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Protein

Spermatogenesis-defective protein 39 homolog

Gene

VIPAS39

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Proposed to be involved in endosomal maturation implicating in part VPS33B. In epithelial cells, the VPS33B:VIPAS39 complex may play a role in the apical RAB11A-dependent recycling pathway and in the maintenance of the apical-basolateral polarity (PubMed:20190753). May play a role in lysosomal trafficking, probably via association with the core HOPS complex in a discrete population of endosomes; the functions seems to be indepenedent of VPS33B (PubMed:19109425). May play a role in vesicular trafficking during spermatogenesis (By similarity). May be involved in direct or indirect transcriptional regulation of E-cadherin (By similarity).By similarity2 Publications

GO - Biological processi

  • cell differentiation Source: UniProtKB-KW
  • endosome to lysosome transport Source: UniProtKB
  • intracellular protein transport Source: UniProtKB
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • spermatogenesis Source: UniProtKB-KW
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

Differentiation, Protein transport, Spermatogenesis, Transcription, Transcription regulation, Transport

Names & Taxonomyi

Protein namesi
Recommended name:
Spermatogenesis-defective protein 39 homolog
Short name:
hSPE-39
Alternative name(s):
VPS33B-interacting protein in apical-basolateral polarity regulator
VPS33B-interacting protein in polarity and apical restriction
Gene namesi
Name:VIPAS39
Synonyms:C14orf133, SPE39, VIPAR
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 14

Organism-specific databases

HGNCiHGNC:20347. VIPAS39.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • cytoplasmic, membrane-bounded vesicle Source: UniProtKB-SubCell
  • early endosome Source: UniProtKB
  • late endosome Source: UniProtKB
  • recycling endosome Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Cytoplasmic vesicle, Endosome

Pathology & Biotechi

Involvement in diseasei

Arthrogryposis, renal dysfunction and cholestasis syndrome 2 (ARCS2)
The disease is caused by mutations affecting the gene represented in this entry. In liver, CEACAM5 and ABCB11 are mislocalized and E-cadherin expression is decreased.
Disease descriptionA multisystem disorder, characterized by neurogenic arthrogryposis multiplex congenita, renal tubular dysfunction and neonatal cholestasis with bile duct hypoplasia and low gamma glutamyl transpeptidase activity. Platelet dysfunction is common.
See also OMIM:613404

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi213 – 2131L → P: Disrupts endodsomal colocalization with VPS33B. 1 Publication

Organism-specific databases

MalaCardsiVIPAS39.
MIMi613404. phenotype.
Orphaneti2697. Arthrogryposis - renal dysfunction - cholestasis.
PharmGKBiPA165479332.

Polymorphism and mutation databases

BioMutaiVIPAS39.
DMDMi41016926.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 493493Spermatogenesis-defective protein 39 homologPRO_0000089935Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei21 – 211PhosphothreonineBy similarity
Modified residuei117 – 1171PhosphothreonineBy similarity
Modified residuei121 – 1211PhosphoserineCombined sources
Modified residuei124 – 1241PhosphoserineBy similarity
Modified residuei132 – 1321PhosphothreonineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ9H9C1.
MaxQBiQ9H9C1.
PaxDbiQ9H9C1.
PRIDEiQ9H9C1.

PTM databases

iPTMnetiQ9H9C1.
PhosphoSiteiQ9H9C1.

Expressioni

Gene expression databases

BgeeiQ9H9C1.
CleanExiHS_C14orf133.
ExpressionAtlasiQ9H9C1. baseline and differential.
GenevisibleiQ9H9C1. HS.

Organism-specific databases

HPAiHPA003589.
HPA003593.

