Q8WX92 (NELFB_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Negative elongation factor B
Short name=NELF-B

Alternative name(s):
Cofactor of BRCA1

Gene names

Name:	COBRA1
Synonyms:	KIAA1182, NELFB

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	580 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Essential component of the NELF complex, a complex that negatively regulates the elongation of transcription by RNA polymerase II. The NELF complex, which acts via an association with the DSIF complex and causes transcriptional pausing, is counteracted by the P-TEFb kinase complex. May be able to induce chromatin unfolding. Ref.7 Ref.8
Subunit structure	The NELF complex is composed of 4 subunits: WHSC2/NELF-A, COBRA1/NELF-B, TH1L (isoform NELF-C or isoform NELF-D) and RDBP/NELF-E. Interacts with the first BRCT repeat of BRCA1. Ref.1
Subcellular location	Nucleus Ref.1.
Tissue specificity	Widely expressed. Expressed in heart, brain, lung, placenta, liver, skeletal muscle, kidney and pancreas. Ref.7
Sequence similarities	Belongs to the NELF-B family.
Sequence caution	The sequence AAH11892.1 differs from that shown. Reason: Erroneous initiation. The sequence BAB14157.1 differs from that shown. Reason: Erroneous initiation. The sequence CAB43381.3 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Molecular function	Repressor
PTM	Acetylation Phosphoprotein
Technical term	Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	negative regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: InterPro positive regulation of viral transcription Traceable author statement. Source: Reactome transcription elongation from RNA polymerase II promoter Traceable author statement. Source: Reactome viral reproduction Traceable author statement. Source: Reactome
Cellular component	cytoplasm Inferred from direct assay. Source: LIFEdb nucleoplasm Traceable author statement. Source: Reactome
Molecular function	protein binding Inferred from physical interaction Ref.1. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
BRCA1	P38398	5	EBI-347721,EBI-349905
DENR	O43583	2	EBI-347721,EBI-716083
FYN	P06241	2	EBI-347721,EBI-515315
GRB2	P62993	2	EBI-347721,EBI-401755
HSPA9	P38646	2	EBI-347721,EBI-354932
KHDRBS3	O75525	2	EBI-347721,EBI-722504
MGST1	P10620	2	EBI-347721,EBI-2691601
NCK1	P16333	6	EBI-347721,EBI-389883
PIK3R1	P27986	2	EBI-347721,EBI-79464

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 580	580	Negative elongation factor B		PRO_0000219129
Amino acid modifications
	Modified residue	519	1	N6-acetyllysine Ref.14
	Modified residue	557	1	Phosphoserine Ref.9 Ref.10 Ref.11 Ref.12 Ref.13
Experimental info
	Sequence conflict	156	1	L → F in BAB14157. Ref.2
	Sequence conflict	182	1	S → A Ref.5

