SP140 (SP140 nuclear body protein)

Gene

• Entrez ID: 11262
• Gene name: SP140 nuclear body protein
• Gene symbol: SP140
• Synonyms (NCBI Gene): LYSP100, LYSP100-A, LYSP100-B
• Chromosome: 2
• Chromosome location: 2q37.1
• Summary: This gene encodes a member of the SP100 family of proteins, which are share common domains including an N-terminal homogeneously staining region domain followed by a SP100/autoimmune regulator/NucP41/P75/deformed epidermal autoregulatory factor domain, a

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1381182	hsa-miR-4749-3p	CLIP-seq
MIRT2114073	hsa-miR-1236	CLIP-seq
MIRT2114074	hsa-miR-3064-5p	CLIP-seq
MIRT2114075	hsa-miR-3156-3p	CLIP-seq
MIRT2114076	hsa-miR-4292	CLIP-seq
MIRT2114077	hsa-miR-4301	CLIP-seq
MIRT2114078	hsa-miR-4308	CLIP-seq
MIRT2114079	hsa-miR-550b	CLIP-seq
MIRT2114080	hsa-miR-670	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA
GO:0001650	Component	Fibrillar center	IDA
GO:0003677	Function	DNA binding	IEA
GO:0005515	Function	Protein binding	IPI	24267382, 32911434
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	25593309
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	TAS	8910577
GO:0005730	Component	Nucleolus	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005739	Component	Mitochondrion	IDA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0006952	Process	Defense response	IEA
GO:0006952	Process	Defense response	TAS	8910577
GO:0008270	Function	Zinc ion binding	IEA
GO:0016605	Component	PML body	IEA
GO:0046872	Function	Metal ion binding	IEA

Other IDs

• MIM: 608602
• HGNC: 17133
• e!Ensembl: ENSG00000079263

Protein

• UniProt ID: Q13342
• Protein name: Nuclear body protein SP140 (Lymphoid-restricted homolog of Sp100) (LYSp100) (Nuclear autoantigen Sp-140) (Speckled 140 kDa)
• Protein function: Component of the nuclear body, also known as nuclear domain 10, PML oncogenic domain, and KR body (PubMed:8910577). May be involved in the pathogenesis of acute promyelocytic leukemia and viral infection (PubMed:8910577). May play a role in chro
• PDB: 2MD7, 2MD8, 6G8R, 8J70, 8J71
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF03172	HSR	38 → 136	HSR domain	Domain
  PF01342	SAND	584 → 660	SAND domain	Family
  PF00439	Bromodomain	766 → 840	Bromodomain	Domain

• Tissue specificity: TISSUE SPECIFICITY: High levels in spleen and peripheral blood leukocytes, much lower levels in tonsils, thymus, prostate, ovary, small intestine, and colon (PubMed:8695863, PubMed:8910577). Very low levels in heart, brain, placenta, lung, liver, skeletal
• Sequence:

  MAQQGQQGQMASGDSNLNFRMVAEIQNVEGQNLQEQVCPEPIFRFFRENKVEIASAITRP
  FPFLMGLRDRSFISEQMYEHFQEAFRNLVPVTRVMYCVLSELEKTFGWSHLEALFSRINL
  MAYPDLNEIYRSFQNVCYEHSPLQMNNVNDLEDRPRLLPYGKQENSNACHEMDDIAVPQE
  ALSSSPRCEPGFSSESCEQLALPKAGGGDAEDAPSLLPGGGVSCKLAIQIDEGESEEMPK
  LLPYDTEVLESNGMIDAARTYSTAPGEKQGEEEGRNSPRKRNQDKEKYQESPEGRDKETF
  DLKTPQVTNEGEPEKGLCLLPGEGEEGSDDCSEMCDGEEPQEASSSLARCGSVSCLSAET
  FDLKTPQVTNEGEPEKELSLLPGEGEEGSDDCSEMCDGEERQEASSSLARRGSVSSELEN
  HPMNEEGESEELASSLLYDNVPGAEQSAYENEKCSCVMCFSEEVPGSPEARTESDQACGT
  MDTVDIANNSTLGKPKRKRRKKRGHGWSRMRMRRQENSQQNDNSKADGQVVSSEKKANVN
  LKDLSKIRGRKRGKPGTRFTQSDRAAQKRVRSRASRKHKDETVDFKAPLLPVTCGGVKGI
  LHKKKLQQGILVKCIQTEDGKWFTPTEFEIKGGHARSKNWRLSVRCGGWPLRWLMENGFL
  PDPPRIRYRKKKRILKSQNNSSVDPCMRNLDECEVCRDGGELFCCDTCSRVFHEDCHIPP
  VEAERTPWNCIFCRMKESPGSQQCCQESEVLERQMCPEEQLKCEFLLLKVYCCSESSFFA
  KIPYYYYIREACQGLKEPMWLDKIKKRLNEHGYPQVEGFVQDMRLIFQNHRASYKYKDFG
  QMGFRLEAEFEKNFKEVFAIQETNGNN

