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Protein

Protein YIPF3

Gene

YIPF3

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

Functioni

Involved in the maintenance of the Golgi structure. May play a role in hematopoiesis.2 Publications

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Differentiation

Protein family/group databases

TCDBi9.B.135.2.1. the membrane trafficking yip (yip) family.

Names & Taxonomyi

Protein namesi
Recommended name:
Protein YIPF3
Alternative name(s):
Killer lineage protein 1
Natural killer cell-specific antigen KLIP1
YIP1 family member 3
Cleaved into the following chain:
Gene namesi
Name:YIPF3
Synonyms:C6orf109, KLIP1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

HGNCiHGNC:21023. YIPF3.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini2 – 148147CytoplasmicSequence analysisAdd
BLAST
Transmembranei149 – 16921HelicalSequence analysisAdd
BLAST
Topological domaini170 – 18718LumenalSequence analysisAdd
BLAST
Transmembranei188 – 20821HelicalSequence analysisAdd
BLAST
Topological domaini209 – 2146CytoplasmicSequence analysis
Transmembranei215 – 23723HelicalSequence analysisAdd
BLAST
Topological domaini238 – 2403LumenalSequence analysis
Transmembranei241 – 26323HelicalSequence analysisAdd
BLAST
Topological domaini264 – 27411CytoplasmicSequence analysisAdd
BLAST
Transmembranei275 – 29521HelicalSequence analysisAdd
BLAST
Topological domaini296 – 35055LumenalSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Cytoplasm, Golgi apparatus, Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134946615.

Polymorphism and mutation databases

BioMutaiYIPF3.
DMDMi74752534.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedCombined sources
Chaini2 – 350349Protein YIPF3PRO_0000244446Add
BLAST
Chaini2 – ?Protein YIPF3, 36 kDa form IIIPRO_0000418216

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanineCombined sources
Glycosylationi333 – 3331O-linked (GalNAc...)1 Publication
Glycosylationi334 – 3341O-linked (GalNAc...)1 Publication
Glycosylationi337 – 3371N-linked (GlcNAc...)1 Publication
Glycosylationi339 – 3391O-linked (GalNAc...)1 Publication
Glycosylationi346 – 3461O-linked (GalNAc...)3 Publications

Post-translational modificationi

N-glycosylated in the ER (40 kDa form I), then O-glycosylated in the Golgi apparatus (46 kDa form II), the C-terminal lumenal region is later removed in the Golgi apparatus to produce a 36 kDa form III. O-glycosylated with core 1-like and core 2-like glycans. O-glycan heterogeneity at Thr-346: HexNAc (minor), HexHexNAc (major), Hex1HexNAc2 (minor), Hex2HexNAc2 (minor) and dHex1Hex2HexNAc2 (minor).4 Publications

Keywords - PTMi

Acetylation, Glycoprotein

Proteomic databases

EPDiQ9GZM5.
MaxQBiQ9GZM5.
PaxDbiQ9GZM5.
PRIDEiQ9GZM5.

PTM databases

iPTMnetiQ9GZM5.
PhosphoSiteiQ9GZM5.
SwissPalmiQ9GZM5.
UniCarbKBiQ9GZM5.

Expressioni

Tissue specificityi

Expressed by nucleated hematopoietic cells (at protein level).1 Publication

Developmental stagei

Expressed in fetal liver (at protein level). Expressed in embryonic hematopoiesis sites.1 Publication

Gene expression databases

BgeeiQ9GZM5.
CleanExiHS_YIPF3.
ExpressionAtlasiQ9GZM5. baseline and differential.
GenevisibleiQ9GZM5. HS.

Organism-specific databases

HPAiHPA014859.
HPA063699.

Interactioni

Subunit structurei

Interacts with YIPF4.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
KRTAP10-8P604103EBI-743787,EBI-10171774
KRTAP3-2Q9BYR73EBI-743787,EBI-751260
KRTAP5-9P263713EBI-743787,EBI-3958099
KRTAP9-4Q9BYQ23EBI-743787,EBI-10185730
NOTCH2NLQ7Z3S93EBI-743787,EBI-945833
YIPF4Q9BSR84EBI-743787,EBI-751253

Protein-protein interaction databases

BioGridi117370. 101 interactions.
IntActiQ9GZM5. 8 interactions.
MINTiMINT-1454282.
STRINGi9606.ENSP00000361499.

