Human Gene RTF1 (uc001zny.3) Description and Page Index
  Description: Homo sapiens Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae) (RTF1), mRNA.
RefSeq Summary (NM_015138): This locus may represent a gene involved in regulation of transcription elongation and chromatin remodeling, based on studies of similar proteins in other organisms. The encoded protein may bind single-stranded DNA. [provided by RefSeq, Sep 2010]. 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 :: D87440.2, BC015052.2 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr15:41,709,302-41,775,761 Size: 66,460 Total Exon Count: 18 Strand: +
Coding Region
   Position: hg19 chr15:41,709,314-41,772,885 Size: 63,572 Coding Exon Count: 18 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:41,709,302-41,775,761)mRNA (may differ from genome)Protein (710 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: RTF1_HUMAN
DESCRIPTION: RecName: Full=RNA polymerase-associated protein RTF1 homolog;
FUNCTION: Component of the PAF1 complex (PAF1C) which has multiple functions during transcription by RNA polymerase II and is implicated in regulation of development and maintenance of embryonic stem cell pluripotency. PAF1C associates with RNA polymerase II through interaction with POLR2A CTD non- phosphorylated and 'Ser-2'- and 'Ser-5'-phosphorylated forms and is involved in transcriptional elongation, acting both indepentently and synergistically with TCEA1 and in cooperation with the DSIF complex and HTATSF1. PAF1C is required for transcription of Hox and Wnt target genes. PAF1C is involved in hematopoiesis and stimulates transcriptional activity of MLL1; it promotes leukemogenesis though association with MLL-rearranged oncoproteins, such as MLL-MLLT3/AF9 and MLL-MLLT1/ENL. PAF1C is involved in histone modifications such as ubiquitination of histone H2B and methylation on histone H3 'Lys-4' (H3K4me3). PAF1C recruits the RNF20/40 E3 ubiquitin-protein ligase complex and the E2 enzyme UBE2A or UBE2B to chromatin which mediate monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1); UB2A/B-mediated H2B ubiquitination is proposed to be coupled to transcription. PAF1C is involved in mRNA 3' end formation probably through association with cleavage and poly(A) factors. In case of infection by influenza A strain H3N2, PAF1C associates with viral NS1 protein, thereby regulating gene transcription. Binds single- stranded DNA. Required for maximal induction of heat-shock genes. Required for the trimethylation of histone H3 'Lys-4' (H3K4me3) on genes involved in stem cell pluripotency; this function is synergistic with CXXC1 indicative for an involvement of a SET1 complex (By similarity).
SUBUNIT: Component of the PAF1 complex, which consists of CDC73, PAF1, LEO1, CTR9, RTF1 and WDR61; the association of RTF1 appears to be less stable than that of other subunits. At least in HeLa cells a N-terminal shorter form of RTF1 is also found in the complex.
INTERACTION: Q6P1J9:CDC73; NbExp=12; IntAct=EBI-1055239, EBI-930143; Q8N7H5:PAF1; NbExp=16; IntAct=EBI-1055239, EBI-2607770;
SUBCELLULAR LOCATION: Nucleus, nucleoplasm (By similarity).
DOMAIN: The Plus3 domain mediates single-stranded DNA-binding.
SIMILARITY: Contains 1 Plus3 domain.
CAUTION: It is uncertain whether Met-1 or Met-41 is the initiator.
SEQUENCE CAUTION: Sequence=AAH15052.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAA13382.2; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RTF1
CDC HuGE Published Literature: RTF1
Positive Disease Associations: Cholesterol, LDL
Related Studies:
  1. Cholesterol, LDL
    , , . [PubMed 0]

-  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: 24.12 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 661.00 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
3' UTR -916.542876-0.319 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
IPR004343 - Plus-3
IPR018144 - Plus3-dom_subgr

Pfam Domains:
PF03126 - Plus-3 domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help

2BZE
- NMR MuPIT

2DB9
- NMR MuPIT

3U1U
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q92541
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 BrowserGenome BrowserGenome Browser
Gene Details  Gene DetailsGene DetailsGene Details
Gene Sorter  Gene SorterGene SorterGene Sorter
  EnsemblFlyBaseWormBaseSGD
  Protein SequenceProtein SequenceProtein SequenceProtein Sequence
  AlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001076 transcription factor activity, RNA polymerase II transcription factor binding
GO:0003677 DNA binding
GO:0003697 single-stranded DNA binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:1990269 RNA polymerase II C-terminal domain phosphoserine binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001711 endodermal cell fate commitment
GO:0001832 blastocyst growth
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0006368 transcription elongation from RNA polymerase II promoter
GO:0016055 Wnt signaling pathway
GO:0016567 protein ubiquitination
GO:0016570 histone modification
GO:0019827 stem cell population maintenance
GO:0032968 positive regulation of transcription elongation from RNA polymerase II promoter
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0051571 positive regulation of histone H3-K4 methylation
GO:0080182 histone H3-K4 trimethylation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0016593 Cdc73/Paf1 complex


