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Protein

Glycophorin-B

Gene

GYPB

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

Functioni

This protein is a minor sialoglycoprotein in erythrocyte membranes.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei33 – 331Not glycosylated
Sitei34 – 341Not glycosylated

Keywords - Molecular functioni

Blood group antigen

Keywords - Ligandi

Sialic acid

Names & Taxonomyi

Protein namesi
Recommended name:
Glycophorin-B
Alternative name(s):
PAS-3
SS-active sialoglycoprotein
Sialoglycoprotein delta
CD_antigen: CD235b
Gene namesi
Name:GYPB
Synonyms:GPB
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 4

Organism-specific databases

HGNCiHGNC:4703. GYPB.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini20 – 5940ExtracellularSequence AnalysisAdd
BLAST
Transmembranei60 – 8122HelicalSequence AnalysisAdd
BLAST
Topological domaini82 – 9110CytoplasmicSequence Analysis

GO - Cellular componenti

  • integral component of plasma membrane Source: ProtInc
  • plasma membrane Source: ProtInc
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Organism-specific databases

MIMi111740. gene+phenotype.
PharmGKBiPA29081.

Polymorphism and mutation databases

BioMutaiGYPB.
DMDMi380865467.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 19193 PublicationsAdd
BLAST
Chaini20 – 9172Glycophorin-BPRO_0000012136Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi36 – 361O-linked (GalNAc...)1 Publication
Glycosylationi38 – 381O-linked (GalNAc...)1 Publication

Post-translational modificationi

The N-terminal extracellular domain is heavily glycosylated on serine and threonine residues.1 Publication

Keywords - PTMi

Glycoprotein

PTM databases

UniCarbKBiP06028.

Expressioni

Gene expression databases

BgeeiP06028.
CleanExiHS_GYPB.
ExpressionAtlasiP06028. baseline and differential.
GenevisibleiP06028. HS.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
UBQLN1Q9UMX03EBI-10194756,EBI-741480
UBQLN1Q9UMX0-23EBI-10194756,EBI-10173939

Protein-protein interaction databases

BioGridi109249. 1 interaction.
IntActiP06028. 1 interaction.
STRINGi9606.ENSP00000427690.

Structurei

3D structure databases

ProteinModelPortaliP06028.
SMRiP06028. Positions 49-91.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the glycophorin-A family.Curated

Keywords - Domaini

Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

GeneTreeiENSGT00610000087442.
HOGENOMiHOG000089933.
HOVERGENiHBG005850.
InParanoidiP06028.
KOiK06575.
OMAiIFEMTAV.
PhylomeDBiP06028.
TreeFamiTF338555.

Family and domain databases

InterProiIPR001195. Glycophorin.
IPR018938. Glycophorin_CS.
[Graphical view]
PANTHERiPTHR13813. PTHR13813. 1 hit.
PROSITEiPS00312. GLYCOPHORIN_A. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

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

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

Isoform 1 (identifier: P06028-1) [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
MYGKIIFVLL LSEIVSISAL STTEVAMHTS TSSSVTKSYI SSQTNGETGQ
60 70 80 90
LVHRFTVPAP VVIILIILCV MAGIIGTILL ISYSIRRLIK A
Length:91
Mass (Da):9,782
Last modified:March 21, 2012 - v3
Checksum:iEF15A64BAA929B7B
GO
Isoform 2 (identifier: P06028-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     13-45: Missing.

Show »
Length:58
Mass (Da):6,352
Checksum:i1DE98AE83FBB43A2
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti69 – 691C → S AA sequence (PubMed:3595615).Curated
Sequence conflicti69 – 691C → S AA sequence (PubMed:3571235).Curated

Polymorphismi

Along with GYPA, GYPB is responsible for the MNS blood group system. The molecular basis of the S/s blood group antigen is a single variation in position 48; Thr-48 corresponds to s=MSN4 and Met-48 to S=MNS3.

