Q13342 (LY10_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	867 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript 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.
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.
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.

Ontologies

Keywords
Cellular component	Cytoplasm Nucleus
Coding sequence diversity	Alternative splicing Polymorphism
Domain	Bromodomain Zinc-finger
Ligand	DNA-binding Metal-binding Zinc
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	defense response Traceable author statement Ref.2. Source: ProtInc
Cellular_component	cytoplasm Inferred from direct assay. Source: HPA nuclear envelope Traceable author statement Ref.1. Source: ProtInc nucleolus Inferred from direct assay. Source: HPA nucleoplasm Traceable author statement Ref.1. Source: ProtInc
Molecular_function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW sequence-specific DNA binding transcription factor activity Traceable author statement Ref.1. Source: ProtInc zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

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 key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 867	867	Nuclear body protein SP140		PRO_0000211206
Regions
	Domain	22 – 138	117	HSR
	Domain	580 – 661	82	SAND
	Domain	796 – 829	34	Bromo
	Zinc finger	690 – 736	47	PHD-type
	Motif	495 – 514	20	Nuclear localization signal Potential
	Compositional bias	784 – 787	4	Poly-Tyr
Natural variations
	Alternative sequence	136 – 172	37	VCYEH…ACHEM → ENLSSSAVLCQLVSPNKDWR SHEESLAHTGTLRRSCM in isoform 4.		VSP_043235
	Alternative sequence	173 – 687	515	Missing in isoform 4.		VSP_043236
	Alternative sequence	248 – 297	50	Missing in isoform Sp140.		VSP_000558
	Alternative sequence	340 – 400	61	Missing in isoform Sp140.		VSP_000559
	Alternative sequence	353 – 386	34	Missing in isoform LYSp100-A.		VSP_000560
	Alternative sequence	405 – 446	42	SSSLA…PGAEQ → QKQGRKVIKRVAQWILWILQ TTPLWENPRGKEEKRGGMAG AE in isoform LYSp100-A.		VSP_000561
	Alternative sequence	447 – 867	421	Missing in isoform LYSp100-A.		VSP_000562
	Natural variant	356	1	L → F. Corresponds to variant rs3820975 [ dbSNP | Ensembl ].		VAR_055555
	Natural variant	512	1	M → T. Corresponds to variant rs4972945 [ dbSNP | Ensembl ].		VAR_055556
	Natural variant	516	1	E → K. Ref.2 Corresponds to variant rs4972946 [ dbSNP | Ensembl ].		VAR_055557
	Natural variant	558	1	R → C. Corresponds to variant rs11887179 [ dbSNP | Ensembl ].		VAR_055558
Experimental info
	Sequence conflict	186	1	P → A in AAB18616. Ref.1
	Sequence conflict	186	1	P → A in AAB18617. Ref.1
	Sequence conflict	186	1	P → A in AAC50817. Ref.2
	Sequence conflict	219 – 221	3	Missing in AAC50817. Ref.2
	Sequence conflict	356 – 358	3	LSA → FST in AAB18617. Ref.1
	Sequence conflict	838	1	D → G in AAB18617. Ref.1
	Sequence conflict	862	1	E → G in AAB18617. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Isoform LYSp100-B [UniParc]. Last modified December 16, 2008. Version 2. Checksum: 355601D1D4689A74	FASTA	867	98,223
	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
	Isoform LYSp100-A [UniParc]. Checksum: 093D90128FEBE1EE	FASTA	412	46,151
	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 GSEGSDDCSE 370 380 390 400 410 MCDGEERQEA QKQGRKVIKR VAQWILWILQ TTPLWENPRG KEEKRGGMAG AE
	Isoform Sp140 [UniParc]. Checksum: 9EA10C9CA02D7239	FASTA	756	86,181
	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 LLPYDTEETF DLKTPQVTNE GEPEKGLCLL PGEGEEGSDD CSEMCDGEER QEASSSLARR 310 320 330 340 350 360 GSVSSELENH PMNEEGESEE LASSLLYDNV PGAEQSAYEN EKCSCVMCFS EEVPGSPEAR 370 380 390 400 410 420 TESDQACGTM DTVDIANNST LGKPKRKRRK KRGHGWSRMR MRRQENSQQN DNSKADGQVV 430 440 450 460 470 480 SSEKKANVNL KDLSKIRGRK RGKPGTRFTQ SDRAAQKRVR SRASRKHKDE TVDFKAPLLP 490 500 510 520 530 540 VTCGGVKGIL HKKKLQQGIL VKCIQTEDGK WFTPTEFEIK GGHARSKNWR LSVRCGGWPL 550 560 570 580 590 600 RWLMENGFLP DPPRIRYRKK KRILKSQNNS SVDPCMRNLD ECEVCRDGGE LFCCDTCSRV 610 620 630 640 650 660 FHEDCHIPPV EAERTPWNCI FCRMKESPGS QQCCQESEVL ERQMCPEEQL KCEFLLLKVY 670 680 690 700 710 720 CCSESSFFAK IPYYYYIREA CQGLKEPMWL DKIKKRLNEH GYPQVEGFVQ DMRLIFQNHR 730 740 750 ASYKYKDFGQ MGFRLEAEFE KNFKEVFAIQ ETNGNN
	Isoform 4 [UniParc]. Checksum: 7EE207925684DB3A	FASTA	352	41,321
	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 RSFQNENLSS SAVLCQLVSP NKDWRSHEES LAHTGTLRRS CMRNLDECEV 190 200 210 220 230 240 CRDGGELFCC DTCSRVFHED CHIPPVEAER TPWNCIFCRM KESPGSQQCC QESEVLERQM 250 260 270 280 290 300 CPEEQLKCEF LLLKVYCCSE SSFFAKIPYY YYIREACQGL KEPMWLDKIK KRLNEHGYPQ 310 320 330 340 350 VEGFVQDMRL IFQNHRASYK YKDFGQMGFR LEAEFEKNFK EVFAIQETNG NN

