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Protein

RNA polymerase II elongation factor ELL3

Gene

ELL3

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

Functioni

Enhancer-binding elongation factor that specifically binds enhancers in embryonic stem cells (ES cells), marks them, and is required for their future activation during stem cell specification. Does not only bind to enhancer regions of active genes, but also marks the enhancers that are in a poised or inactive state in ES cells and is required for establishing proper RNA polymerase II occupancy at developmentally regulated genes in a cohesin-dependent manner. Probably required for priming developmentally regulated genes for later recruitment of the super elongation complex (SEC), for transcriptional activation during differentiation. Required for recruitment of P-TEFb within SEC during differentiation. Probably preloaded on germ cell chromatin, suggesting that it may prime gene activation by marking enhancers as early as in the germ cells. Promoting epithelial-mesenchymal transition (EMT) (By similarity). Elongation factor component of the super elongation complex (SEC), a complex required to increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by the polymerase at multiple sites along the DNA. Component of the little elongation complex (LEC), a complex required to regulate small nuclear RNA (snRNA) gene transcription by RNA polymerase II and III (PubMed:22195968).By similarity2 Publications

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Transcription, Transcription regulation

Enzyme and pathway databases

ReactomeiR-HSA-6807505. RNA polymerase II transcribes snRNA genes.

Names & Taxonomyi

Protein namesi
Recommended name:
RNA polymerase II elongation factor ELL3
Gene namesi
Name:ELL3
OrganismiHomo sapiens (Human)Imported
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 15

Organism-specific databases

HGNCiHGNC:23113. ELL3.

Subcellular locationi

  • Nucleus 1 Publication

GO - Cellular componenti

  • nucleolus Source: HPA
  • nucleoplasm Source: HPA
  • nucleus Source: UniProtKB
  • transcription elongation factor complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA128394728.

Polymorphism and mutation databases

BioMutaiELL3.
DMDMi48428154.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 397397RNA polymerase II elongation factor ELL3PRO_0000146736Add
BLAST

Proteomic databases

EPDiQ9HB65.
MaxQBiQ9HB65.
PaxDbiQ9HB65.
PeptideAtlasiQ9HB65.
PRIDEiQ9HB65.

Expressioni

Tissue specificityi

Testis specific.1 Publication

Gene expression databases

BgeeiQ9HB65.
CleanExiHS_ELL3.
ExpressionAtlasiQ9HB65. baseline and differential.
GenevisibleiQ9HB65. HS.

Organism-specific databases

HPAiHPA028938.

Interactioni

Subunit structurei

Interacts with AFF4 (By similarity). Component of the super elongation complex (SEC), at least composed of EAF1, EAF2, CDK9, MLLT3/AF9, AFF (AFF1 or AFF4), the P-TEFb complex and ELL (ELL, ELL2 or ELL3). Component of the little elongation complex (LEC), at least composed of ELL (ELL, ELL2 or ELL3), ZC3H8, ICE1 and ICE2.By similarity1 Publication

Protein-protein interaction databases

BioGridi123198. 17 interactions.
IntActiQ9HB65. 6 interactions.
MINTiMINT-1398616.
STRINGi9606.ENSP00000320346.

Structurei

3D structure databases

ProteinModelPortaliQ9HB65.
SMRiQ9HB65. Positions 287-393.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the ELL/occludin family.Curated

Phylogenomic databases

eggNOGiKOG4796. Eukaryota.
ENOG410ZNGU. LUCA.
GeneTreeiENSGT00550000074378.
HOGENOMiHOG000231840.
HOVERGENiHBG051462.
InParanoidiQ9HB65.
KOiK15183.
OMAiLHCLGPL.
OrthoDBiEOG7P02HN.
PhylomeDBiQ9HB65.
TreeFamiTF337345.