Structurei

3D structure databases

ProteinModelPortaliQ9GZM5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the YIP1 family.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410IPBK. Eukaryota.
ENOG4111EUH. LUCA.
GeneTreeiENSGT00510000047963.
HOVERGENiHBG055544.
InParanoidiQ9GZM5.
OrthoDBiEOG769ZK3.
PhylomeDBiQ9GZM5.
TreeFamiTF314073.

Family and domain databases

InterProiIPR026637. YIPF3.
[Graphical view]
PANTHERiPTHR15627:SF14. PTHR15627:SF14. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q9GZM5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MATTAAPAGG ARNGAGPEWG GFEENIQGGG SAVIDMENMD DTSGSSFEDM
60 70 80 90 100
GELHQRLREE EVDADAADAA AAEEEDGEFL GMKGFKGQLS RQVADQMWQA
110 120 130 140 150
GKRQASRAFS LYANIDILRP YFDVEPAQVR SRLLESMIPI KMVNFPQKIA
160 170 180 190 200
GELYGPLMLV FTLVAILLHG MKTSDTIIRE GTLMGTAIGT CFGYWLGVSS
210 220 230 240 250
FIYFLAYLCN AQITMLQMLA LLGYGLFGHC IVLFITYNIH LHALFYLFWL
260 270 280 290 300
LVGGLSTLRM VAVLVSRTVG PTQRLLLCGT LAALHMLFLL YLHFAYHKVV
310 320 330 340 350
EGILDTLEGP NIPPIQRVPR DIPAMLPAAR LPTTVLNATA KAVAVTLQSH
Length:350
Mass (Da):38,248
Last modified:March 1, 2001 - v1
Checksum:iED7A566716A6B364
GO

Sequence cautioni

The sequence CAI42626.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti103 – 1031R → G in CAG38572 (Ref. 6) Curated
Sequence conflicti142 – 1421M → V in BAA91439 (PubMed:14702039).Curated
Sequence conflicti161 – 1611F → L in AAM21161 (PubMed:12490290).Curated
Sequence conflicti305 – 3051D → V in CAB43375 (PubMed:11230166).Curated
Sequence conflicti305 – 3051D → V in CAG38572 (Ref. 6) Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti5 – 51A → V.
Corresponds to variant rs2231763 [ dbSNP | Ensembl ].
VAR_026906

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF162672 mRNA. Translation: AAM21161.1.
AK000946 mRNA. Translation: BAA91439.1.
AK021655 mRNA. Translation: BAB13866.1.
AK022757 mRNA. Translation: BAB14231.1.
AL355802 Genomic DNA. Translation: CAI42626.1. Sequence problems.
BC019297 mRNA. Translation: AAH19297.1.
AL050274 mRNA. Translation: CAB43375.2.
CR533541 mRNA. Translation: CAG38572.1.
CCDSiCCDS4899.1.
PIRiT08721.
RefSeqiNP_056203.2. NM_015388.3.
UniGeneiHs.440950.

Genome annotation databases

EnsembliENST00000372422; ENSP00000361499; ENSG00000137207.
GeneIDi25844.
KEGGihsa:25844.
UCSCiuc003ovl.2. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF162672 mRNA. Translation: AAM21161.1.
AK000946 mRNA. Translation: BAA91439.1.
AK021655 mRNA. Translation: BAB13866.1.
AK022757 mRNA. Translation: BAB14231.1.
AL355802 Genomic DNA. Translation: CAI42626.1. Sequence problems.
BC019297 mRNA. Translation: AAH19297.1.
AL050274 mRNA. Translation: CAB43375.2.
CR533541 mRNA. Translation: CAG38572.1.
CCDSiCCDS4899.1.
PIRiT08721.
RefSeqiNP_056203.2. NM_015388.3.
UniGeneiHs.440950.