Interactioni

Subunit structurei

Interacts with VPS33B (PubMed:19109425, PubMed:23901104). Associates with the homotypic fusion and vacuole protein sorting (HOPS) complex; impaired by VPS33B (PubMed:19109425, PubMed:23918659, PubMed:22753090). A possible interaction with VPS33A is reported conflictingly (PubMed:19109425, PubMed:23901104). Interacts with RAB11A (PubMed:20190753).3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
Vps11Q91W863EBI-749080,EBI-2527812From a different organism.
Vps16Q920Q44EBI-749080,EBI-775797From a different organism.
Vps18Q8R3075EBI-749080,EBI-2527788From a different organism.
VPS33BQ9H26729EBI-749080,EBI-749072
VPS41P497544EBI-749080,EBI-2130459

Protein-protein interaction databases

BioGridi121974. 15 interactions.
IntActiQ9H9C1. 10 interactions.
MINTiMINT-1451086.
STRINGi9606.ENSP00000339122.

Structurei

3D structure databases

ProteinModelPortaliQ9H9C1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the SPE39 family.Curated

Phylogenomic databases

eggNOGiKOG4677. Eukaryota.
ENOG410XR4F. LUCA.
GeneTreeiENSGT00390000013955.
HOGENOMiHOG000070044.
HOVERGENiHBG051031.
InParanoidiQ9H9C1.
OrthoDBiEOG7RV9G5.
PhylomeDBiQ9H9C1.
TreeFamiTF319640.

Family and domain databases

InterProiIPR006925. Vps16_C.
[Graphical view]
PfamiPF04840. Vps16_C. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9H9C1-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MNRTKGDEEE YWNSSKFKAF TFDDEDDELS QLKESKRAVN SLRDFVDDDD
60 70 80 90 100
DDDLERVSWS GEPVGSISWS IRETAGNSGS THEGREQLKS RNSFSSYAQL
110 120 130 140 150
PKPTSTYSLS SFFRGRTRPG SFQSLSDALS DTPAKSYAPE LGRPKGEYRD
160 170 180 190 200
YSNDWSPSDT VRRLRKGKVC SLERFRSLQD KLQLLEEAVS MHDGNVITAV
210 220 230 240 250
LIFLKRTLSK EILFRELEVR QVALRHLIHF LKEIGDQKLL LDLFRFLDRT
260 270 280 290 300
EELALSHYRE HLNIQDPDKR KEFLKTCVGL PFSAEDSAHI QDHYTLLERQ
310 320 330 340 350
IIIEANDRHL ESAGQTEIFR KHPRKASILN MPLVTTLFYS CFYHYTEAEG
360 370 380 390 400
TFSSPVNLKK TFKIPDKQYV LTALAARAKL RAWNDVDALF TTKNWLGYTK
410 420 430 440 450
KRAPIGFHRV VEILHKNNAP VQILQEYVNL VEDVDTKLNL ATKFKCHDVV
460 470 480 490
IDTYRDLKDR QQLLAYRSKV DKGSAEEEKI DALLSSSQIR WKN
Length:493
Mass (Da):57,005
Last modified:March 1, 2001 - v1
Checksum:iCF05C38EB922D192
GO
Isoform 2 (identifier: Q9H9C1-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     67-115: Missing.

Note: No experimental confirmation available.
Show »
Length:444
Mass (Da):51,581
Checksum:i62293CF96A0DF07A
GO

Sequence cautioni

The sequence AAD09624.1 differs from that shown. Reason: Erroneous gene model prediction. Curated
The sequence BAB14951.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti280 – 2801L → S in BAB14237 (PubMed:14702039).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei67 – 11549Missing in isoform 2. 1 PublicationVSP_043055Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK024661 mRNA. Translation: BAB14951.1. Different initiation.
AK022769 mRNA. Translation: BAB14237.1.
AK022925 mRNA. Translation: BAB14310.1.
AK298354 mRNA. Translation: BAG60598.1.
AF111168 Genomic DNA. Translation: AAD09624.1. Sequence problems.
BC015054 mRNA. Translation: AAH15054.1.
CCDSiCCDS53905.1. [Q9H9C1-2]
CCDS9862.1. [Q9H9C1-1]
RefSeqiNP_001180243.1. NM_001193314.1. [Q9H9C1-1]
NP_001180244.1. NM_001193315.1. [Q9H9C1-1]
NP_001180245.1. NM_001193316.1. [Q9H9C1-2]
NP_001180246.1. NM_001193317.1. [Q9H9C1-1]
NP_071350.2. NM_022067.3. [Q9H9C1-1]
UniGeneiHs.16157.