• Sequence length: 867

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ANKYLOSING SPONDYLITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHOLANGIOCARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHRONIC LYMPHOCYTIC LEUKEMIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLORECTAL CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CROHN'S DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEPATIC VENOOCCLUSIVE DISEASE WITH IMMUNODEFICIENCY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HODGKINS LYMPHOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INFLAMMATORY BOWEL DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LEUKEMIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LEUKEMIA, LYMPHOCYTIC, CHRONIC, B-CELL	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LIVER CIRRHOSIS, EXPERIMENTAL	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LYMPHOID LEUKEMIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MULTIPLE MYELOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MULTIPLE SCLEROSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-HODGKINS LYMPHOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PSORIASIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SARCOIDOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCLEROSING CHOLANGITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ULCERATIVE COLITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Acute Promyelocytic Leukemia	Promyelocytic Leukemia	BEFREE	8910577		★☆☆☆☆ Found in Text Mining only
Ankylosing spondylitis	Ankylosing Spondylitis	GWASCAT_DG	26974007		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autoimmune Diseases	Autoimmune Diseases	BEFREE	30102396		★☆☆☆☆ Found in Text Mining only
Cholangiocarcinoma	Cholangiocarcinoma	GWASCAT_DG	28779025		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangitis, Sclerosing	Cholangitis	GWASCAT_DG	26974007, 28779025		★☆☆☆☆ Found in Text Mining only
Chronic Lymphocytic Leukemia	Lymphocytic Leukemia	BEFREE	18758461, 20731705, 26152201		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Chronic Lymphocytic Leukemia	Lymphocytic Leukemia	GWASDB_DG	18758461, 22700719, 23770605, 24292274		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Chronic Lymphocytic Leukemia	Lymphocytic Leukemia	GWASCAT_DG	18758461, 22700719, 23770605, 24292274, 28112199, 28165464		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Chronic Lymphocytic Leukemia	Lymphocytic Leukemia	CTD_human_DG	18758461		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Crohn Disease	Crohn Disease	GWASDB_DG	21102463, 23128233		★☆☆☆☆ Found in Text Mining only
Crohn Disease	Crohn Disease	GWASCAT_DG	21102463, 23128233, 26192919, 26974007, 28067908		★☆☆☆☆ Found in Text Mining only
Crohn Disease	Crohn Disease	BEFREE	26152201, 28783698, 30102396		★☆☆☆☆ Found in Text Mining only
Crohn Disease	Crohn disease	Pubtator	35986286, 40226707	Associate	★☆☆☆☆ Found in Text Mining only
Depressive Disorder	Major depressive disorder	Pubtator	40226707	Associate	★☆☆☆☆ Found in Text Mining only
Ehlers-Danlos Syndrome	Ehlers-Danlos Syndrome	BEFREE	26888452		★☆☆☆☆ Found in Text Mining only
Erectile dysfunction	Erectile Dysfunction	GWASDB_DG	22704111		★☆☆☆☆ Found in Text Mining only
Gastrointestinal Neoplasms	Gastrointestinal neoplasm	Pubtator	40226707	Associate	★☆☆☆☆ Found in Text Mining only
Hepatic venoocclusive disease with immunodeficiency	Hepatic Venoocclusive Disease With Immunodeficiency	CLINVAR_DG	16648851, 22621957		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hodgkin Disease	Hodgkin Disease	GWASCAT_DG	28112199		★☆☆☆☆ Found in Text Mining only
Immune System Diseases	Immune System Diseases	BEFREE	30102396		★☆☆☆☆ Found in Text Mining only
Inflammatory Bowel Diseases	Inflammatory Bowel Disease	GWASCAT_DG	26192919		★☆☆☆☆ Found in Text Mining only
Inflammatory Bowel Diseases	Inflammatory Bowel Disease	BEFREE	30102396		★☆☆☆☆ Found in Text Mining only
Leukemia	Leukemia	Pubtator	37370186	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Leukemia Promyelocytic Acute	Promyelocytic leukemia	Pubtator	8910577	Associate	★☆☆☆☆ Found in Text Mining only
Liver Cirrhosis Biliary	Liver cirrhosis	Pubtator	24267382, 8910577	Associate	★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	36600652	Associate	★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	30465816		★☆☆☆☆ Found in Text Mining only
Melanoma	Melanoma	Pubtator	36600652	Associate	★☆☆☆☆ Found in Text Mining only
Mucocutaneous Lymph Node Syndrome	Kawasaki disease	BEFREE	24635044		★☆☆☆☆ Found in Text Mining only
Mucocutaneous Lymph Node Syndrome	Kawasaki disease	Pubtator	24635044	Stimulate	★☆☆☆☆ Found in Text Mining only
Multiple Myeloma	Multiple myeloma	Pubtator	24429703, 25743686	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Multiple Myeloma	Multiple myeloma	GWASCAT_DG	28112199		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Multiple Sclerosis	Multiple Sclerosis	GWASCAT_DG	21833088, 24076602		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Multiple Sclerosis	Multiple Sclerosis	GWASDB_DG	21833088		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Multiple Sclerosis	Multiple Sclerosis	BEFREE	26152201, 30102396		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Multiple Sclerosis	Multiple sclerosis	Pubtator	36405756	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nasopharyngeal carcinoma	Nasopharyngeal Carcinoma	GWASDB_DG	20512145		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	22235315		★☆☆☆☆ Found in Text Mining only
Osteosarcoma	Osteosarcoma	Pubtator	38225273	Associate	★☆☆☆☆ Found in Text Mining only
Psoriasis	Psoriasis	GWASCAT_DG	26974007		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoidosis	Sarcoidosis	GWASCAT_DG	26051272		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sleep Apnea Obstructive	Sleep apnea	Pubtator	26888452	Associate	★☆☆☆☆ Found in Text Mining only
Sleep Apnea Syndromes	Sleep apnea	Pubtator	26888452	Associate	★☆☆☆☆ Found in Text Mining only
Sleep Apnea, Obstructive	Sleep Apnea	BEFREE	26888452		★☆☆☆☆ Found in Text Mining only
Sleep-Disordered Breathing	Sleep Apnea	BEFREE	26888452		★☆☆☆☆ Found in Text Mining only
Small Lymphocytic Lymphoma	Lymphocytic Leukemia	GWASCAT_DG	18758461, 22700719, 23770605, 24292274, 28112199, 28165464		★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Squamous cell carcinoma	Pubtator	33361747, 36600652	Associate	★☆☆☆☆ Found in Text Mining only
Ulcerative Colitis	Ulcerative colitis	GWASCAT_DG	26974007		★★☆☆☆ Found in Text Mining + Unknown/Other Associations