3D structure databases

ProteinModelPortaliQ9GZM5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi117370. 101 interactions.
IntActiQ9GZM5. 8 interactions.
MINTiMINT-1454282.
STRINGi9606.ENSP00000361499.

Protein family/group databases

TCDBi9.B.135.2.1. the membrane trafficking yip (yip) family.

PTM databases

iPTMnetiQ9GZM5.
PhosphoSiteiQ9GZM5.
SwissPalmiQ9GZM5.
UniCarbKBiQ9GZM5.

Polymorphism and mutation databases

BioMutaiYIPF3.
DMDMi74752534.

Proteomic databases

EPDiQ9GZM5.
MaxQBiQ9GZM5.
PaxDbiQ9GZM5.
PRIDEiQ9GZM5.

Protocols and materials databases

DNASUi25844.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000372422; ENSP00000361499; ENSG00000137207.
GeneIDi25844.
KEGGihsa:25844.
UCSCiuc003ovl.2. human.

Organism-specific databases

CTDi25844.
GeneCardsiYIPF3.
HGNCiHGNC:21023. YIPF3.
HPAiHPA014859.
HPA063699.
MIMi609775. gene.
neXtProtiNX_Q9GZM5.
PharmGKBiPA134946615.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IPBK. Eukaryota.
ENOG4111EUH. LUCA.
GeneTreeiENSGT00510000047963.
HOVERGENiHBG055544.
InParanoidiQ9GZM5.
OrthoDBiEOG769ZK3.
PhylomeDBiQ9GZM5.
TreeFamiTF314073.

Miscellaneous databases

ChiTaRSiYIPF3. human.
GeneWikiiYIPF3.
GenomeRNAii25844.
NextBioi47175.
PROiQ9GZM5.
SOURCEiSearch...

Gene expression databases

BgeeiQ9GZM5.
CleanExiHS_YIPF3.
ExpressionAtlasiQ9GZM5. baseline and differential.
GenevisibleiQ9GZM5. HS.

Family and domain databases

InterProiIPR026637. YIPF3.
[Graphical view]
PANTHERiPTHR15627:SF14. PTHR15627:SF14. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Characterization of a novel hematopoietic marker expressed from early embryonic hematopoietic stem cells to adult mature lineages."
    Prost S., LeDiscorde M., Haddad R., Gluckman J.-C., Canque B., Kirszenbaum M.
    Blood Cells Mol. Dis. 29:236-248(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, DEVELOPMENTAL STAGE, TISSUE SPECIFICITY, GLYCOSYLATION, SUBCELLULAR LOCATION.
    Tissue: Lung.
  2. "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].
    Tissue: Embryo.
  3. "The DNA sequence and analysis of human chromosome 6."
    Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D.
    , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.
    Nature 425:805-811(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "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].
    Tissue: Skin.
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 7-350.
    Tissue: Fetal kidney.
  6. "Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
    Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.
    Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 36-350.
  7. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  8. Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH YIPF4, GLYCOSYLATION AT THR-333; THR-334; ASN-337 AND THR-346.
  9. "Human urinary glycoproteomics; attachment site specific analysis of N-and O-linked glycosylations by CID and ECD."
    Halim A., Nilsson J., Ruetschi U., Hesse C., Larson G.
    Mol. Cell. Proteomics 0:0-0(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: GLYCOSYLATION AT THR-346, STRUCTURE OF CARBOHYDRATES, IDENTIFICATION BY MASS SPECTROMETRY.
  10. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS], IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  11. "LC-MS/MS characterization of O-glycosylation sites and glycan structures of human cerebrospinal fluid glycoproteins."
    Halim A., Ruetschi U., Larson G., Nilsson J.
    J. Proteome Res. 12:573-584(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: GLYCOSYLATION AT THR-339 AND THR-346, IDENTIFICATION BY MASS SPECTROMETRY.

Entry informationi

Entry nameiYIPF3_HUMAN
AccessioniPrimary (citable) accession number: Q9GZM5
Secondary accession number(s): Q5JTD2
, Q6FI85, Q8NI57, Q9NWE3, Q9Y3U9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 27, 2006
Last sequence update: March 1, 2001
Last modified: April 13, 2016
This is version 116 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 6
    Human chromosome 6: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. 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.