Genome annotation databases

EnsembliENST00000327028; ENSP00000313098; ENSG00000151445. [Q9H9C1-2]
ENST00000343765; ENSP00000339122; ENSG00000151445. [Q9H9C1-1]
ENST00000448935; ENSP00000404815; ENSG00000151445. [Q9H9C1-2]
ENST00000553888; ENSP00000452181; ENSG00000151445. [Q9H9C1-1]
ENST00000557658; ENSP00000452191; ENSG00000151445. [Q9H9C1-1]
GeneIDi63894.
KEGGihsa:63894.
UCSCiuc001xtt.3. human. [Q9H9C1-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK024661 mRNA. Translation: BAB14951.1. Different initiation.
AK022769 mRNA. Translation: BAB14237.1.
AK022925 mRNA. Translation: BAB14310.1.
AK298354 mRNA. Translation: BAG60598.1.
AF111168 Genomic DNA. Translation: AAD09624.1. Sequence problems.
BC015054 mRNA. Translation: AAH15054.1.
CCDSiCCDS53905.1. [Q9H9C1-2]
CCDS9862.1. [Q9H9C1-1]
RefSeqiNP_001180243.1. NM_001193314.1. [Q9H9C1-1]
NP_001180244.1. NM_001193315.1. [Q9H9C1-1]
NP_001180245.1. NM_001193316.1. [Q9H9C1-2]
NP_001180246.1. NM_001193317.1. [Q9H9C1-1]
NP_071350.2. NM_022067.3. [Q9H9C1-1]
UniGeneiHs.16157.

3D structure databases

ProteinModelPortaliQ9H9C1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121974. 15 interactions.
IntActiQ9H9C1. 10 interactions.
MINTiMINT-1451086.
STRINGi9606.ENSP00000339122.

PTM databases

iPTMnetiQ9H9C1.
PhosphoSiteiQ9H9C1.

Polymorphism and mutation databases

BioMutaiVIPAS39.
DMDMi41016926.

Proteomic databases

EPDiQ9H9C1.
MaxQBiQ9H9C1.
PaxDbiQ9H9C1.
PRIDEiQ9H9C1.

Protocols and materials databases

DNASUi63894.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000327028; ENSP00000313098; ENSG00000151445. [Q9H9C1-2]
ENST00000343765; ENSP00000339122; ENSG00000151445. [Q9H9C1-1]
ENST00000448935; ENSP00000404815; ENSG00000151445. [Q9H9C1-2]
ENST00000553888; ENSP00000452181; ENSG00000151445. [Q9H9C1-1]
ENST00000557658; ENSP00000452191; ENSG00000151445. [Q9H9C1-1]
GeneIDi63894.
KEGGihsa:63894.
UCSCiuc001xtt.3. human. [Q9H9C1-1]

Organism-specific databases

CTDi63894.
GeneCardsiVIPAS39.
HGNCiHGNC:20347. VIPAS39.
HPAiHPA003589.
HPA003593.
MalaCardsiVIPAS39.
MIMi613401. gene.
613404. phenotype.
neXtProtiNX_Q9H9C1.
Orphaneti2697. Arthrogryposis - renal dysfunction - cholestasis.
PharmGKBiPA165479332.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG4677. Eukaryota.
ENOG410XR4F. LUCA.
GeneTreeiENSGT00390000013955.
HOGENOMiHOG000070044.
HOVERGENiHBG051031.
InParanoidiQ9H9C1.
OrthoDBiEOG7RV9G5.
PhylomeDBiQ9H9C1.
TreeFamiTF319640.

Miscellaneous databases

GenomeRNAii63894.
PROiQ9H9C1.
SOURCEiSearch...

