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Q13342 (SP140_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 132. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Nuclear body protein SP140
Alternative name(s):
Lymphoid-restricted homolog of Sp100
Short name=LYSp100
Nuclear autoantigen Sp-140
Speckled 140 kDa
Gene names
Name:SP140
Synonyms:LYSP100
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length867 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Component of the nuclear body, also known as nuclear domain 10, PML oncogenic domain, and KR body. May be involved in the pathogenesis of acute promyelocytic leukemia and viral infection. May play a role in chromatin-mediated regulation of gene expression although it doesn't bind to histone H3 tails. Ref.5

Subunit structure

Interacts with PIN1. Ref.5

Subcellular location

Nucleus. Cytoplasm. Note: Localized to nuclear structures termed LANDS, for LYSp100-associated nuclear domains. LANDS are globular, electron-dense structures most often found in the nucleoplasm, but also found at the nuclear membrane and in the cytoplasm, suggesting that these structures may traffic between the cytoplasm and the nucleus.

Tissue specificity

High levels in spleen and peripheral blood leukocytes, much lower levels in thymus, prostate, ovary, small intestine, and colon. Very low levels in heart, brain, placenta, lung, liver, skeletal muscle, kidney, and pancreas.

Induction

By interferons.

Post-translational modification

Phosphorylation at Thr-726 promotes binding of PIN1 and subsequent isomerization of Pro-727.

Miscellaneous

This antigen is recognized by autoantibodies from patients with primary biliary cirrhosis.

Sequence similarities

Contains 1 bromo domain.

Contains 1 HSR domain.

Contains 1 PHD-type zinc finger.

Contains 1 SAND domain.

Sequence caution

The sequence AAB18617.1 differs from that shown. Reason: Frameshift at position 862.

The sequence AAX93282.1 differs from that shown. Reason: Erroneous gene model prediction.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

PIN1Q135264EBI-2865100,EBI-714158

Alternative products

This entry describes 4 isoforms produced by alternative splicing. [Align] [Select]
Isoform LYSp100-B (identifier: Q13342-1)

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.
Isoform LYSp100-A (identifier: Q13342-2)

The sequence of this isoform differs from the canonical sequence as follows:
     353-386: Missing.
     405-446: SSSLARRGSV...LYDNVPGAEQ → QKQGRKVIKR...EKRGGMAGAE
     447-867: Missing.
Isoform Sp140 (identifier: Q13342-3)

The sequence of this isoform differs from the canonical sequence as follows:
     248-297: Missing.
     340-400: Missing.
Isoform 4 (identifier: Q13342-4)

The sequence of this isoform differs from the canonical sequence as follows:
     136-172: VCYEHSPLQMNNVNDLEDRPRLLPYGKQENSNACHEM → ENLSSSAVLCQLVSPNKDWRSHEESLAHTGTLRRSCM
     173-687: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 867867Nuclear body protein SP140
PRO_0000211206

Regions

Domain22 – 138117HSR
Domain580 – 66182SAND
Domain796 – 82934Bromo
Zinc finger690 – 73647PHD-type
Motif495 – 51420Nuclear localization signal Potential
Compositional bias784 – 7874Poly-Tyr

Amino acid modifications

Modified residue7261Phosphothreonine Ref.5

Natural variations

Alternative sequence136 – 17237VCYEH…ACHEM → ENLSSSAVLCQLVSPNKDWR SHEESLAHTGTLRRSCM in isoform 4.
VSP_043235
Alternative sequence173 – 687515Missing in isoform 4.
VSP_043236
Alternative sequence248 – 29750Missing in isoform Sp140.
VSP_000558
Alternative sequence340 – 40061Missing in isoform Sp140.
VSP_000559
Alternative sequence353 – 38634Missing in isoform LYSp100-A.
VSP_000560
Alternative sequence405 – 44642SSSLA…PGAEQ → QKQGRKVIKRVAQWILWILQ TTPLWENPRGKEEKRGGMAG AE in isoform LYSp100-A.
VSP_000561
Alternative sequence447 – 867421Missing in isoform LYSp100-A.
VSP_000562
Natural variant3561L → F.
Corresponds to variant rs3820975 [ dbSNP | Ensembl ].
VAR_055555
Natural variant5121M → T.
Corresponds to variant rs4972945 [ dbSNP | Ensembl ].
VAR_055556
Natural variant5161E → K. Ref.2
Corresponds to variant rs4972946 [ dbSNP | Ensembl ].
VAR_055557
Natural variant5581R → C.
Corresponds to variant rs11887179 [ dbSNP | Ensembl ].
VAR_055558

