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Q9H3P2 (NELFA_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 119. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | 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:
Negative elongation factor A

Short name=NELF-A
Alternative name(s):
Wolf-Hirschhorn syndrome candidate 2 protein
Gene names
Name:NELFA
Synonyms:WHSC2
ORF Names:P/OKcl.15
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length528 AA.
Sequence statusComplete.
Protein existenceEvidence 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. Probably required to interact with the RNA polymerase II complex. Ref.9 Ref.11 Ref.12

Subunit structure

The NELF complex is composed of NELFA, NELFB, NELFCD (isoform NELF-Cor isoform NELF-D)and NELFE. Interacts with the RNA polymerase II complex when it is not phosphorylated by P-TEFb. Ref.8

Subcellular location

Nucleus Ref.10.

Tissue specificity

Ubiquitous. Expressed in heart, brain, placenta, liver, skeletal muscle, kidney and pancreas. Expressed at lower level in adult lung. Expressed in fetal brain, lung, liver and kidney. Ref.1 Ref.10 Ref.12

Domain

The HDAg-like domain is essential for transcriptional repression, and mediates the interaction with the RNA polymerase II complex. Ref.12

Sequence similarities

Belongs to the NELF-A family.

Contains 1 HDAg-like domain.

Caution

Ref.12 has shown that it is not involved in Wolf-Hirschhorn syndrome.

Sequence caution

The sequence AAC72982.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence BAG54283.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

The sequence CAM15219.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

The sequence EAW82546.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

NELFCDQ8IXH7-43EBI-5461341,EBI-6109710

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9H3P2-1)

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 2 (identifier: Q9H3P2-7)

The sequence of this isoform differs from the canonical sequence as follows:
     1-263: Missing.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 528528Negative elongation factor A
PRO_0000219126

Regions

Domain189 – 24860HDAg-like

Amino acid modifications

Modified residue1571Phosphothreonine Ref.13 Ref.16 Ref.17
Modified residue2771Phosphothreonine Ref.17
Modified residue3631Phosphoserine Ref.14 Ref.17

Natural variations

Alternative sequence1 – 263263Missing in isoform 2.
VSP_035589
Natural variant3351S → A.
Corresponds to variant rs2234569 [ dbSNP | Ensembl ].
VAR_059459

Experimental info

Sequence conflict371V → I in BAB18651. Ref.2
Sequence conflict401N → NIRLCFHGLSSASLLTAAVI DN in BAB18651. Ref.2

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified November 4, 2008. Version 3.
Checksum: 4F33C3BC68BDC798

FASTA52857,277
        10         20         30         40         50         60 
MASMRESDTG LWLHNKLGAT DELWAPPSIA SLLTAAVIDN IRLCFHGLSS AVKLKLLLGT 

        70         80         90        100        110        120 
LHLPRRTVDE MKGALMEIIQ LASLDSDPWV LMVADILKSF PDTGSLNLEL EEQNPNVQDI 

       130        140        150        160        170        180 
LGELREKVGE CEASAMLPLE CQYLNKNALT TLAGPLTPPV KHFQLKRKPK SATLRAELLQ 

       190        200        210        220        230        240 
KSTETAQQLK RSAGVPFHAK GRGLLRKMDT TTPLKGIPKQ APFRSPTAPS VFSPTGNRTP 

       250        260        270        280        290        300 
IPPSRTLLRK ERGVKLLDIS ELDMVGAGRE AKRRRKTLDA EVVEKPAKEE TVVENATPDY 

       310        320        330        340        350        360 
AAGLVSTQKL GSLNNEPALP STSYLPSTPS VVPASSYIPS SETPPAPSSR EASRPPEEPS 

       370        380        390        400        410        420 
APSPTLPAQF KQRAPMYNSG LSPATPTPAA PTSPLTPTTP PAVAPTTQTP PVAMVAPQTQ 

       430        440        450        460        470        480 
APAQQQPKKN LSLTREQMFA AQEMFKTANK VTRPEKALIL GFMAGSRENP CQEQGDVIQI 

       490        500        510        520 
KLSEHTEDLP KADGQGSTTM LVDTVFEMNY ATGQWTRFKK YKPMTNVS 

« Hide

Isoform 2 [UniParc].

