Human Gene NELFCD (uc002yag.4) Description and Page Index
  Description: Homo sapiens negative elongation factor complex member C/D (NELFCD), mRNA.
RefSeq Summary (NM_198976): The NELF complex of proteins interacts with the DSIF protein complex to repress transcriptional elongation by RNA polymerase II. The protein encoded by this gene is an essential part of the NELF complex. Alternative translation initiation site usage results in the formation of two isoforms with different N-termini. [provided by RefSeq, Jul 2008]. CCDS Note: The coding region has been updated to shorten the N-terminus to one that is more supported by conservation. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR3476690.1126501.1, BC014952.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## CDS uses downstream in-frame AUG :: upstream AUG and CDS extension is not conserved RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr20:57,556,263-57,570,188 Size: 13,926 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr20:57,556,311-57,569,731 Size: 13,421 Coding Exon Count: 15 

Page IndexSequence and LinksMalaCardsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:57,556,263-57,570,188)mRNA (may differ from genome)Protein (599 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsGeneNetworkH-INV
HGNCHPRDLynxMGIOMIMPubMed
Stanford SOURCEUniProtKBWikipedia

-  MalaCards Disease Associations
  MalaCards Gene Search: NELFCD
Diseases sorted by gene-association score: hiv-1 (3), hyperlucent lung (2), ascaridiasis (2), buruli ulcer (2), pancoast tumor (2), pericardial tuberculosis (1), eumycotic mycetoma (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 59.07 RPKM in Pituitary
Total median expression: 1391.07 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -24.2048-0.504 Picture PostScript Text
3' UTR -132.70457-0.290 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR006942 - TH1

Pfam Domains:
PF04858 - TH1 protein

ModBase Predicted Comparative 3D Structure on H0UI80
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserNo orthologNo ortholog
Gene Details  Gene Details  
Gene Sorter  Gene Sorter  
  EnsemblFlyBase  
  Protein SequenceProtein Sequence  
  AlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0045892 negative regulation of transcription, DNA-templated

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AK304310 - Homo sapiens cDNA FLJ59161 complete cds, highly similar to Negative elongation factor C/D.
AK293410 - Homo sapiens cDNA FLJ56424 complete cds, highly similar to Negative elongation factor C/D.
BC014952 - Homo sapiens TH1-like (Drosophila), mRNA (cDNA clone MGC:22971 IMAGE:4860894), complete cds.
BX647417 - Homo sapiens mRNA; cDNA DKFZp686F23158 (from clone DKFZp686F23158).
AJ238379 - Homo sapiens mRNA for putative TH1 protein.
AF161479 - Homo sapiens HSPC130 mRNA, complete cds.
KJ898905 - Synthetic construct Homo sapiens clone ccsbBroadEn_08299 TH1L gene, encodes complete protein.
JF432711 - Synthetic construct Homo sapiens clone IMAGE:100073951 TH1-like (Drosophila) (TH1L) gene, encodes complete protein.
AB528731 - Synthetic construct DNA, clone: pF1KB9910, Homo sapiens TH1L gene for TH1-like protein, without stop codon, in Flexi system.
AK023927 - Homo sapiens cDNA FLJ13865 fis, clone THYRO1001204, weakly similar to Homo sapiens cathepsin Z precursor (CTSZ) gene.
AK023310 - Homo sapiens cDNA FLJ13248 fis, clone OVARC1000703.
AK001316 - Homo sapiens cDNA FLJ10454 fis, clone NT2RP1001011, weakly similar to Drosophila melanogaster putative 43 kDa protein mRNA.
JD027412 - Sequence 8436 from Patent EP1572962.
JD033526 - Sequence 14550 from Patent EP1572962.
JD022813 - Sequence 3837 from Patent EP1572962.
JD032195 - Sequence 13219 from Patent EP1572962.
AJ238376 - Homo sapiens mRNA for putative protein TH1, partial, clone IMAGE ID 255931.
AJ238374 - Homo sapiens mRNA for putative protein TH1, partial, clone IMAGE ID 785447.
AJ238375 - Homo sapiens mRNA for putative protein TH1, partial, clone IMAGE ID 612462.
AK127431 - Homo sapiens cDNA FLJ45523 fis, clone BRTHA2026071.
JD374037 - Sequence 355061 from Patent EP1572962.
JD156291 - Sequence 137315 from Patent EP1572962.
JD177088 - Sequence 158112 from Patent EP1572962.
JD272727 - Sequence 253751 from Patent EP1572962.
JD404338 - Sequence 385362 from Patent EP1572962.
JD555513 - Sequence 536537 from Patent EP1572962.
JD486304 - Sequence 467328 from Patent EP1572962.
JD563753 - Sequence 544777 from Patent EP1572962.
JD552754 - Sequence 533778 from Patent EP1572962.
JD349145 - Sequence 330169 from Patent EP1572962.
JD382536 - Sequence 363560 from Patent EP1572962.
JD061737 - Sequence 42761 from Patent EP1572962.
JD556873 - Sequence 537897 from Patent EP1572962.
JD492537 - Sequence 473561 from Patent EP1572962.
JD513832 - Sequence 494856 from Patent EP1572962.
JD069294 - Sequence 50318 from Patent EP1572962.
JD516605 - Sequence 497629 from Patent EP1572962.
JD300220 - Sequence 281244 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: H0UI80, H0UI80_HUMAN, hCG_28547, NM_198976, NP_945327, TH1L, uc002yag.3
UCSC ID: uc002yag.4
RefSeq Accession: NM_198976
Protein: H0UI80 CCDS: CCDS13473.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_198976.2
exon count: 15CDS single in 3' UTR: no RNA size: 2320
ORF size: 1800CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3637.50frame shift in genome: no % Coverage: 99.35
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 309# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.