Sequences

	Sequence		Length	Mass (Da)
	Q8WX92 [UniParc]. Last modified March 1, 2002. Version 1. Checksum: C0A4F7F2BEE52CBD	FASTA	580	65,697
	10 20 30 40 50 60 MFAGLQDLGV ANGEDLKETL TNCTEPLKAI EQFQTENGVL LPSLQSALPF LDLHGTPRLE 70 80 90 100 110 120 FHQSVFDELR DKLLERVSAI ASEGKAEERY KKLEDLLEKS FSLVKMPSLQ PVVMCVMKHL 130 140 150 160 170 180 PKVPEKKLKL VMADKELYRA CAVEVKRQIW QDNQALFGDE VSPLLKQYIL EKESALFSTE 190 200 210 220 230 240 LSVLHNFFSP SPKTRRQGEV VQRLTRMVGK NVKLYDMVLQ FLRTLFLRTR NVHYCTLRAE 250 260 270 280 290 300 LLMSLHDLDV GEICTVDPCH KFTWCLDACI RERFVDSKRA RELQGFLDGV KKGQEQVLGD 310 320 330 340 350 360 LSMILCDPFA INTLALSTVR HLQELVGQET LPRDSPDLLL LLRLLALGQG AWDMIDSQVF 370 380 390 400 410 420 KEPKMEVELI TRFLPMLMSF LVDDYTFNVD QKLPAEEKAP VSYPNTLPES FTKFLQEQRM 430 440 450 460 470 480 ACEVGLYYVL HITKQRNKNA LLRLLPGLVE TFGDLAFGDI FLHLLTGNLA LLADEFALED 490 500 510 520 530 540 FCSSLFDGFF LTASPRKENV HRHALRLLIH LHPRVAPSKL EALQKALEPT GQSGEAVKEL 550 560 570 580 YSQLGEKLEQ LDHRKPSPAQ AAETPALELP LPSVPAPAPL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"BRCA1-induced large-scale chromatin unfolding and allele-specific effects of cancer-predisposing mutations." Ye Q., Hu Y.-F., Zhong H., Nye A.C., Belmont A.S., Li R. J. Cell Biol. 155:911-921(2001) [PubMed: 11739404] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], SUBCELLULAR LOCATION, INTERACTION WITH BRCA1. Tissue: Ovary.
[2]	"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: 14702039] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Brain.
[3]	"DNA sequence and analysis of human chromosome 9." Humphray S.J., Oliver K., Hunt A.R., Plumb R.W., Loveland J.E., Howe K.L., Andrews T.D., Searle S., Hunt S.E., Scott C.E., Jones M.C., Ainscough R., Almeida J.P., Ambrose K.D., Ashwell R.I.S., Babbage A.K., Babbage S., Bagguley C.L. , Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beasley H., Beasley O., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y., Burford D., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Chen Y., Clarke G., Clark S.Y., Clee C.M., Clegg S., Collier R.E., Corby N., Crosier M., Cummings A.T., Davies J., Dhami P., Dunn M., Dutta I., Dyer L.W., Earthrowl M.E., Faulkner L., Fleming C.J., Frankish A., Frankland J.A., French L., Fricker D.G., Garner P., Garnett J., Ghori J., Gilbert J.G.R., Glison C., Grafham D.V., Gribble S., Griffiths C., Griffiths-Jones S., Grocock R., Guy J., Hall R.E., Hammond S., Harley J.L., Harrison E.S.I., Hart E.A., Heath P.D., Henderson C.D., Hopkins B.L., Howard P.J., Howden P.J., Huckle E., Johnson C., Johnson D., Joy A.A., Kay M., Keenan S., Kershaw J.K., Kimberley A.M., King A., Knights A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C., Lloyd D.M., Lovell J., Martin S., Mashreghi-Mohammadi M., Matthews L., McLaren S., McLay K.E., McMurray A., Milne S., Nickerson T., Nisbett J., Nordsiek G., Pearce A.V., Peck A.I., Porter K.M., Pandian R., Pelan S., Phillimore B., Povey S., Ramsey Y., Rand V., Scharfe M., Sehra H.K., Shownkeen R., Sims S.K., Skuce C.D., Smith M., Steward C.A., Swarbreck D., Sycamore N., Tester J., Thorpe A., Tracey A., Tromans A., Thomas D.W., Wall M., Wallis J.M., West A.P., Whitehead S.L., Willey D.L., Williams S.A., Wilming L., Wray P.W., Young L., Ashurst J.L., Coulson A., Blocker H., Durbin R.M., Sulston J.E., Hubbard T., Jackson M.J., Bentley D.R., Beck S., Rogers J., Dunham I. Nature 429:369-374(2004) [PubMed: 15164053] [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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 31-580. Tissue: Lung.
[5]	"Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs." Wiemann S., Weil B., Wellenreuther R., Gassenhuber J., Glassl S., Ansorge W., Boecher M., Bloecker H., Bauersachs S., Blum H., Lauber J., Duesterhoeft A., Beyer A., Koehrer K., Strack N., Mewes H.-W., Ottenwaelder B., Obermaier B. , Tampe J., Heubner D., Wambutt R., Korn B., Klein M., Poustka A. Genome Res. 11:422-435(2001) [PubMed: 11230166] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 182-580. Tissue: Uterus.
[6]	"Characterization of cDNA clones selected by the GeneMark analysis from size-fractionated cDNA libraries from human brain." Hirosawa M., Nagase T., Ishikawa K., Kikuno R., Nomura N., Ohara O. DNA Res. 6:329-336(1999) [PubMed: 10574461] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 371-580. Tissue: Brain.