References

	« Hide 'large scale' referencesShow '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. , 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).
+	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.
IPI	IPI00012793. IPI00219535. IPI00219536. IPI00431685.
PIR	G02099.
RefSeq	NP_001005176.1. NM_001005176.2. NP_009168.4. NM_007237.4.
UniGene	Hs.632549.
3D structure databases
ProteinModelPortal	Q13342.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q13342. 2 interactions.
STRING	9606.ENSP00000375899.
PTM databases
PhosphoSite	Q13342.
Polymorphism databases
DMDM	218511671.
Proteomic databases
PaxDb	Q13342.
PRIDE	Q13342.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000373645; ENSP00000362749; ENSG00000079263. ENST00000392045; ENSP00000375899; ENSG00000079263.
GeneID	11262.
KEGG	hsa:11262.
UCSC	uc002vql.3. human. uc002vqn.3. human.
Organism-specific databases
CTD	11262.
GeneCards	GC02P231090.
HGNC	HGNC:17133. SP140.
HPA	HPA006162.
MIM	608602. gene.
neXtProt	NX_Q13342.
PharmGKB	PA38205.
GenAtlas	Search...
Phylogenomic databases
eggNOG	NOG300534.
HOGENOM	HOG000089984.
HOVERGEN	HBG006294.
InParanoid	Q13342.
OMA	MCFSEEV.
OrthoDB	EOG44QT09.
Gene expression databases
ArrayExpress	Q13342.
Bgee	Q13342.
CleanEx	HS_SP140.
Genevestigator	Q13342.
GermOnline	ENSG00000079263. Homo sapiens.
Family and domain databases
Gene3D	1.20.920.10. 1 hit. 3.10.390.10. 1 hit. 3.30.40.10. 1 hit.
InterPro	IPR001487. 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]
Pfam	PF00439. Bromodomain. 1 hit. PF00628. PHD. 1 hit. PF01342. SAND. 1 hit. PF03172. Sp100. 1 hit. [Graphical view]
SMART	SM00297. BROMO. 1 hit. SM00249. PHD. 1 hit. SM00258. SAND. 1 hit. [Graphical view]
SUPFAM	SSF47370. Bromodomain. 1 hit. SSF57903. FYVE_PHD_ZnF. 1 hit. SSF63763. SAND_like. 1 hit.
PROSITE	PS00633. BROMODOMAIN_1. False negative. PS50014. 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]
ProtoNet	Search...
Other
ChiTaRS	SP140. human.
GenomeRNAi	11262.
NextBio	42859.
SOURCE	Search...

Entry information

Entry name

LY10_HUMAN

Accession

Primary (citable) accession number: Q13342
Secondary accession number(s): Q13341 , Q4ZG66, Q53TG1, Q6NSG4, Q92881, Q96TG3

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 15, 1999
Last sequence update:	December 16, 2008
Last modified:	May 1, 2013
This is version 120 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.