Experimental info

Sequence conflict1861P → A in AAB18616. Ref.1
Sequence conflict1861P → A in AAB18617. Ref.1
Sequence conflict1861P → A in AAC50817. Ref.2
Sequence conflict219 – 2213Missing in AAC50817. Ref.2
Sequence conflict356 – 3583LSA → FST in AAB18617. Ref.1
Sequence conflict8381D → G in AAB18617. Ref.1
Sequence conflict8621E → G in AAB18617. Ref.1

Secondary structure

........... 867
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform LYSp100-B [UniParc].

Last modified December 16, 2008. Version 2.
Checksum: 355601D1D4689A74

FASTA86798,223
        10         20         30         40         50         60 
MAQQGQQGQM ASGDSNLNFR MVAEIQNVEG QNLQEQVCPE PIFRFFRENK VEIASAITRP 

        70         80         90        100        110        120 
FPFLMGLRDR SFISEQMYEH FQEAFRNLVP VTRVMYCVLS ELEKTFGWSH LEALFSRINL 

       130        140        150        160        170        180 
MAYPDLNEIY RSFQNVCYEH SPLQMNNVND LEDRPRLLPY GKQENSNACH EMDDIAVPQE 

       190        200        210        220        230        240 
ALSSSPRCEP GFSSESCEQL ALPKAGGGDA EDAPSLLPGG GVSCKLAIQI DEGESEEMPK 

       250        260        270        280        290        300 
LLPYDTEVLE SNGMIDAART YSTAPGEKQG EEEGRNSPRK RNQDKEKYQE SPEGRDKETF 

       310        320        330        340        350        360 
DLKTPQVTNE GEPEKGLCLL PGEGEEGSDD CSEMCDGEEP QEASSSLARC GSVSCLSAET 

       370        380        390        400        410        420 
FDLKTPQVTN EGEPEKELSL LPGEGEEGSD DCSEMCDGEE RQEASSSLAR RGSVSSELEN 

       430        440        450        460        470        480 
HPMNEEGESE ELASSLLYDN VPGAEQSAYE NEKCSCVMCF SEEVPGSPEA RTESDQACGT 

       490        500        510        520        530        540 
MDTVDIANNS TLGKPKRKRR KKRGHGWSRM RMRRQENSQQ NDNSKADGQV VSSEKKANVN 

       550        560        570        580        590        600 
LKDLSKIRGR KRGKPGTRFT QSDRAAQKRV RSRASRKHKD ETVDFKAPLL PVTCGGVKGI 

       610        620        630        640        650        660 
LHKKKLQQGI LVKCIQTEDG KWFTPTEFEI KGGHARSKNW RLSVRCGGWP LRWLMENGFL 

       670        680        690        700        710        720 
PDPPRIRYRK KKRILKSQNN SSVDPCMRNL DECEVCRDGG ELFCCDTCSR VFHEDCHIPP 

       730        740        750        760        770        780 
VEAERTPWNC IFCRMKESPG SQQCCQESEV LERQMCPEEQ LKCEFLLLKV YCCSESSFFA 

       790        800        810        820        830        840 
KIPYYYYIRE ACQGLKEPMW LDKIKKRLNE HGYPQVEGFV QDMRLIFQNH RASYKYKDFG 

       850        860 
QMGFRLEAEF EKNFKEVFAI QETNGNN 

« Hide

Isoform LYSp100-A [UniParc].

Checksum: 093D90128FEBE1EE
Show »

FASTA41246,151
Isoform Sp140 [UniParc].

Checksum: 9EA10C9CA02D7239
Show »

FASTA75686,181
Isoform 4 [UniParc].