-  Descriptions from all associated GenBank mRNAs
  AK292302 - Homo sapiens cDNA FLJ75793 complete cds.
D87440 - Homo sapiens mRNA for KIAA0252 gene, partial cds.
BC015052 - Homo sapiens Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae), mRNA (cDNA clone MGC:9613 IMAGE:3909737), complete cds.
JD462646 - Sequence 443670 from Patent EP1572962.
JD487460 - Sequence 468484 from Patent EP1572962.
JD211213 - Sequence 192237 from Patent EP1572962.
AB383821 - Synthetic construct DNA, clone: pF1KSDA0252, Homo sapiens RTF1 gene for RNA polymerase-associated protein RTF1 homolog, complete cds, without stop codon, in Flexi system.
JD044949 - Sequence 25973 from Patent EP1572962.
JD404821 - Sequence 385845 from Patent EP1572962.
JD302663 - Sequence 283687 from Patent EP1572962.
JD073577 - Sequence 54601 from Patent EP1572962.
JD097540 - Sequence 78564 from Patent EP1572962.
JD166906 - Sequence 147930 from Patent EP1572962.
JD548318 - Sequence 529342 from Patent EP1572962.
JD105110 - Sequence 86134 from Patent EP1572962.
JD390518 - Sequence 371542 from Patent EP1572962.
JD109348 - Sequence 90372 from Patent EP1572962.
JD218130 - Sequence 199154 from Patent EP1572962.
JD119066 - Sequence 100090 from Patent EP1572962.
JD054233 - Sequence 35257 from Patent EP1572962.
JD153863 - Sequence 134887 from Patent EP1572962.
JD107297 - Sequence 88321 from Patent EP1572962.
JD124080 - Sequence 105104 from Patent EP1572962.
JD255506 - Sequence 236530 from Patent EP1572962.
JD400902 - Sequence 381926 from Patent EP1572962.
JD475395 - Sequence 456419 from Patent EP1572962.
JD413096 - Sequence 394120 from Patent EP1572962.
JD384921 - Sequence 365945 from Patent EP1572962.
JD396077 - Sequence 377101 from Patent EP1572962.
JD294028 - Sequence 275052 from Patent EP1572962.
JD481488 - Sequence 462512 from Patent EP1572962.
JD421900 - Sequence 402924 from Patent EP1572962.
JD533705 - Sequence 514729 from Patent EP1572962.
JD511438 - Sequence 492462 from Patent EP1572962.
JD363230 - Sequence 344254 from Patent EP1572962.
JD376816 - Sequence 357840 from Patent EP1572962.
JD411063 - Sequence 392087 from Patent EP1572962.
JD395633 - Sequence 376657 from Patent EP1572962.
JD425618 - Sequence 406642 from Patent EP1572962.
JD112496 - Sequence 93520 from Patent EP1572962.
JD089587 - Sequence 70611 from Patent EP1572962.
JD135531 - Sequence 116555 from Patent EP1572962.
JD339515 - Sequence 320539 from Patent EP1572962.
JD215551 - Sequence 196575 from Patent EP1572962.
JD518788 - Sequence 499812 from Patent EP1572962.
JD184308 - Sequence 165332 from Patent EP1572962.
JD371165 - Sequence 352189 from Patent EP1572962.
JD337336 - Sequence 318360 from Patent EP1572962.
JD446838 - Sequence 427862 from Patent EP1572962.
JD273648 - Sequence 254672 from Patent EP1572962.
JD413171 - Sequence 394195 from Patent EP1572962.
JD055784 - Sequence 36808 from Patent EP1572962.
JD393017 - Sequence 374041 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q92541 (Reactome details) participates in the following event(s):

R-HSA-112379 Recruitment of elongation factors to form elongation complex
R-HSA-8942099 RNF20:RNF40 binds PAF complex, Ubiquitin:UBE2A,B (Ubiquitin:RAD6), WAC and Histone H2B
R-HSA-113429 Elongating transcript encounters a lesion in the template
R-HSA-112385 Addition of nucleotides leads to transcript elongation
R-HSA-113411 2-4 nt.backtracking of Pol II complex on the template leading to elongation pausing
R-HSA-113412 Pol II elongation complex moves on the template as transcript elongates
R-HSA-113414 7-14 nt. Backtracking of Pol II complex on the template leading to elongation arrest
R-HSA-112392 Resumption of elongation after recovery from pausing
R-HSA-113413 TFIIS-mediated recovery of elongation from arrest
R-HSA-112395 Abortive termination of elongation after arrest
R-HSA-112396 Separation of elongating transcript from template
R-HSA-112382 Formation of RNA Pol II elongation complex
R-HSA-8866654 E3 ubiquitin ligases ubiquitinate target proteins
R-HSA-674695 RNA Polymerase II Pre-transcription Events
R-HSA-75955 RNA Polymerase II Transcription Elongation
R-HSA-8852135 Protein ubiquitination
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-597592 Post-translational protein modification
R-HSA-74160 Gene expression (Transcription)
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: KIAA0252, NM_015138, NP_055953, Q92541, Q96BX6, RTF1_HUMAN
UCSC ID: uc001zny.3
RefSeq Accession: NM_015138
Protein: Q92541 (aka RTF1_HUMAN)
CCDS: CCDS32200.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_015138.4
exon count: 18CDS single in 3' UTR: no RNA size: 5038
ORF size: 2133CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4366.00frame shift in genome: no % Coverage: 99.66
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# 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.