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Protein

Signal-regulatory protein beta-1 isoform 3

Gene

SIRPB1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Immunoglobulin-like cell surface receptor involved in the negative regulation of receptor tyrosine kinase-coupled signaling processes.By similarity

Names & Taxonomyi

Protein namesi
Recommended name:
Signal-regulatory protein beta-1 isoform 3
Short name:
SIRP-beta-1 isoform 3
Gene namesi
Name:SIRPB1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 20

Organism-specific databases

HGNCiHGNC:15928. SIRPB1.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini30 – 371342ExtracellularSequence analysisAdd
BLAST
Transmembranei372 – 39221HelicalSequence analysisAdd
BLAST
Topological domaini393 – 3986CytoplasmicSequence analysis

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA38051.

Polymorphism and mutation databases

BioMutaiZNF786.
DMDMi205829937.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2929Sequence analysisAdd
BLAST
Chaini30 – 398369Signal-regulatory protein beta-1 isoform 3PRO_0000349108Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi54 ↔ 120PROSITE-ProRule annotation1 Publication
Disulfide bondi169 ↔ 227PROSITE-ProRule annotation
Glycosylationi244 – 2441N-linked (GlcNAc...)Sequence analysis
Disulfide bondi272 ↔ 330PROSITE-ProRule annotation
Glycosylationi291 – 2911N-linked (GlcNAc...)Sequence analysis
Glycosylationi318 – 3181N-linked (GlcNAc...)Sequence analysis

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

EPDiQ5TFQ8.
MaxQBiQ5TFQ8.
PaxDbiQ5TFQ8.
PRIDEiQ5TFQ8.

Expressioni

Gene expression databases

BgeeiQ5TFQ8.
CleanExiHS_SIRPB1.
ExpressionAtlasiQ5TFQ8. baseline and differential.
GenevisibleiQ5TFQ8. HS.

Interactioni

Protein-protein interaction databases

BioGridi115609. 5 interactions.
STRINGi9606.ENSP00000279477.

Structurei

Secondary structure

1
398
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi40 – 456Combined sources
Beta strandi50 – 523Combined sources
Beta strandi55 – 573Combined sources
Beta strandi65 – 695Combined sources
Beta strandi76 – 805Combined sources
Beta strandi89 – 935Combined sources
Beta strandi95 – 973Combined sources
Beta strandi105 – 1073Combined sources
Helixi112 – 1143Combined sources
Beta strandi116 – 1249Combined sources
Beta strandi127 – 1293Combined sources
Beta strandi131 – 1355Combined sources
Beta strandi139 – 1446Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2JJVX-ray1.80A/B30-148[»]
ProteinModelPortaliQ5TFQ8.
SMRiQ5TFQ8. Positions 30-347.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5TFQ8.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini31 – 136106Ig-like V-typeAdd
BLAST
Domaini147 – 246100Ig-like C1-type 1Add
BLAST
Domaini253 – 34795Ig-like C1-type 2Add
BLAST

Sequence similaritiesi

Keywords - Domaini

Immunoglobulin domain, Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410IKYM. Eukaryota.
ENOG410YKK2. LUCA.
GeneTreeiENSGT00440000033339.
HOGENOMiHOG000230874.
HOVERGENiHBG056632.
OMAiLSETIRX.

Family and domain databases

Gene3Di2.60.40.10. 3 hits.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003597. Ig_C1-set.
IPR003599. Ig_sub.
IPR013106. Ig_V-set.
[Graphical view]
PfamiPF07654. C1-set. 2 hits.
PF07686. V-set. 1 hit.
[Graphical view]
SMARTiSM00409. IG. 2 hits.
SM00407. IGc1. 2 hits.
SM00406. IGv. 1 hit.
[Graphical view]
SUPFAMiSSF48726. SSF48726. 3 hits.
PROSITEiPS50835. IG_LIKE. 3 hits.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

