XM_063270826.1 → XP_063126896.1  synaptojanin-1 isoform X30

  29. XM_039088699.2 → XP_038944627.1  synaptojanin-1 isoform X21

    UniProtKB/TrEMBL
    D4ABN3
    Conserved Domains (4) summary
    cd09098
    Location:576 → 911
    INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
    COG5329
    Location:100 → 523
    COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
    PRK07764
    Location:1110 → 1317
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    cl17169
    Location:910 → 1052
    RRM_SF; RNA recognition motif (RRM) superfamily

  30. XM_039088700.2 → XP_038944628.1  synaptojanin-1 isoform X21

    UniProtKB/TrEMBL
    D4ABN3
    Conserved Domains (4) summary
    cd09098
    Location:576 → 911
    INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
    COG5329
    Location:100 → 523
    COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
    PRK07764
    Location:1110 → 1317
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    cl17169
    Location:910 → 1052
    RRM_SF; RNA recognition motif (RRM) superfamily

  31. XM_039088702.2 → XP_038944630.1  synaptojanin-1 isoform X22

    UniProtKB/TrEMBL
    D4ABN3
    Conserved Domains (4) summary
    cd09098
    Location:576 → 911
    INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
    COG5329
    Location:100 → 523
    COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
    PRK07764
    Location:1110 → 1317
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    cl17169
    Location:910 → 1052
    RRM_SF; RNA recognition motif (RRM) superfamily

  32. XM_063270818.1 → XP_063126888.1  synaptojanin-1 isoform X21

  33. XM_063270828.1 → XP_063126898.1  synaptojanin-1 isoform X32

  34. XM_063270824.1 → XP_063126894.1  synaptojanin-1 isoform X28

  35. XM_063270820.1 → XP_063126890.1  synaptojanin-1 isoform X24

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q62910.3 GenPept UniProtKB/Swiss-Prot:Q62910

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