Q8IXH7 (NELFD_HUMAN) Reviewed, UniProtKB/Swiss-Prot
Last modified
January 25, 2012.
Version 93.
History...
Names·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
Names·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize orderNames and origin
| Protein names | Recommended name: Negative elongation factor C/D Short name=NELF-C/D Alternative name(s): TH1-like protein | ||||||
| Gene names |
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| 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 | 590 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. 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.1 Ref.6 |
| 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. The sequence BAA91618.1 differs from that shown. Reason: Erroneous initiation. The sequence BAB14519.1 differs from that shown. Reason: Erroneous initiation. The sequence CAB64339.1 differs from that shown. Reason: Erroneous initiation. |
Ontologies
| Keywords | |
|---|---|
| Biological process | Transcription Transcription regulation |
| Cellular component | Nucleus |
| Coding sequence diversity | Alternative initiation Alternative splicing |
| Molecular function | Repressor |
| PTM | 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 transcriptionTraceable author statement. Source: Reactome transcription elongation from RNA polymerase II promoterTraceable author statement. Source: Reactome viral reproductionTraceable author statement. Source: Reactome |
| Cellular component | nucleoplasm Traceable author statement. Source: Reactome |
| Molecular function | protein binding Inferred from physical interaction. Source: IntAct |
| Complete GO annotation... | |
Binary interactions
With | Entry | #Exp. | IntAct | Notes |
|---|---|---|---|---|
| ARAF | P10398 | 5 | EBI-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 key | Position(s) | Length | Description | Graphical view | Feature identifier | ||||
Molecule processing | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Chain | 1 – 590 | 590 | Negative elongation factor C/D | PRO_0000019456 | |||||
Amino acid modifications | |||||||||
| Modified residue | 280 | 1 | Phosphothreonine Ref.9 | ||||||
| Modified residue | 285 | 1 | Phosphothreonine Ref.9 | ||||||
| Modified residue | 289 | 1 | Phosphotyrosine Ref.9 | ||||||
| Modified residue | 301 | 1 | Phosphoserine Ref.9 | ||||||
Natural variations | |||||||||
| Alternative sequence | 1 – 9 | 9 | Missing in isoform NELF-D. | VSP_018769 | |||||
| Alternative sequence | 178 – 201 | 24 | LISDA…QLEVF → VGRVLELRRKVFMNVYFWLL VCFL in isoform 3. | VSP_008950 | |||||
| Alternative sequence | 202 – 590 | 389 | Missing in isoform 3. | VSP_008951 | |||||
Experimental info | |||||||||
| Sequence conflict | 117 | 1 | N → D in BAA91618. Ref.3 | ||||||
| Sequence conflict | 306 | 1 | N → S in BAB14729. Ref.3 | ||||||
| Sequence conflict | 430 | 1 | W → R in BAA91618. Ref.3 | ||||||
| Sequence conflict | 497 | 1 | L → P in BAA91618. Ref.3 | ||||||
| Sequence conflict | 573 | 1 | D → V in BAA91618. Ref.3 | ||||||
Sequences
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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. 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. 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. 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] | "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 THR-280; THR-285; TYR-289 AND SER-301, MASS SPECTROMETRY. Tissue: Embryonic kidney. |
| [10] | "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 | 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. |
| IPI | IPI00164949. IPI00387090. IPI00759539. |
| RefSeq | NP_945327.1. NM_198976.1. |
| UniGene | Hs.517148. |
3D structure databases | |
| ProteinModelPortal | Q8IXH7. |
| ModBase | Search... |
Protein-protein interaction databases | |
| DIP | DIP-34061N. |
| IntAct | Q8IXH7. 14 interactions. |
| MINT | MINT-260753. |
| STRING | Q8IXH7. |
Polymorphism databases | |
| DMDM | 38372376. |
Proteomic databases | |
| PRIDE | Q8IXH7. |
Protocols and materials databases | |
| StructuralBiologyKnowledgebase | Search... |
Genome annotation databases | |
| Ensembl | ENST00000344018; ENSP00000342300; ENSG00000101158. |
| GeneID | 51497. |
| KEGG | hsa:51497. |
| UCSC | uc002yag.1. human. |
Organism-specific databases | |
| CTD | 51497. |
| GeneCards | GC20P057556. |
| H-InvDB | HIX0015956. HIX0138057. |
| HGNC | HGNC:15934. TH1L. |
| MIM | 605297. gene. |
| neXtProt | NX_Q8IXH7. |
| PharmGKB | PA38055. |
| GenAtlas | Search... |
Phylogenomic databases | |
| eggNOG | prNOG13799. |
| GeneTree | ENSGT00390000001799. |
| HOVERGEN | HBG052597. |
| InParanoid | Q8IXH7. |
| OMA | PDYIMEP. |
| OrthoDB | EOG4V170G. |
| PhylomeDB | Q8IXH7. |
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 | Q8IXH7. |
| Bgee | Q8IXH7. |
| Genevestigator | Q8IXH7. |
| GermOnline | ENSG00000101158. Homo sapiens. |
Family and domain databases | |
| InterPro | IPR006942. TH1. [Graphical view] |
| KO | K15181. |
| PANTHER | PTHR12144. TH1. 1 hit. |
| Pfam | PF04858. TH1. 1 hit. [Graphical view] |
| ProtoNet | Search... |
Other | |
| NextBio | 55171. |
| SOURCE | Search... |
Entry information
| Entry name | NELFD_HUMAN | ||||||||
| Accession | Primary (citable) accession number: Q8IXH7 Secondary accession number(s): B4DE06 Q9UGN3 | ||||||||
| Entry history |
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| 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. | ||||||||
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 |

Clusters with