Family and domain databases

InterProiIPR031176. ELL/occludin.
IPR031175. ELL3.
IPR019464. ELL_N.
IPR010844. Occludin_ELL.
[Graphical view]
PANTHERiPTHR23288. PTHR23288. 1 hit.
PTHR23288:SF18. PTHR23288:SF18. 1 hit.
PfamiPF10390. ELL. 1 hit.
PF07303. Occludin_ELL. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

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

Isoform 1 (identifier: Q9HB65-1) [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
MEELQEPLRG QLRLCFTQAA RTSLLLLRLN DAALRALQEC QRQQVRPVIA
60 70 80 90 100
FQGHRGYLRL PGPGWSCLFS FIVSQCCQEG AGGSLDLVCQ RFLRSGPNSL
110 120 130 140 150
HCLGSLRERL IIWAAMDSIP APSSVQGHNL TEDARHPESW QNTGGYSEGD
160 170 180 190 200
AVSQPQMALE EVSVSDPLAS NQGQSLPGSS REHMAQWEVR SQTHVPNREP
210 220 230 240 250
VQALPSSASR KRLDKKRSVP VATVELEEKR FRTLPLVPSP LQGLTNQDLQ
260 270 280 290 300
EGEDWEQEDE DMDPRLEHSS SVQEDSESPS PEDIPDYLLQ YRAIHSAEQQ
310 320 330 340 350
HAYEQDFETD YAEYRILHAR VGTASQRFIE LGAEIKRVRR GTPEYKVLED
360 370 380 390
KIIQEYKKFR KQYPSYREEK RRCEYLHQKL SHIKGLILEF EEKNRGS
Length:397
Mass (Da):45,361
Last modified:June 7, 2004 - v2
Checksum:i9DC16B3D6E184FA7
GO
Isoform 2 (identifier: Q9HB65-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-56: MEELQEPLRGQLRLCFTQAARTSLLLLRLNDAALRALQECQRQQVRPVIAFQGHRG → MGLTVSFHPQ

Note: No experimental confirmation available.
Show »
Length:351
Mass (Da):40,033
Checksum:i599EC16BD47AC009
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti5 – 51Q → H in AAG13463 (PubMed:10882741).Curated
Sequence conflicti278 – 2781S → P in BAG54320 (PubMed:14702039).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti11 – 111Q → E.
Corresponds to variant rs2277531 [ dbSNP | Ensembl ].
VAR_018992
Natural varianti140 – 1401W → R.
Corresponds to variant rs35454865 [ dbSNP | Ensembl ].
VAR_053074

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 5656MEELQ…QGHRG → MGLTVSFHPQ in isoform 2. 1 PublicationVSP_045937Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF276512 mRNA. Translation: AAG13463.1.
AK026290 mRNA. Translation: BAB15432.1.
AK057528 mRNA. Translation: BAG51928.1.
AK126384 mRNA. Translation: BAG54320.1.
CR457358 mRNA. Translation: CAG33639.1.
AC018512 Genomic DNA. No translation available.
CH471082 Genomic DNA. Translation: EAW77238.1.
BC006548 mRNA. Translation: AAH06548.1.
BC019293 mRNA. Translation: AAH19293.1.
CCDSiCCDS10102.1. [Q9HB65-1]
RefSeqiNP_079441.1. NM_025165.2. [Q9HB65-1]
UniGeneiHs.706346.

Genome annotation databases

EnsembliENST00000319359; ENSP00000320346; ENSG00000128886. [Q9HB65-1]
GeneIDi80237.
KEGGihsa:80237.
UCSCiuc001zsw.2. human. [Q9HB65-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF276512 mRNA. Translation: AAG13463.1.
AK026290 mRNA. Translation: BAB15432.1.
AK057528 mRNA. Translation: BAG51928.1.
AK126384 mRNA. Translation: BAG54320.1.
CR457358 mRNA. Translation: CAG33639.1.
AC018512 Genomic DNA. No translation available.
CH471082 Genomic DNA. Translation: EAW77238.1.
BC006548 mRNA. Translation: AAH06548.1.
BC019293 mRNA. Translation: AAH19293.1.
CCDSiCCDS10102.1. [Q9HB65-1]
RefSeqiNP_079441.1. NM_025165.2. [Q9HB65-1]
UniGeneiHs.706346.

3D structure databases

ProteinModelPortaliQ9HB65.
SMRiQ9HB65. Positions 287-393.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi123198. 17 interactions.
IntActiQ9HB65. 6 interactions.
MINTiMINT-1398616.
STRINGi9606.ENSP00000320346.

Polymorphism and mutation databases

BioMutaiELL3.
DMDMi48428154.

Proteomic databases

EPDiQ9HB65.
MaxQBiQ9HB65.
PaxDbiQ9HB65.
PeptideAtlasiQ9HB65.
PRIDEiQ9HB65.

