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Reviewed, UniProtKB/Swiss-Prot Q8IXH7 (NELFD_HUMAN)

Last modified July 7, 2009. Version 64. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data | Customize display text xml rdf/xml gff fasta
Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Alternative products · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

Names and origin

Protein namesRecommended name:
    Negative elongation factor C/D
      Short name=NELF-C/D
Alternative name(s):
    TH1-like protein
Gene names
Name: TH1L
Synonyms: NELFD, TH1
ORF Names: HSPC130
OrganismHomo sapiens (Human) [Complete proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length590 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is not processed.
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. Ref.6 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 ARAF1. Ref.7

Subcellular location

Nucleus Probable.

Tissue specificity

Widely expressed. Expressed in heart, brain, lung, placenta, liver, skeletal and cardiac muscle, adrenal, thyroid, kidney and pancreas. Ref.6 Ref.1

Sequence similarities

Belongs to the NELF-D family.

Sequence caution

The sequence AAF29094.1 differs from that shown. Reason: Frameshift at positions 462 and 464.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentNucleus
   Coding sequence diversityAlternative initiation
Alternative splicing
   Molecular functionRepressor
   Technical termComplete proteome
Direct protein sequencing
Gene Ontology (GO)
   Biological processnegative regulation of transcription

Inferred from electronic annotation. Source: InterPro

regulation of transcription, DNA-dependent

Inferred from electronic annotation. Source: UniProtKB-KW

transcription

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular componentnucleoplasm

Inferred from Experiment. Source: Reactome

   Molecular functionprotein binding

Inferred from physical interaction. Source: IntAct

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

ARAFP103984EBI-536725,EBI-365961

Alternative products

This entry describes 3 isoforms produced by alternative splicing and alternative initiation. [Align] [Select]
Isoform NELF-C (identifier: Q8IXH7-1)

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 3 (identifier: Q8IXH7-3)

The sequence of this isoform differs from the canonical sequence as follows:
     178-201: LISDAGYQGEITSVSTACQQLEVF → VGRVLELRRKVFMNVYFWLLVCFL
     202-590: Missing.
Note: No experimental confirmation available.
Isoform NELF-D (identifier: Q8IXH7-4)

The sequence of this isoform differs from the canonical sequence as follows:
     1-9: Missing.
Note: Produced by alternative initiation at Met-10 of isoform NELF-C.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 590590Negative elongation factor C/D
PRO_0000019456

Natural variations

Alternative sequence1 – 99Missing in isoform NELF-D.
VSP_018769
Alternative sequence178 – 20124LISDA…QLEVF → VGRVLELRRKVFMNVYFWLL VCFL in isoform 3.
VSP_008950
Alternative sequence202 – 590389Missing in isoform 3.
VSP_008951

Experimental info

Sequence conflict1171N → D in BAA91618. Ref.3
Sequence conflict3061N → S in BAB14729. Ref.3
Sequence conflict4301W → R in BAA91618. Ref.3
Sequence conflict4971L → P in BAA91618. Ref.3
Sequence conflict5731D → V in BAA91618. Ref.3

Sequences

Sequence LengthMass (Da)Tools
Isoform NELF-C [UniParc].

Last modified November 14, 2003. Version 2.
Checksum: 425437DC46DAF953

FASTA59066,247
        10         20         30         40         50         60 
MAGAVPGAIM DEDYYGSAAE WGDEADGGQQ EDDSGEGEDD AEVQQECLHK FSTRDYIMEP 

        70         80         90        100        110        120 
SIFNTLKRYF QAGGSPENVI QLLSENYTAV AQTVNLLAEW LIQTGVEPVQ VQETVENHLK 

       130        140        150        160        170        180 
SLLIKHFDPR KADSIFTEEG ETPAWLEQMI AHTTWRDLFY KLAEAHPDCL MLNFTVKLIS 

       190        200        210        220        230        240 
DAGYQGEITS VSTACQQLEV FSRVLRTSLA TILDGGEENL EKNLPEFAKM VCHGEHTYLF 

       250        260        270        280        290        300 
AQAMMSVLAQ EEQGGSAVRR IAQEVQRFAQ EKGHDASQIT LALGTAASYP RACQALGAML 