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

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 3 (identifier: Q5TFQ8-1) [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
MPVPASWPHL PSPFLLMTLL LGRLTGVAGE EELQVIQPDK SISVAAGESA
60 70 80 90 100
TLHCTVTSLI PVGPIQWFRG AGPGRELIYN QKEGHFPRVT TVSDLTKRNN
110 120 130 140 150
MDFSIRISNI TPADAGTYYC VKFRKGSPDH VEFKSGAGTE LSVRAKPSAP
160 170 180 190 200
VVSGPAARAT PQHTVSFTCE SHGFSPRDIT LKWFKNGNEL SDFQTNVDPA
210 220 230 240 250
GDSVSYSIHS TAKVVLTRED VHSQVICEVA HVTLQGDPLR GTANLSETIR
260 270 280 290 300
VPPTLEVTQQ PVRAENQVNV TCQVRKFYPQ RLQLTWLENG NVSRTETAST
310 320 330 340 350
LTENKDGTYN WMSWLLVNVS AHRDDVKLTC QVEHDGQPAV SKSHDLKVSA
360 370 380 390
HPKEQGSNTA PGPALASAAP LLIAFLLGPK VLLVVGVSVI YVYWKQKA
Length:398
Mass (Da):43,359
Last modified:February 5, 2008 - v1
Checksum:i7F3B930235BD556C
GO
Isoform 1 (identifier: O00241-1) [UniParc]FASTAAdd to basket

The sequence of this isoform can be found in the external entry O00241.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Length:398
Mass (Da):43,211
GO
Isoform 2 (identifier: O00241-2) [UniParc]FASTAAdd to basket

The sequence of this isoform can be found in the external entry O00241.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: No experimental confirmation available.
Length:181
Mass (Da):19,394
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti23 – 231R → G.2 Publications
Corresponds to variant rs1535882 [ dbSNP | Ensembl ].
VAR_056077
Natural varianti51 – 511T → I.
Corresponds to variant rs1135196 [ dbSNP | Ensembl ].
VAR_059411

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK289866 mRNA. Translation: BAF82555.1.
BX537992 mRNA. Translation: CAD97951.1.
AL049634, AL138804, AL592544 Genomic DNA. Translation: CAI21866.1.
AL592544, AL049634, AL138804 Genomic DNA. Translation: CAI21700.1.
CCDSiCCDS46571.1. [Q5TFQ8-1]
RefSeqiNP_001129316.1. NM_001135844.2. [Q5TFQ8-1]
XP_011527432.1. XM_011529130.1. [Q5TFQ8-1]
XP_011527433.1. XM_011529131.1. [Q5TFQ8-1]
UniGeneiHs.664861.

Genome annotation databases

EnsembliENST00000279477; ENSP00000279477; ENSG00000101307. [Q5TFQ8-1]
ENST00000568365; ENSP00000456826; ENSG00000101307. [Q5TFQ8-1]
GeneIDi10326.
UCSCiuc002wfl.5. human. [Q5TFQ8-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK289866 mRNA. Translation: BAF82555.1.
BX537992 mRNA. Translation: CAD97951.1.
AL049634, AL138804, AL592544 Genomic DNA. Translation: CAI21866.1.
AL592544, AL049634, AL138804 Genomic DNA. Translation: CAI21700.1.
CCDSiCCDS46571.1. [Q5TFQ8-1]
RefSeqiNP_001129316.1. NM_001135844.2. [Q5TFQ8-1]
XP_011527432.1. XM_011529130.1. [Q5TFQ8-1]
XP_011527433.1. XM_011529131.1. [Q5TFQ8-1]
UniGeneiHs.664861.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2JJVX-ray1.80A/B30-148[»]
ProteinModelPortaliQ5TFQ8.
SMRiQ5TFQ8. Positions 30-347.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi115609. 5 interactions.
STRINGi9606.ENSP00000279477.

Polymorphism and mutation databases

BioMutaiZNF786.
DMDMi205829937.

Proteomic databases

EPDiQ5TFQ8.
MaxQBiQ5TFQ8.
PaxDbiQ5TFQ8.
PRIDEiQ5TFQ8.

Protocols and materials databases

DNASUi10326.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000279477; ENSP00000279477; ENSG00000101307. [Q5TFQ8-1]
ENST00000568365; ENSP00000456826; ENSG00000101307. [Q5TFQ8-1]
GeneIDi10326.
UCSCiuc002wfl.5. human. [Q5TFQ8-1]

Organism-specific databases

CTDi10326.
GeneCardsiSIRPB1.
HGNCiHGNC:15928. SIRPB1.
neXtProtiNX_Q5TFQ8.
PharmGKBiPA38051.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IKYM. Eukaryota.
ENOG410YKK2. LUCA.
GeneTreeiENSGT00440000033339.
HOGENOMiHOG000230874.
HOVERGENiHBG056632.
OMAiLSETIRX.