Gene expression databases

BgeeiQ9H9C1.
CleanExiHS_C14orf133.
ExpressionAtlasiQ9H9C1. baseline and differential.
GenevisibleiQ9H9C1. HS.

Family and domain databases

InterProiIPR006925. Vps16_C.
[Graphical view]
PfamiPF04840. Vps16_C. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
    Tissue: Kidney.
  2. "The DNA sequence and analysis of human chromosome 14."
    Heilig R., Eckenberg R., Petit J.-L., Fonknechten N., Da Silva C., Cattolico L., Levy M., Barbe V., De Berardinis V., Ureta-Vidal A., Pelletier E., Vico V., Anthouard V., Rowen L., Madan A., Qin S., Sun H., Du H.
    , Pepin K., Artiguenave F., Robert C., Cruaud C., Bruels T., Jaillon O., Friedlander L., Samson G., Brottier P., Cure S., Segurens B., Aniere F., Samain S., Crespeau H., Abbasi N., Aiach N., Boscus D., Dickhoff R., Dors M., Dubois I., Friedman C., Gouyvenoux M., James R., Madan A., Mairey-Estrada B., Mangenot S., Martins N., Menard M., Oztas S., Ratcliffe A., Shaffer T., Trask B., Vacherie B., Bellemere C., Belser C., Besnard-Gonnet M., Bartol-Mavel D., Boutard M., Briez-Silla S., Combette S., Dufosse-Laurent V., Ferron C., Lechaplais C., Louesse C., Muselet D., Magdelenat G., Pateau E., Petit E., Sirvain-Trukniewicz P., Trybou A., Vega-Czarny N., Bataille E., Bluet E., Bordelais I., Dubois M., Dumont C., Guerin T., Haffray S., Hammadi R., Muanga J., Pellouin V., Robert D., Wunderle E., Gauguet G., Roy A., Sainte-Marthe L., Verdier J., Verdier-Discala C., Hillier L.W., Fulton L., McPherson J., Matsuda F., Wilson R., Scarpelli C., Gyapay G., Wincker P., Saurin W., Quetier F., Waterston R., Hood L., Weissenbach J.
    Nature 421:601-607(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Skin.
  4. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-132, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  5. "SPE-39 family proteins interact with the HOPS complex and function in lysosomal delivery."
    Zhu G.D., Salazar G., Zlatic S.A., Fiza B., Doucette M.M., Heilman C.J., Levey A.I., Faundez V., L'hernault S.W.
    Mol. Biol. Cell 20:1223-1240(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH VPS33A; VPS33B AND HOPS COMPLEX, SUBCELLULAR LOCATION.
  6. "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
    Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
    Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-121, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Leukemic T-cell.
  7. Cited for: FUNCTION, INTERACTION WITH RAB11A AND VPS33B, SUBCELLULAR LOCATION, INVOLVEMENT IN ARCS1.
  8. "On the endosomal function and gene nomenclature of human SPE-39."
    L'Hernault S.W., Faundez V.
    Nat. Genet. 43:176-176(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE NOMENCLATURE.
  9. "Vps33b pathogenic mutations preferentially affect VIPAS39/SPE-39-positive endosomes."
    Tornieri K., Zlatic S.A., Mullin A.P., Werner E., Harrison R., L'hernault S.W., Faundez V.
    Hum. Mol. Genet. 22:5215-5228(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH VPS33B.
  10. Cited for: SUBCELLULAR LOCATION, SUBUNIT, MUTAGENESIS OF LEU-213.
  11. Cited for: INTERACTION WITH VPS33B.
  12. "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome."
    Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L., Ye M., Zou H.
    J. Proteomics 96:253-262(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-121, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.

Entry informationi

Entry nameiSPE39_HUMAN
AccessioniPrimary (citable) accession number: Q9H9C1
Secondary accession number(s): B4DPI6
, O95434, Q9H7E1, Q9H9I9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 16, 2004
Last sequence update: March 1, 2001
Last modified: June 8, 2016
This is version 123 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 14
    Human chromosome 14: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.