       310        320        330        340        350        360 
SKGALNPADI TVLFKMFTSM DPPPVELIRV PAFLDLFMQS LFKPGARINQ DHKHKYIHIL 

       370        380        390        400        410        420 
AYAASVVETW KKNKRVSINK DELKSTSKAV ETVHNLCCNE NKGASELVAE LSTLYQCIRF 

       430        440        450        460        470        480 
PVVAMGVLKW VDWTVSEPRY FQLQTDHTPV HLALLDEIST CHQLLHPQVL QLLVKLFETE 

       490        500        510        520        530        540 
HSQLDVMEQL ELKKTLLDRM VHLLSRGYVL PVVSYIRKCL EKLDTDISLI RYFVTEVLDV 

       550        560        570        580        590 
IAPPYTSDFV QLFLPILEND SIAGTIKTEG EHDPVTEFIA HCKSNFIMVN 

« Hide

Isoform 3.

Checksum: 28EA9E5A52CD68FF
Show »

FASTA20122,903
Isoform NELF-D.

Checksum: DD20EFAF08DE67E8
Show »

FASTA58165,479

References

« Hide 'large scale' references
[1]"Characterization of TH1 and CTSZ, two non-imprinted genes downstream of GNAS1 in chromosome 20q13."
Bonthron D.T., Hayward B.E., Moran V., Strain L.
Hum. Genet. 107:165-175(2000) [PubMed: 11030415] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE (ISOFORM NELF-C), TISSUE SPECIFICITY.
[2]"Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells."
Zhang Q.-H., Ye M., Wu X.-Y., Ren S.-X., Zhao M., Zhao C.-J., Fu G., Shen Y., Fan H.-Y., Lu G., Zhong M., Xu X.-R., Han Z.-G., Zhang J.-W., Tao J., Huang Q.-H., Zhou J., Hu G.-X. expand/collapse author list , Gu J., Chen S.-J., Chen Z.
Genome Res. 10:1546-1560(2000) [PubMed: 11042152] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM NELF-C).
Tissue: Umbilical cord blood.
[3]"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: 14702039] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS NELF-C AND 3).
Tissue: Ovarian carcinoma, Teratocarcinoma and Thyroid.
[4]"The DNA sequence and comparative analysis of human chromosome 20."
Deloukas P., Matthews L.H., Ashurst J.L., Burton J., Gilbert J.G.R., Jones M., Stavrides G., Almeida J.P., Babbage A.K., Bagguley C.L., Bailey J., Barlow K.F., Bates K.N., Beard L.M., Beare D.M., Beasley O.P., Bird C.P., Blakey S.E. expand/collapse author list , Bridgeman A.M., Brown A.J., Buck D., Burrill W.D., Butler A.P., Carder C., Carter N.P., Chapman J.C., Clamp M., Clark G., Clark L.N., Clark S.Y., Clee C.M., Clegg S., Cobley V.E., Collier R.E., Connor R.E., Corby N.R., Coulson A., Coville G.J., Deadman R., Dhami P.D., Dunn M., Ellington A.G., Frankland J.A., Fraser A., French L., Garner P., Grafham D.V., Griffiths C., Griffiths M.N.D., Gwilliam R., Hall R.E., Hammond S., Harley J.L., Heath P.D., Ho S., Holden J.L., Howden P.J., Huckle E., Hunt A.R., Hunt S.E., Jekosch K., Johnson C.M., Johnson D., Kay M.P., Kimberley A.M., King A., Knights A., Laird G.K., Lawlor S., Lehvaeslaiho M.H., Leversha M.A., Lloyd C., Lloyd D.M., Lovell J.D., Marsh V.L., Martin S.L., McConnachie L.J., McLay K., McMurray A.A., Milne S.A., Mistry D., Moore M.J.F., Mullikin J.C., Nickerson T., Oliver K., Parker A., Patel R., Pearce T.A.V., Peck A.I., Phillimore B.J.C.T., Prathalingam S.R., Plumb R.W., Ramsay H., Rice C.M., Ross M.T., Scott C.E., Sehra H.K., Shownkeen R., Sims S., Skuce C.D., Smith M.L., Soderlund C., Steward C.A., Sulston J.E., Swann R.M., Sycamore N., Taylor R., Tee L., Thomas D.W., Thorpe A., Tracey A., Tromans A.C., Vaudin M., Wall M., Wallis J.M., Whitehead S.L., Whittaker P., Willey D.L., Williams L., Williams S.A., Wilming L., Wray P.W., Hubbard T., Durbin R.M., Bentley D.R., Beck S., Rogers J.
Nature 414:865-871(2001) [PubMed: 11780052] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"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] (ISOFORM NELF-C).
Tissue: Skin.
[6]"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 126-139; 223-230; 303-315 AND 476-491, IDENTIFICATION IN A NELF COMPLEX, ALTERNATIVE INITIATION, FUNCTION, TISSUE SPECIFICITY.
[7]"Identification of TH1 as an interaction partner of A-Raf kinase."
Yin X.L., Chen S., Gu J.X.
Mol. Cell. Biochem. 231:69-74(2002) [PubMed: 11952167] [Abstract]
Cited for: INTERACTION WITH ARAF1.
[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]Colinge J., Superti-Furga G., Bennett K.L.
Submitted (OCT-2008) to UniProtKB
Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
+Additional computationally mapped references.