Miscellaneous databases

EvolutionaryTraceiQ5TFQ8.
GenomeRNAii10326.
NextBioi39145.

Gene expression databases

BgeeiQ5TFQ8.
CleanExiHS_SIRPB1.
ExpressionAtlasiQ5TFQ8. baseline and differential.
GenevisibleiQ5TFQ8. HS.

Family and domain databases

Gene3Di2.60.40.10. 3 hits.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003597. Ig_C1-set.
IPR003599. Ig_sub.
IPR013106. Ig_V-set.
[Graphical view]
PfamiPF07654. C1-set. 2 hits.
PF07686. V-set. 1 hit.
[Graphical view]
SMARTiSM00409. IG. 2 hits.
SM00407. IGc1. 2 hits.
SM00406. IGv. 1 hit.
[Graphical view]
SUPFAMiSSF48726. SSF48726. 3 hits.
PROSITEiPS50835. IG_LIKE. 3 hits.
[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], VARIANT GLY-23.
    Tissue: Caudate nucleus.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT GLY-23.
    Tissue: Esophageal carcinoma.
  3. "The DNA sequence and comparative analysis of human chromosome 20."
    Deloukas P., Matthews L.H., Ashurst J.L., Burton J., Gilbert J.G.R., Jones M., Stavrides G., Almeida J.P., Babbage A.K., Bagguley C.L., Bailey J., Barlow K.F., Bates K.N., Beard L.M., Beare D.M., Beasley O.P., Bird C.P., Blakey S.E.
    , Bridgeman A.M., Brown A.J., Buck D., Burrill W.D., Butler A.P., Carder C., Carter N.P., Chapman J.C., Clamp M., Clark G., Clark L.N., Clark S.Y., Clee C.M., Clegg S., Cobley V.E., Collier R.E., Connor R.E., Corby N.R., Coulson A., Coville G.J., Deadman R., Dhami P.D., Dunn M., Ellington A.G., Frankland J.A., Fraser A., French L., Garner P., Grafham D.V., Griffiths C., Griffiths M.N.D., Gwilliam R., Hall R.E., Hammond S., Harley J.L., Heath P.D., Ho S., Holden J.L., Howden P.J., Huckle E., Hunt A.R., Hunt S.E., Jekosch K., Johnson C.M., Johnson D., Kay M.P., Kimberley A.M., King A., Knights A., Laird G.K., Lawlor S., Lehvaeslaiho M.H., Leversha M.A., Lloyd C., Lloyd D.M., Lovell J.D., Marsh V.L., Martin S.L., McConnachie L.J., McLay K., McMurray A.A., Milne S.A., Mistry D., Moore M.J.F., Mullikin J.C., Nickerson T., Oliver K., Parker A., Patel R., Pearce T.A.V., Peck A.I., Phillimore B.J.C.T., Prathalingam S.R., Plumb R.W., Ramsay H., Rice C.M., Ross M.T., Scott C.E., Sehra H.K., Shownkeen R., Sims S., Skuce C.D., Smith M.L., Soderlund C., Steward C.A., Sulston J.E., Swann R.M., Sycamore N., Taylor R., Tee L., Thomas D.W., Thorpe A., Tracey A., Tromans A.C., Vaudin M., Wall M., Wallis J.M., Whitehead S.L., Whittaker P., Willey D.L., Williams L., Williams S.A., Wilming L., Wray P.W., Hubbard T., Durbin R.M., Bentley D.R., Beck S., Rogers J.
    Nature 414:865-871(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "Paired receptor specificity explained by structures of signal regulatory proteins alone and complexed with CD47."
    Hatherley D., Graham S.C., Turner J., Harlos K., Stuart D.I., Barclay A.N.
    Mol. Cell 31:266-277(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 30-148, DISULFIDE BOND.

Entry informationi

Entry nameiSIRBL_HUMAN
AccessioniPrimary (citable) accession number: Q5TFQ8
Secondary accession number(s): Q7Z3B9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 2, 2008
Last sequence update: February 5, 2008
Last modified: May 11, 2016
This is version 80 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 20
    Human chromosome 20: 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.