Checksum: 7EE207925684DB3A
Show »

FASTA35241,321

References

« Hide 'large scale' references
[1]"LYSP100-associated nuclear domains (LANDs): description of a new class of subnuclear structures and their relationship to PML nuclear bodies."
Dent A.L., Yewdell J., Puvion-Dutilleul F., Koken M.H.M., de The H., Staudt L.M.
Blood 88:1423-1426(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS LYSP100-A AND LYSP100-B).
[2]"Identification and characterization of a leukocyte-specific component of the nuclear body."
Bloch D.B., de la Monte S.M., Guigaouri P., Filippov A., Bloch K.D.
J. Biol. Chem. 271:29198-29204(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM SP140), VARIANT LYS-516.
Tissue: Placenta.
[3]"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. expand/collapse author list , 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].
[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] (ISOFORM 4).
[5]"Structure of human Sp140 PHD finger: an atypical fold interacting with Pin1."
Zucchelli C., Tamburri S., Quilici G., Palagano E., Berardi A., Saare M., Peterson P., Bachi A., Musco G.
FEBS J. 281:216-231(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 687-738, FUNCTION, PHOSPHORYLATION AT THR-726, INTERACTION WITH PIN1.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U36499 mRNA. Translation: AAB18616.1.
U36500 mRNA. Translation: AAB18617.1. Frameshift.
U63420 mRNA. Translation: AAC50817.1.
AC009949 Genomic DNA. Translation: AAX88868.1.
AC009950 Genomic DNA. Translation: AAX93282.1. Sequence problems.
BC070160 mRNA. Translation: AAH70160.1.
CCDSCCDS42831.1. [Q13342-1]
PIRG02099.
RefSeqNP_001005176.1. NM_001005176.2.
NP_001265380.1. NM_001278451.1.
NP_001265381.1. NM_001278452.1.
NP_001265382.1. NM_001278453.1.
NP_009168.4. NM_007237.4. [Q13342-1]
UniGeneHs.632549.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2MD7NMR-B687-738[»]
2MD8NMR-C687-738[»]
ProteinModelPortalQ13342.
SMRQ13342. Positions 580-669, 687-858.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid116422. 2 interactions.
IntActQ13342. 3 interactions.
MINTMINT-6631209.
STRING9606.ENSP00000375899.

PTM databases

PhosphoSiteQ13342.

Polymorphism databases

DMDM218511671.

Proteomic databases

MaxQBQ13342.
PaxDbQ13342.
PRIDEQ13342.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000373645; ENSP00000362749; ENSG00000079263.
ENST00000392045; ENSP00000375899; ENSG00000079263. [Q13342-1]
GeneID11262.
KEGGhsa:11262.
UCSCuc002vqk.2. human. [Q13342-2]
uc002vql.3. human. [Q13342-1]
uc002vqn.3. human. [Q13342-3]

Organism-specific databases

CTD11262.
GeneCardsGC02P231090.
HGNCHGNC:17133. SP140.
HPAHPA006162.
MIM608602. gene.
neXtProtNX_Q13342.
PharmGKBPA38205.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG300534.
HOGENOMHOG000089984.
HOVERGENHBG006294.
InParanoidQ13342.
OMAGILVKCI.
OrthoDBEOG7G1V5G.
PhylomeDBQ13342.
TreeFamTF335091.

Gene expression databases

ArrayExpressQ13342.
BgeeQ13342.
CleanExHS_SP140.
GenevestigatorQ13342.

Family and domain databases

Gene3D1.20.920.10. 1 hit.
3.10.390.10. 1 hit.
3.30.40.10. 1 hit.
InterProIPR001487. Bromodomain.
IPR000770. SAND_dom.
IPR010919. SAND_dom-like.
IPR004865. Sp100.
IPR019786. Zinc_finger_PHD-type_CS.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamPF00439. Bromodomain. 1 hit.
PF00628. PHD. 1 hit.
PF01342. SAND. 1 hit.
PF03172. Sp100. 1 hit.
[Graphical view]
SMARTSM00297. BROMO. 1 hit.
SM00249. PHD. 1 hit.
SM00258. SAND. 1 hit.
[Graphical view]
SUPFAMSSF47370. SSF47370. 1 hit.
SSF57903. SSF57903. 1 hit.
SSF63763. SSF63763. 1 hit.
PROSITEPS50014. BROMODOMAIN_2. 1 hit.
PS51414. HSR. 1 hit.
PS50864. SAND. 1 hit.
PS01359. ZF_PHD_1. 1 hit.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSSP140. human.
GenomeRNAi11262.
NextBio42859.
PROQ13342.
SOURCESearch...

Entry information

Entry nameSP140_HUMAN
AccessionPrimary (citable) accession number: Q13342
Secondary accession number(s): Q13341 expand/collapse secondary AC list , Q4ZG66, Q53TG1, Q6NSG4, Q92881, Q96TG3
Entry history
Integrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: December 16, 2008
Last modified: July 9, 2014
This is version 132 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 2

Human chromosome 2: entries, gene names and cross-references to MIM