[7]	"Human transcription elongation factor NELF: identification of novel subunits and reconstitution of the functionally active complex." Narita T., Yamaguchi Y., Yano K., Sugimoto S., Chanarat S., Wada T., Kim D.-K., Hasegawa J., Omori M., Inukai N., Endoh M., Yamada T., Handa H. Mol. Cell. Biol. 23:1863-1873(2003) [PubMed: 12612062] [Abstract] Cited for: PROTEIN SEQUENCE OF 173-186; 399-412 AND 548-560, IDENTIFICATION IN A NELF COMPLEX, FUNCTION, TISSUE SPECIFICITY.
[8]	"NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation." Yamaguchi Y., Takagi T., Wada T., Yano K., Furuya A., Sugimoto S., Hasegawa J., Handa H. Cell 97:41-51(1999) [PubMed: 10199401] [Abstract] Cited for: FUNCTION OF THE NELF COMPLEX.
[9]	"Large-scale characterization of HeLa cell nuclear phosphoproteins." Beausoleil S.A., Jedrychowski M., Schwartz D., Elias J.E., Villen J., Li J., Cohn M.A., Cantley L.C., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 101:12130-12135(2004) [PubMed: 15302935] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-557, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[10]	"A probability-based approach for high-throughput protein phosphorylation analysis and site localization." Beausoleil S.A., Villen J., Gerber S.A., Rush J., Gygi S.P. Nat. Biotechnol. 24:1285-1292(2006) [PubMed: 16964243] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-557, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[11]	"A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed: 18669648] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-557, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[12]	"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach." Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S. Anal. Chem. 81:4493-4501(2009) [PubMed: 19413330] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-557, MASS SPECTROMETRY. Tissue: Embryonic kidney.
[13]	"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions." Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K. Sci. Signal. 2:RA46-RA46(2009) [PubMed: 19690332] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-557, MASS SPECTROMETRY. Tissue: Leukemic T-cell.
[14]	"Lysine acetylation targets protein complexes and co-regulates major cellular functions." Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T., Olsen J.V., Mann M. Science 325:834-840(2009) [PubMed: 19608861] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-519, MASS SPECTROMETRY.
[15]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed: 21269460] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF464935 mRNA. Translation: AAL69965.1. AK022651 mRNA. Translation: BAB14157.1. Different initiation. AK091056 mRNA. Translation: BAG52272.1. BX255925 Genomic DNA. Translation: CAM24149.1. BC011892 mRNA. Translation: AAH11892.1. Different initiation. AL050280 mRNA. Translation: CAB43381.3. Different initiation. AB033008 mRNA. Translation: BAA86496.1.
IPI	IPI00103483.
PIR	T08747.
RefSeq	NP_056271.2. NM_015456.3.
UniGene	Hs.655043.
3D structure databases
ProteinModelPortal	Q8WX92.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-32670N.
IntAct	Q8WX92. 15 interactions.
MINT	MINT-1033357.
STRING	Q8WX92.
PTM databases
PhosphoSite	Q8WX92.
Polymorphism databases
DMDM	38372378.
Proteomic databases
PeptideAtlas	Q8WX92.
PRIDE	Q8WX92.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000343053; ENSP00000339495; ENSG00000188986.
GeneID	25920.
KEGG	hsa:25920.
UCSC	uc004cmm.2. human.
Organism-specific databases
CTD	25920.
GeneCards	GC09P140149.
H-InvDB	HIX0021915.
HGNC	HGNC:24324. COBRA1.
HPA	HPA020259.
MIM	611180. gene.
neXtProt	NX_Q8WX92.
PharmGKB	PA162382703.
HUGE	Search...
GenAtlas	Search...
Phylogenomic databases
GeneTree	ENSGT00390000012665.
HOGENOM	HBG716510.
HOVERGEN	HBG052596.
InParanoid	Q8WX92.
OMA	EFALEDF.
OrthoDB	EOG4MGS77.
PhylomeDB	Q8WX92.
Enzyme and pathway databases
Reactome	REACT_1788. Transcription. REACT_1892. Elongation arrest and recovery. REACT_6185. HIV Infection. REACT_71. Gene Expression. REACT_769. Pausing and recovery of elongation.
Gene expression databases
ArrayExpress	Q8WX92.
Bgee	Q8WX92.
CleanEx	HS_COBRA1.
Genevestigator	Q8WX92.
GermOnline	ENSG00000188986. Homo sapiens.
Family and domain databases
InterPro	IPR010405. COBRA1. [Graphical view]
KO	K15180.
PANTHER	PTHR13503. COBRA1. 1 hit.
Pfam	PF06209. COBRA1. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	47437.
SOURCE	Search...

Entry information

Entry name

NELFB_HUMAN

Accession

Primary (citable) accession number: Q8WX92
Secondary accession number(s): A2BFA3 , Q96EW5, Q9H9R4, Q9ULN8, Q9Y3W0

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 14, 2003
Last sequence update:	March 1, 2002
Last modified:	January 25, 2012
This is version 97 of the entry and version 1 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.