Human Gene SYPL1 (uc003vdp.4) Description and Page Index
  Description: Homo sapiens synaptophysin-like 1 (SYPL1), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr7:105,730,814-105,753,093 Size: 22,280 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr7:105,732,251-105,752,975 Size: 20,725 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr7:105,730,814-105,753,093)mRNA (may differ from genome)Protein (259 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDHuman Cortex Gene ExpressionLynx
MGIneXtProtOMIMPubMedStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Synaptophysin-like protein 1; AltName: Full=Pantophysin;
SUBCELLULAR LOCATION: Cytoplasmic vesicle membrane; Multi-pass membrane protein (By similarity). Melanosome. Note=Cytoplasmic transport vesicles (By similarity). Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
SIMILARITY: Belongs to the synaptophysin/synaptobrevin family.
SIMILARITY: Contains 1 MARVEL domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SYPL1
CDC HuGE Published Literature: SYPL1
Positive Disease Associations: Waist Circumference , Waist-Hip Ratio
Related Studies:
  1. Waist Circumference
    , , . [PubMed 0]
  2. Waist-Hip Ratio
    , , . [PubMed 0]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 95.67 RPKM in Brain - Spinal cord (cervical c-1)
Total median expression: 2170.01 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -57.90118-0.491 Picture PostScript Text
3' UTR -346.731437-0.241 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR008253 - Marvel
IPR021128 - MARVEL-like_dom
IPR001285 - Synaptophysin/porin

Pfam Domains:
PF01284 - Membrane-associating domain

ModBase Predicted Comparative 3D Structure on Q16563
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0007268 chemical synaptic transmission

Cellular Component:
GO:0005887 integral component of plasma membrane
GO:0008021 synaptic vesicle
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030141 secretory granule
GO:0030285 integral component of synaptic vesicle membrane
GO:0030659 cytoplasmic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0042470 melanosome
GO:0070062 extracellular exosome

-  Descriptions from all associated GenBank mRNAs
  KJ892238 - Synthetic construct Homo sapiens clone ccsbBroadEn_01632 SYPL1 gene, encodes complete protein.
HQ448071 - Synthetic construct Homo sapiens clone IMAGE:100071451; CCSB012111_02 synaptophysin-like 1 (SYPL1) gene, encodes complete protein.
KJ892239 - Synthetic construct Homo sapiens clone ccsbBroadEn_01633 SYPL1 gene, encodes complete protein.
LF209514 - JP 2014500723-A/17017: Polycomb-Associated Non-Coding RNAs.
X68194 - H.sapiens h-Sp1 mRNA.
BC016835 - Homo sapiens synaptophysin-like 1, mRNA (cDNA clone MGC:10011 IMAGE:3883697), complete cds.
AK128279 - Homo sapiens cDNA FLJ46416 fis, clone THYMU3011827, highly similar to Homo sapiens synaptophysin-like protein (SYPL).
S72481 - pantophysin [human, keratinocyte line HaCaT, mRNA, 2106 nt].
BC020938 - Homo sapiens synaptophysin-like 1, mRNA (cDNA clone MGC:24750 IMAGE:4282246), complete cds.
JD494713 - Sequence 475737 from Patent EP1572962.
LF329223 - JP 2014500723-A/136726: Polycomb-Associated Non-Coding RNAs.
JD563191 - Sequence 544215 from Patent EP1572962.
JD234368 - Sequence 215392 from Patent EP1572962.
JD539113 - Sequence 520137 from Patent EP1572962.
LF329222 - JP 2014500723-A/136725: Polycomb-Associated Non-Coding RNAs.
JD136641 - Sequence 117665 from Patent EP1572962.
JD237116 - Sequence 218140 from Patent EP1572962.
AK292230 - Homo sapiens cDNA FLJ75789 complete cds, highly similar to Homo sapiens synaptophysin-like 1 (SYPL1), transcript variant 1, mRNA.
LF329221 - JP 2014500723-A/136724: Polycomb-Associated Non-Coding RNAs.
BC061887 - Homo sapiens synaptophysin-like 1, mRNA (cDNA clone MGC:75065 IMAGE:5171714), complete cds.
AK128299 - Homo sapiens cDNA FLJ46439 fis, clone THYMU3015962, highly similar to Homo sapiens synaptophysin-like protein (SYPL).
X61382 - H.sapiens mRNA for a novel synaptophysin related protein.
LF329220 - JP 2014500723-A/136723: Polycomb-Associated Non-Coding RNAs.
CU687506 - Synthetic construct Homo sapiens gateway clone IMAGE:100021608 5' read SYPL1 mRNA.
EU831812 - Synthetic construct Homo sapiens clone HAIB:100066841; DKFZo008F0821 synaptophysin-like 1 protein (SYPL1) gene, encodes complete protein.
EU831889 - Synthetic construct Homo sapiens clone HAIB:100066918; DKFZo004F0822 synaptophysin-like 1 protein (SYPL1) gene, encodes complete protein.
JD033041 - Sequence 14065 from Patent EP1572962.
JD019629 - Sequence 653 from Patent EP1572962.
CU677735 - Synthetic construct Homo sapiens gateway clone IMAGE:100020639 5' read SYPL1 mRNA.
MA564800 - JP 2018138019-A/136726: Polycomb-Associated Non-Coding RNAs.
MA564799 - JP 2018138019-A/136725: Polycomb-Associated Non-Coding RNAs.
MA564798 - JP 2018138019-A/136724: Polycomb-Associated Non-Coding RNAs.
MA564797 - JP 2018138019-A/136723: Polycomb-Associated Non-Coding RNAs.
MA445091 - JP 2018138019-A/17017: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_006754, NP_874384, Q16563, Q96AR8, SYPL, SYPL1_HUMAN, uc003vdp.3
UCSC ID: uc003vdp.4
RefSeq Accession: NM_006754
Protein: Q16563 (aka SYPL1_HUMAN)
CCDS: CCDS5736.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_006754.3
exon count: 6CDS single in 3' UTR: no RNA size: 2335
ORF size: 780CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1760.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.