Cross-references

Sequence databases

AJ238374 mRNA. Translation: CAB64337.1.
AJ238375 mRNA. Translation: CAB64373.1.
AJ238379 mRNA. Translation: CAB64339.1. Different initiation.
AF161479 mRNA. Translation: AAF29094.1. Frameshift.
AK001316 mRNA. Translation: BAA91618.1. Different initiation.
AK023310 mRNA. Translation: BAB14519.1. Different initiation.
AK023927 mRNA. Translation: BAB14729.1.
AK293410 mRNA. Translation: BAG56917.1.
AL109840 Genomic DNA. Translation: CAC09368.1.
BC014952 mRNA. Translation: AAH14952.1.
IPIIPI00164949.
IPI00387090.
IPI00759539.
RefSeqNP_945327.1.
UniGeneHs.517148

3D structure databases

ModBaseSearch...

Protein-protein interaction databases

IntActQ8IXH7. 11 interactions.

Proteomic databases

PRIDEQ8IXH7.

Genome annotation databases

EnsemblENSG00000101158. Homo sapiens. [Contig view]
GeneID51497.
KEGGhsa:51497.
UCSCuc002yag.1. human.

Organism-specific databases

GeneCardsGC20P056989.
H-InvDBHIX0015956.
HGNCHGNC:15934. TH1L.
MIM605297. gene.
PharmGKBPA38055.
GenAtlasSearch...

Phylogenomic databases

HOVERGENQ8IXH7.
OMAQ8IXH7. CKSNFIM.

Enzyme and pathway databases

ReactomeREACT_1788. Transcription.
REACT_1892. Elongation arrest and recovery.
REACT_6143. Pausing and recovery of Tat-mediated HIV-1 elongation.
REACT_6185. HIV Infection.
REACT_6244. Pausing and recovery of HIV-1 elongation.
REACT_6259. HIV-1 elongation arrest and recovery.
REACT_6344. Tat-mediated HIV-1 elongation arrest and recovery.
REACT_71. Gene Expression.
REACT_769. Pausing and recovery of elongation.

Gene expression databases

BgeeQ8IXH7.
GermOnlineENSG00000101158. Homo sapiens.

Family and domain databases

InterProIPR006942. TH1.
[Graphical view]
PANTHERPTHR12144. TH1. 1 hit.
PfamPF04858. TH1. 1 hit.
[Graphical view]
ProtoNetSearch...

Other Resources

NextBio55171.
SOURCESearch...

Entry information

Entry nameNELFD_HUMAN
AccessionPrimary (citable) accession number: Q8IXH7
Secondary accession number(s): B4DE06 expand/collapse secondary AC list , Q9BYL2, Q9H405, Q9H888, Q9H8T3, Q9NVX5, Q9P029, Q9UGN1, Q9UGN2, Q9UGN3
Entry history
Integrated into UniProtKB/Swiss-Prot: November 14, 2003
Last sequence update: November 14, 2003
Last modified: July 7, 2009
This is version 64 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectHPI (Human Proteome Initiative)

Relevant documents

Human chromosome 20

Human chromosome 20: entries, gene names and cross-references to MIM

MIM cross-references

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

SIMILARITY comments

Index of protein domains and families

Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Alternative products · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents