Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Negative elongation factor A

Gene

NELFA

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.3 Publications

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Enzyme and pathway databases

BioCyciZFISH:G66-30814-MONOMER.
ReactomeiR-HSA-112382. Formation of RNA Pol II elongation complex.
R-HSA-112387. Elongation arrest and recovery.
R-HSA-113418. Formation of the Early Elongation Complex.
R-HSA-167152. Formation of HIV elongation complex in the absence of HIV Tat.
R-HSA-167158. Formation of the HIV-1 Early Elongation Complex.
R-HSA-167200. Formation of HIV-1 elongation complex containing HIV-1 Tat.
R-HSA-167238. Pausing and recovery of Tat-mediated HIV elongation.
R-HSA-167242. Abortive elongation of HIV-1 transcript in the absence of Tat.
R-HSA-167243. Tat-mediated HIV elongation arrest and recovery.
R-HSA-167246. Tat-mediated elongation of the HIV-1 transcript.
R-HSA-167287. HIV elongation arrest and recovery.
R-HSA-167290. Pausing and recovery of HIV elongation.
R-HSA-674695. RNA Polymerase II Pre-transcription Events.
R-HSA-6796648. TP53 Regulates Transcription of DNA Repair Genes.
R-HSA-75955. RNA Polymerase II Transcription Elongation.

Names & Taxonomyi

Protein namesi
Recommended name:
Negative elongation factor A
Short name:
NELF-A
Alternative name(s):
Wolf-Hirschhorn syndrome candidate 2 protein
Gene namesi
Name:NELFA
Synonyms:WHSC2
ORF Names:P/OKcl.15
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 4

Organism-specific databases

HGNCiHGNC:12768. NELFA.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: HPA
  • NELF complex Source: UniProtKB
  • nucleoplasm Source: HPA
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi7469.
OpenTargetsiENSG00000185049.
Orphaneti280. Wolf-Hirschhorn syndrome.
PharmGKBiPA37371.

Polymorphism and mutation databases

BioMutaiNELFA.
DMDMi212276499.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002191261 – 528Negative elongation factor AAdd BLAST528

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei157PhosphothreonineCombined sources1
Modified residuei225PhosphoserineCombined sources1
Modified residuei233PhosphoserineCombined sources1
Modified residuei277PhosphothreonineCombined sources1
Modified residuei363PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ9H3P2.
MaxQBiQ9H3P2.
PaxDbiQ9H3P2.
PeptideAtlasiQ9H3P2.
PRIDEiQ9H3P2.

PTM databases

iPTMnetiQ9H3P2.
PhosphoSitePlusiQ9H3P2.

Expressioni

Tissue specificityi

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.3 Publications

Gene expression databases

BgeeiENSG00000185049.
CleanExiHS_WHSC2.
ExpressionAtlasiQ9H3P2. baseline and differential.
GenevisibleiQ9H3P2. HS.

Organism-specific databases

HPAiCAB009960.
HPA039858.
HPA043931.

Interactioni

Subunit structurei

The NELF complex is composed of NELFA, NELFB, NELFCD (isoform NELF-C or isoform NELF-D) and NELFE. Interacts with the RNA polymerase II complex when it is not phosphorylated by P-TEFb.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
NELFCDQ8IXH73EBI-5461341,EBI-536725
NELFCDQ8IXH7-44EBI-5461341,EBI-6109710
SIAH1Q8IUQ43EBI-5461341,EBI-747107

Protein-protein interaction databases

BioGridi113307. 29 interactors.
DIPiDIP-48478N.
IntActiQ9H3P2. 17 interactors.
MINTiMINT-3067399.
STRINGi9606.ENSP00000372335.

Structurei

Secondary structure

1528
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi9 – 17Combined sources9
Helixi29 – 32Combined sources4
Helixi35 – 44Combined sources10
Helixi45 – 47Combined sources3
Helixi50 – 59Combined sources10
Helixi60 – 62Combined sources3
Helixi65 – 70Combined sources6
Helixi72 – 82Combined sources11
Helixi88 – 96Combined sources9
Helixi100 – 103Combined sources4
Helixi115 – 130Combined sources16
Helixi139 – 143Combined sources5
Helixi146 – 153Combined sources8
Beta strandi163 – 167Combined sources5
Helixi171 – 180Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5L3XX-ray2.75A6-182[»]
ProteinModelPortaliQ9H3P2.
SMRiQ9H3P2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini189 – 248HDAg-likeAdd BLAST60

Domaini

The HDAg-like domain is essential for transcriptional repression, and mediates the interaction with the RNA polymerase II complex.1 Publication

Sequence similaritiesi

Belongs to the NELF-A family.Curated
Contains 1 HDAg-like domain.Curated

Phylogenomic databases

eggNOGiENOG410IGI5. Eukaryota.
ENOG410XRP9. LUCA.
GeneTreeiENSGT00390000005342.
HOGENOMiHOG000113765.
HOVERGENiHBG052595.
InParanoidiQ9H3P2.
KOiK15179.
PhylomeDBiQ9H3P2.
TreeFamiTF324956.

Family and domain databases

InterProiIPR026305. NELF-A.
[Graphical view]
PANTHERiPTHR13328. PTHR13328. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9H3P2-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MASMRESDTG LWLHNKLGAT DELWAPPSIA SLLTAAVIDN IRLCFHGLSS
60 70 80 90 100
AVKLKLLLGT LHLPRRTVDE MKGALMEIIQ LASLDSDPWV LMVADILKSF
110 120 130 140 150
PDTGSLNLEL EEQNPNVQDI LGELREKVGE CEASAMLPLE CQYLNKNALT
160 170 180 190 200
TLAGPLTPPV KHFQLKRKPK SATLRAELLQ KSTETAQQLK RSAGVPFHAK
210 220 230 240 250
GRGLLRKMDT TTPLKGIPKQ APFRSPTAPS VFSPTGNRTP IPPSRTLLRK
260 270 280 290 300
ERGVKLLDIS ELDMVGAGRE AKRRRKTLDA EVVEKPAKEE TVVENATPDY
310 320 330 340 350
AAGLVSTQKL GSLNNEPALP STSYLPSTPS VVPASSYIPS SETPPAPSSR
360 370 380 390 400
EASRPPEEPS APSPTLPAQF KQRAPMYNSG LSPATPTPAA PTSPLTPTTP
410 420 430 440 450
PAVAPTTQTP PVAMVAPQTQ APAQQQPKKN LSLTREQMFA AQEMFKTANK
460 470 480 490 500
VTRPEKALIL GFMAGSRENP CQEQGDVIQI KLSEHTEDLP KADGQGSTTM
510 520
LVDTVFEMNY ATGQWTRFKK YKPMTNVS
Length:528
Mass (Da):57,277
Last modified:November 4, 2008 - v3
Checksum:i4F33C3BC68BDC798
GO
Isoform 2 (identifier: Q9H3P2-7) [UniParc]FASTAAdd to basket

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

Show »
Length:265
Mass (Da):28,416
Checksum:i66F97A90BF7F1C62
GO

Sequence cautioni

The sequence AAC72982 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BAG54283 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
The sequence CAM15219 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
The sequence EAW82546 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti37V → I in BAB18651 (PubMed:11280764).Curated1
Sequence conflicti40N → NIRLCFHGLSSASLLTAAVI DN in BAB18651 (PubMed:11280764).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_059459335S → A.Corresponds to variant rs2234569dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0355891 – 263Missing in isoform 2. 1 PublicationAdd BLAST263

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
RefSeqiNP_005654.3. NM_005663.4.
UniGeneiHs.21771.

Genome annotation databases

EnsembliENST00000411638; ENSP00000399165; ENSG00000185049. [Q9H3P2-1]
GeneIDi7469.
KEGGihsa:7469.
UCSCiuc003gem.4. human. [Q9H3P2-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
RefSeqiNP_005654.3. NM_005663.4.
UniGeneiHs.21771.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5L3XX-ray2.75A6-182[»]
ProteinModelPortaliQ9H3P2.
SMRiQ9H3P2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi113307. 29 interactors.
DIPiDIP-48478N.
IntActiQ9H3P2. 17 interactors.
MINTiMINT-3067399.
STRINGi9606.ENSP00000372335.

PTM databases

iPTMnetiQ9H3P2.
PhosphoSitePlusiQ9H3P2.

Polymorphism and mutation databases

BioMutaiNELFA.
DMDMi212276499.

Proteomic databases

EPDiQ9H3P2.
MaxQBiQ9H3P2.
PaxDbiQ9H3P2.
PeptideAtlasiQ9H3P2.
PRIDEiQ9H3P2.

Protocols and materials databases

DNASUi7469.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000411638; ENSP00000399165; ENSG00000185049. [Q9H3P2-1]
GeneIDi7469.
KEGGihsa:7469.
UCSCiuc003gem.4. human. [Q9H3P2-1]

Organism-specific databases

CTDi7469.
DisGeNETi7469.
GeneCardsiNELFA.
HGNCiHGNC:12768. NELFA.
HPAiCAB009960.
HPA039858.
HPA043931.
MIMi606026. gene.
neXtProtiNX_Q9H3P2.
OpenTargetsiENSG00000185049.
Orphaneti280. Wolf-Hirschhorn syndrome.
PharmGKBiPA37371.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IGI5. Eukaryota.
ENOG410XRP9. LUCA.
GeneTreeiENSGT00390000005342.
HOGENOMiHOG000113765.
HOVERGENiHBG052595.
InParanoidiQ9H3P2.
KOiK15179.
PhylomeDBiQ9H3P2.
TreeFamiTF324956.

Enzyme and pathway databases

BioCyciZFISH:G66-30814-MONOMER.
ReactomeiR-HSA-112382. Formation of RNA Pol II elongation complex.
R-HSA-112387. Elongation arrest and recovery.
R-HSA-113418. Formation of the Early Elongation Complex.
R-HSA-167152. Formation of HIV elongation complex in the absence of HIV Tat.
R-HSA-167158. Formation of the HIV-1 Early Elongation Complex.
R-HSA-167200. Formation of HIV-1 elongation complex containing HIV-1 Tat.
R-HSA-167238. Pausing and recovery of Tat-mediated HIV elongation.
R-HSA-167242. Abortive elongation of HIV-1 transcript in the absence of Tat.
R-HSA-167243. Tat-mediated HIV elongation arrest and recovery.
R-HSA-167246. Tat-mediated elongation of the HIV-1 transcript.
R-HSA-167287. HIV elongation arrest and recovery.
R-HSA-167290. Pausing and recovery of HIV elongation.
R-HSA-674695. RNA Polymerase II Pre-transcription Events.
R-HSA-6796648. TP53 Regulates Transcription of DNA Repair Genes.
R-HSA-75955. RNA Polymerase II Transcription Elongation.

Miscellaneous databases

GeneWikiiWHSC2.
GenomeRNAii7469.
PROiQ9H3P2.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000185049.
CleanExiHS_WHSC2.
ExpressionAtlasiQ9H3P2. baseline and differential.
GenevisibleiQ9H3P2. HS.

Family and domain databases

InterProiIPR026305. NELF-A.
[Graphical view]
PANTHERiPTHR13328. PTHR13328. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiNELFA_HUMAN
AccessioniPrimary (citable) accession number: Q9H3P2
Secondary accession number(s): A2A2T1, O95392
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 14, 2003
Last sequence update: November 4, 2008
Last modified: November 30, 2016
This is version 143 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (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.

Miscellaneousi

Caution

PubMed:12612062 has shown that it is not involved in Wolf-Hirschhorn syndrome.Curated

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 4
    Human chromosome 4: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.