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti22 – 221T → S in M(v) antigen. 1 Publication
VAR_047948
Natural varianti48 – 481T → M in S antigen and Mit antigen. 1 Publication
Corresponds to variant rs7683365 [ dbSNP | Ensembl ].
VAR_003192
Natural varianti54 – 541R → H in Mit antigen. 1 Publication
VAR_047949
Natural varianti58 – 581P → R in s(D) antigen. 1 Publication
VAR_047950
Natural varianti84 – 841S → T.3 Publications
Corresponds to variant rs1132783 [ dbSNP | Ensembl ].
VAR_030785

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei13 – 4533Missing in isoform 2. 1 PublicationVSP_047824Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02982 mRNA. Translation: AAA52573.1.
X08055 mRNA. Translation: CAB42645.1.
M24137
, M24130, M24131, M24135 Genomic DNA. Translation: AAA58626.1.
AY950609 mRNA. Translation: AAX53130.1.
AY950610 mRNA. Translation: AAX53131.1.
AY950611 mRNA. Translation: AAX53132.1.
EU338223 mRNA. Translation: ACA96781.1.
EU338235 mRNA. Translation: ACA96793.1.
AC093890 Genomic DNA. No translation available.
AC107223 Genomic DNA. No translation available.
AC110762 Genomic DNA. No translation available.
CH471056 Genomic DNA. Translation: EAX05058.1.
BC069310 mRNA. Translation: AAH69310.1.
BC121077 mRNA. Translation: AAI21078.1.
BC121078 mRNA. Translation: AAI21079.1.
M60708 Genomic DNA. Translation: AAC63048.1.
CCDSiCCDS54809.1. [P06028-1]
PIRiB33931.
RefSeqiNP_001291311.1. NM_001304382.1.
NP_002091.3. NM_002100.5.
UniGeneiHs.654368.

Genome annotation databases

EnsembliENST00000502664; ENSP00000427690; ENSG00000250361.
ENST00000513128; ENSP00000425244; ENSG00000250361. [P06028-2]
GeneIDi2994.
KEGGihsa:2994.

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Web resourcesi

dbRBC/BGMUT

Blood group antigen gene mutation database

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02982 mRNA. Translation: AAA52573.1.
X08055 mRNA. Translation: CAB42645.1.
M24137
, M24130, M24131, M24135 Genomic DNA. Translation: AAA58626.1.
AY950609 mRNA. Translation: AAX53130.1.
AY950610 mRNA. Translation: AAX53131.1.
AY950611 mRNA. Translation: AAX53132.1.
EU338223 mRNA. Translation: ACA96781.1.
EU338235 mRNA. Translation: ACA96793.1.
AC093890 Genomic DNA. No translation available.
AC107223 Genomic DNA. No translation available.
AC110762 Genomic DNA. No translation available.
CH471056 Genomic DNA. Translation: EAX05058.1.
BC069310 mRNA. Translation: AAH69310.1.
BC121077 mRNA. Translation: AAI21078.1.
BC121078 mRNA. Translation: AAI21079.1.
M60708 Genomic DNA. Translation: AAC63048.1.
CCDSiCCDS54809.1. [P06028-1]
PIRiB33931.
RefSeqiNP_001291311.1. NM_001304382.1.
NP_002091.3. NM_002100.5.
UniGeneiHs.654368.

3D structure databases

ProteinModelPortaliP06028.
SMRiP06028. Positions 49-91.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi109249. 1 interaction.
IntActiP06028. 1 interaction.
STRINGi9606.ENSP00000427690.

PTM databases

UniCarbKBiP06028.

Polymorphism and mutation databases

BioMutaiGYPB.
DMDMi380865467.

Protocols and materials databases

DNASUi2994.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000502664; ENSP00000427690; ENSG00000250361.
ENST00000513128; ENSP00000425244; ENSG00000250361. [P06028-2]
GeneIDi2994.
KEGGihsa:2994.

Organism-specific databases

CTDi2994.
GeneCardsiGC04M144918.
HGNCiHGNC:4703. GYPB.
MIMi111740. gene+phenotype.
neXtProtiNX_P06028.
PharmGKBiPA29081.
GenAtlasiSearch...

Phylogenomic databases

GeneTreeiENSGT00610000087442.
HOGENOMiHOG000089933.
HOVERGENiHBG005850.
InParanoidiP06028.
KOiK06575.
OMAiIFEMTAV.
PhylomeDBiP06028.
TreeFamiTF338555.

Miscellaneous databases

GeneWikiiGYPB.
GenomeRNAii2994.
NextBioi11866.
PROiP06028.
SOURCEiSearch...

Gene expression databases

BgeeiP06028.
CleanExiHS_GYPB.
ExpressionAtlasiP06028. baseline and differential.
GenevisibleiP06028. HS.

Family and domain databases

InterProiIPR001195. Glycophorin.
IPR018938. Glycophorin_CS.
[Graphical view]
PANTHERiPTHR13813. PTHR13813. 1 hit.
PROSITEiPS00312. GLYCOPHORIN_A. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Molecular cloning of a human glycophorin B cDNA: nucleotide sequence and genomic relationship to glycophorin A."
    Siebert P.D., Fukuda M.
    Proc. Natl. Acad. Sci. U.S.A. 84:6735-6739(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), VARIANT THR-84.
  2. "Isolation of cDNA clones for human erythrocyte membrane sialoglycoproteins alpha and delta."
    Tate C.G., Tanner M.J.A.
    Biochem. J. 254:743-750(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
  3. "Structural organization of glycophorin A and B genes: glycophorin B gene evolved by homologous recombination at Alu repeat sequences."
    Kudo S., Fukuda M.
    Proc. Natl. Acad. Sci. U.S.A. 86:4619-4623(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANT THR-84.
  4. "Extensive alternative splicing of glycophorins in Southeast Asian populations."
    Hsu K., Chi N., Lin M.
    Submitted (DEC-2007) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), ALTERNATIVE SPLICING.
    Tissue: Blood.
  5. "Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
    Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H.
    , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
    Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  6. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  7. "The low-incidence MNS antigens M(v), s(D), and Mit arise from single amino acid substitutions on GPB."
    Storry J.R., Reid M.E., MacLennan S., Lubenko A., Nortman P.
    Transfusion 41:269-275(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), VARIANT M(V) SER-22, VARIANTS MIT MET-48 AND HIS-54, VARIANT S(D) ARG-58, VARIANT THR-84.
    Tissue: Blood.
  8. "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).
  9. "Molecular genetics of human erythrocyte MiIII and MiVI glycophorins. Use of a pseudoexon in construction of two delta-alpha-delta hybrid genes resulting in antigenic diversification."
    Huang C.-H., Blumenfeld O.O.
    J. Biol. Chem. 266:7248-7255(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 13-58.
    Tissue: Blood.
  10. "Hybrid glycophorins from human erythrocyte membranes. I. Isolation and complete structural analysis of the hybrid sialoglycoprotein from Dantu-positive red cells of the N.E. variety."
    Dahr W., Beyreuther K., Moulds J., Unger P.
    Eur. J. Biochem. 166:31-36(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 20-90.
  11. "Glycophorins B and C from human erythrocyte membranes. Purification and sequence analysis."
    Blanchard D., Dahr W., Hummel M., Latron F., Beyreuther K., Cartron J.-P.
    J. Biol. Chem. 262:5808-5811(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 20-90.
  12. "Molecular basis for the human erythrocyte glycophorin specifying the Miltenberger class I (MiI) phenotype."
    Huang C.-H., Spruell P., Moulds J.J., Blumenfeld O.O.
    Blood 80:257-263(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 20-45.
  13. Cited for: PROTEIN SEQUENCE OF 20-40, GLYCOSYLATION AT THR-36 AND SER-38.

Entry informationi

Entry nameiGLPB_HUMAN
AccessioniPrimary (citable) accession number: P06028
Secondary accession number(s): B8Q174
, E2QBW7, Q0VAF4, Q58HE9, Q58HF0, Q58HF1, Q9UCH7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: March 21, 2012
Last modified: July 22, 2015
This is version 139 of the entry and version 3 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, Direct protein sequencing, Reference proteome

Documents

  1. Blood group antigen proteins
    Nomenclature of blood group antigens and list of entries
  2. Human cell differentiation molecules
    CD nomenclature of surface proteins of human leucocytes and list of entries
  3. Human chromosome 4
    Human chromosome 4: entries, gene names and cross-references to MIM
  4. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  5. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  6. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  7. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.