Checksum: 66F97A90BF7F1C62
Show »

FASTA26528,416

References

« Hide 'large scale' references
[1]"Comparative analysis of a novel gene from the Wolf-Hirschhorn/Pitt-Rogers-Danks syndrome critical region."
Wright T.J., Costa J.L., Naranjo C., Francis-West P., Altherr M.R.
Genomics 59:203-212(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY.
Tissue: Brain.
[2]"Molecular basis of T cell-mediated recognition of pancreatic cancer cells."
Ito M., Shichijo S., Tsuda N., Ochi M., Harashima N., Saito N., Itoh K.
Cancer Res. 61:2038-2046(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
Tissue: Pancreatic cancer.
[3]Mei G., Yu W., Gibbs R.A.
Submitted (FEB-1999) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
Tissue: Brain.
[4]"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. expand/collapse author list , 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] (ISOFORM 1).
Tissue: Testis.
[5]"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].
[6]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[7]"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 1).
Tissue: Placenta.
[8]"Stimulation of RNA polymerase II elongation by hepatitis delta antigen."
Yamaguchi Y., Filipovska J., Yano K., Furuya A., Inukai N., Narita T., Wada T., Sugimoto S., Konarska M.M., Handa H.
Science 293:124-127(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 212-221; 309-321 AND 503-513, IDENTIFICATION IN THE NELF COMPLEX.
[9]"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] [Europe PMC] [Abstract]
Cited for: FUNCTION OF THE NELF COMPLEX.
[10]"Modulation of WHSC2 expression in human endothelial cells."
Mariotti M., Manganini M., Maier J.A.M.
FEBS Lett. 487:166-170(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
[11]"Mapping the Wolf-Hirschhorn syndrome phenotype outside the currently accepted WHS critical region and defining a new critical region, WHSCR-2."
Zollino M., Lecce R., Fischetto R., Murdolo M., Faravelli F., Selicorni A., Butte C., Memo L., Capovilla G., Neri G.
Am. J. Hum. Genet. 72:590-597(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[12]"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] [Europe PMC] [Abstract]
Cited for: FUNCTION, TISSUE SPECIFICITY, DOMAIN.
[13]"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] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-157, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[14]"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] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-363, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[15]"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] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[16]"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] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-157, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Leukemic T-cell.
[17]"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-157; THR-277 AND SER-363, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[18]"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] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF101434 mRNA. Translation: AAC72982.1. Different initiation.
AB044549 mRNA. Translation: BAB18651.1.
AF131751 mRNA. Translation: AAD20034.1.
AK126056 mRNA. Translation: BAG54283.1. Different initiation.
AL132868 Genomic DNA. Translation: CAM15219.1. Different initiation.
CH471131 Genomic DNA. Translation: EAW82546.1. Different initiation.
BC002764 mRNA. Translation: AAH02764.2.
RefSeqNP_005654.3. NM_005663.4.
UniGeneHs.21771.

3D structure databases

ProteinModelPortalQ9H3P2.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid113307. 12 interactions.
DIPDIP-48478N.
IntActQ9H3P2. 6 interactions.
MINTMINT-3067399.
STRING9606.ENSP00000372335.

PTM databases

PhosphoSiteQ9H3P2.

Polymorphism databases

DMDM212276499.

Proteomic databases

MaxQBQ9H3P2.
PaxDbQ9H3P2.
PRIDEQ9H3P2.

Protocols and materials databases

DNASU7469.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000382882; ENSP00000372335; ENSG00000185049.
ENST00000411638; ENSP00000399165; ENSG00000185049. [Q9H3P2-1]
GeneID7469.
KEGGhsa:7469.
UCSCuc003gek.3. human. [Q9H3P2-1]

Organism-specific databases

CTD7469.
GeneCardsGC04M001985.
HGNCHGNC:12768. NELFA.
HPACAB009960.
HPA039858.
HPA043931.
MIM606026. gene.
neXtProtNX_Q9H3P2.
Orphanet280. Wolf-Hirschhorn syndrome.
PharmGKBPA37371.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG10551.
HOGENOMHOG000113765.
HOVERGENHBG052595.
InParanoidQ9H3P2.
KOK15179.
OrthoDBEOG708VZQ.
PhylomeDBQ9H3P2.
TreeFamTF324956.

Enzyme and pathway databases

ReactomeREACT_116125. Disease.
REACT_1788. Transcription.
REACT_1892. Elongation arrest and recovery.
REACT_71. Gene Expression.

Gene expression databases

ArrayExpressQ9H3P2.
BgeeQ9H3P2.
CleanExHS_WHSC2.
GenevestigatorQ9H3P2.

Family and domain databases

InterProIPR026305. NELF-A.
[Graphical view]
PANTHERPTHR13328. PTHR13328. 1 hit.
ProtoNetSearch...

Other

GeneWikiWHSC2.
GenomeRNAi7469.
NextBio29260.
PROQ9H3P2.
SOURCESearch...

Entry information

Entry nameNELFA_HUMAN
AccessionPrimary (citable) accession number: Q9H3P2
Secondary accession number(s): A2A2T1, O95392
Entry history
Integrated into UniProtKB/Swiss-Prot: November 14, 2003
Last sequence update: November 4, 2008
Last modified: July 9, 2014
This is version 119 of the entry and version 3 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

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 4

Human chromosome 4: entries, gene names and cross-references to MIM