Protocols and materials databases

DNASUi80237.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000319359; ENSP00000320346; ENSG00000128886. [Q9HB65-1]
GeneIDi80237.
KEGGihsa:80237.
UCSCiuc001zsw.2. human. [Q9HB65-1]

Organism-specific databases

CTDi80237.
GeneCardsiELL3.
HGNCiHGNC:23113. ELL3.
HPAiHPA028938.
MIMi609885. gene.
neXtProtiNX_Q9HB65.
PharmGKBiPA128394728.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG4796. Eukaryota.
ENOG410ZNGU. LUCA.
GeneTreeiENSGT00550000074378.
HOGENOMiHOG000231840.
HOVERGENiHBG051462.
InParanoidiQ9HB65.
KOiK15183.
OMAiLHCLGPL.
OrthoDBiEOG7P02HN.
PhylomeDBiQ9HB65.
TreeFamiTF337345.

Enzyme and pathway databases

ReactomeiR-HSA-6807505. RNA polymerase II transcribes snRNA genes.

Miscellaneous databases

ChiTaRSiELL3. human.
GenomeRNAii80237.
PROiQ9HB65.
SOURCEiSearch...

Gene expression databases

BgeeiQ9HB65.
CleanExiHS_ELL3.
ExpressionAtlasiQ9HB65. baseline and differential.
GenevisibleiQ9HB65. HS.

Family and domain databases

InterProiIPR031176. ELL/occludin.
IPR031175. ELL3.
IPR019464. ELL_N.
IPR010844. Occludin_ELL.
[Graphical view]
PANTHERiPTHR23288. PTHR23288. 1 hit.
PTHR23288:SF18. PTHR23288:SF18. 1 hit.
PfamiPF10390. ELL. 1 hit.
PF07303. Occludin_ELL. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Identification, cloning, expression, and biochemical characterization of the testis-specific RNA polymerase II elongation factor ELL3."
    Miller T., Williams K., Johnstone R.W., Shilatifard A.
    J. Biol. Chem. 275:32052-32056(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
  2. "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.
    , 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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
    Tissue: Small intestineImported, Testis and Uterus.
  3. "Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
    Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.
    Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
  4. "Analysis of the DNA sequence and duplication history of human chromosome 15."
    Zody M.C., Garber M., Sharpe T., Young S.K., Rowen L., O'Neill K., Whittaker C.A., Kamal M., Chang J.L., Cuomo C.A., Dewar K., FitzGerald M.G., Kodira C.D., Madan A., Qin S., Yang X., Abbasi N., Abouelleil A.
    , Arachchi H.M., Baradarani L., Birditt B., Bloom S., Bloom T., Borowsky M.L., Burke J., Butler J., Cook A., DeArellano K., DeCaprio D., Dorris L. III, Dors M., Eichler E.E., Engels R., Fahey J., Fleetwood P., Friedman C., Gearin G., Hall J.L., Hensley G., Johnson E., Jones C., Kamat A., Kaur A., Locke D.P., Madan A., Munson G., Jaffe D.B., Lui A., Macdonald P., Mauceli E., Naylor J.W., Nesbitt R., Nicol R., O'Leary S.B., Ratcliffe A., Rounsley S., She X., Sneddon K.M.B., Stewart S., Sougnez C., Stone S.M., Topham K., Vincent D., Wang S., Zimmer A.R., Birren B.W., Hood L., Lander E.S., Nusbaum C.
    Nature 440:671-675(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  6. "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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: LungImported.
  7. Cited for: FUNCTION, IDENTIFICATION IN THE SEC COMPLEX, IDENTIFICATION IN THE LEC COMPLEX.
  8. "The super elongation complex (SEC) family in transcriptional control."
    Luo Z., Lin C., Shilatifard A.
    Nat. Rev. Mol. Cell Biol. 13:543-547(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW ON THE SUPER ELONGATION COMPLEX.

Entry informationi

Entry nameiELL3_HUMAN
AccessioniPrimary (citable) accession number: Q9HB65
Secondary accession number(s): B3KQ66
, B3KX08, Q6I9Z7, Q9H634
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2004
Last sequence update: June 7, 2004
Last modified: July 6, 2016
This is version 113 of the entry and version 2 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

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 15
    Human chromosome 15: 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. 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.