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Protein

Heterogeneous nuclear ribonucleoprotein F

Gene

Hnrnpf

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Component of the heterogeneous nuclear ribonucleoprotein (hnRNP) complexes which provide the substrate for the processing events that pre-mRNAs undergo before becoming functional, translatable mRNAs in the cytoplasm. Plays a role in the regulation of alternative splicing events. Binds G-rich sequences in pre-mRNAs and keeps target RNA in an unfolded state (By similarity).By similarity

GO - Molecular functioni

  • nucleotide binding Source: InterPro
  • poly(A) RNA binding Source: Ensembl
  • single-stranded RNA binding Source: UniProtKB
  • TBP-class protein binding Source: RGD
  • transcription factor binding Source: RGD

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiR-RNO-72163. mRNA Splicing - Major Pathway.
R-RNO-72203. Processing of Capped Intron-Containing Pre-mRNA.

Names & Taxonomyi

Protein namesi
Recommended name:
Heterogeneous nuclear ribonucleoprotein F
Short name:
hnRNP F
Cleaved into the following chain:
Gene namesi
Name:Hnrnpf
Synonyms:Hnrpf
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 4

Organism-specific databases

RGDi620366. Hnrnpf.

Subcellular locationi

  • Nucleusnucleoplasm 1 Publication

GO - Cellular componenti

  • catalytic step 2 spliceosome Source: Ensembl
  • cytoplasm Source: Ensembl
  • membrane Source: Ensembl
  • nucleoplasm Source: UniProtKB-SubCell
  • nucleus Source: RGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus, Spliceosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 415415Heterogeneous nuclear ribonucleoprotein FPRO_0000367117Add
BLAST
Initiator methionineiRemoved; alternateBy similarity
Chaini2 – 415414Heterogeneous nuclear ribonucleoprotein F, N-terminally processedPRO_0000253054Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-acetylmethionineBy similarity
Modified residuei2 – 21N-acetylmethionine; in Heterogeneous nuclear ribonucleoprotein F, N-terminally processedBy similarity
Cross-linki72 – 72Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)By similarity
Modified residuei104 – 1041PhosphoserineCombined sources
Modified residuei107 – 1071PhosphoserineBy similarity
Modified residuei161 – 1611PhosphoserineBy similarity
Modified residuei187 – 1871PhosphoserineBy similarity
Modified residuei195 – 1951PhosphoserineCombined sources
Modified residuei200 – 2001N6-acetyllysine; alternateBy similarity
Cross-linki200 – 200Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateBy similarity
Modified residuei224 – 2241N6-acetyllysineBy similarity

Post-translational modificationi

Sumoylated.By similarity

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiQ794E4.
PRIDEiQ794E4.

PTM databases

iPTMnetiQ794E4.
PhosphoSiteiQ794E4.

Expressioni

Tissue specificityi

Detected in liver, thymus, spleen and testis.1 Publication

Gene expression databases

GenevisibleiQ794E4. RN.

Interactioni

Subunit structurei

Identified in the spliceosome C complex. Interacts with AGO1, AGO2, TBP and TXNL4/DIM1 (By similarity).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei16 – 161Interaction with RNABy similarity
Sitei20 – 201Interaction with RNABy similarity
Sitei52 – 521Interaction with RNABy similarity
Sitei75 – 751Interaction with RNABy similarity
Sitei116 – 1161Interaction with RNABy similarity
Sitei120 – 1201Interaction with RNABy similarity
Sitei150 – 1501Interaction with RNABy similarity
Sitei173 – 1731Interaction with RNABy similarity
Sitei294 – 2941Interaction with RNABy similarity
Sitei298 – 2981Interaction with RNABy similarity
Sitei326 – 3261Interaction with RNABy similarity
Sitei349 – 3491Interaction with RNABy similarity

GO - Molecular functioni

  • TBP-class protein binding Source: RGD
  • transcription factor binding Source: RGD

Protein-protein interaction databases

BioGridi249006. 1 interaction.
IntActiQ794E4. 1 interaction.
STRINGi10116.ENSRNOP00000019529.

Structurei

3D structure databases

ProteinModelPortaliQ794E4.
SMRiQ794E4. Positions 1-194, 277-381.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini11 – 9080RRM 1PROSITE-ProRule annotationAdd
BLAST
Domaini111 – 18878RRM 2PROSITE-ProRule annotationAdd
BLAST
Domaini289 – 36678RRM 3PROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni81 – 866Interaction with RNABy similarity
Regioni179 – 1846Interaction with RNABy similarity
Regioni355 – 3606Interaction with RNABy similarity

Domaini

The N-terminal RRM domains are responsible for recognizing the G-tract of BCL-X RNA.By similarity

Sequence similaritiesi

Contains 3 RRM (RNA recognition motif) domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG4211. Eukaryota.
ENOG410Z6M0. LUCA.
GeneTreeiENSGT00760000119102.
HOGENOMiHOG000220896.
HOVERGENiHBG055557.
InParanoidiQ794E4.
KOiK12898.
OMAiFLSECKI.
OrthoDBiEOG7BS4BZ.
PhylomeDBiQ794E4.
TreeFamiTF316157.

Family and domain databases

Gene3Di3.30.70.330. 3 hits.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
IPR012996. Znf_CHHC.
[Graphical view]
PfamiPF00076. RRM_1. 2 hits.
PF08080. zf-RNPHF. 1 hit.
[Graphical view]
SMARTiSM00360. RRM. 3 hits.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 3 hits.
PROSITEiPS50102. RRM. 3 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q794E4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMLGPEGGEG YVVKLRGLPW SCSIEDVQNF LSDCTIHDGV AGVHFIYTRE
60 70 80 90 100
GRQSGEAFVE LESEDDVKLA LKKDRESMGH RYIEVFKSHR TEMDWVLKHS
110 120 130 140 150
GPNSADSAND GFVRLRGLPF GCTKEEIVQF FSGLEIVPNG ITLPVDPEGK
160 170 180 190 200
ITGEAFVQFA SQELAEKALG KHKERIGHRY IEVFKSSQEE VRSYSDPPLK
210 220 230 240 250
FMSVQRPGPY DRPGTARRYI GIVKQAGLDR MRSGAYSAGY GGYEEYSGLS
260 270 280 290 300
DGYGFTTDLF GRDLSYCLSG MYDHRYGDSE FTVQSTTGHC VHMRGLPYKA
310 320 330 340 350
TENDIYNFFS PLNPVRVHIE IGPDGRVTGE ADVEFATHEE AVAAMSKDRA
360 370 380 390 400
NMQHRYIELF LNSTTGASNG AYSSQVMQGM GVSAAQATYS GLESQSVSGC
410
YGAGYSGQNS MGGYD
Length:415
Mass (Da):45,730
Last modified:January 23, 2007 - v3
Checksum:i31E1C9C90A8E051F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB022209 mRNA. Translation: BAA37095.1.
BC097275 mRNA. Translation: AAH97275.1.
BC103634 mRNA. Translation: AAI03635.1.
RefSeqiNP_001032362.1. NM_001037285.1.
NP_001032363.1. NM_001037286.1.
NP_001032364.1. NM_001037287.1.
NP_071792.1. NM_022397.3.
XP_008761484.1. XM_008763262.1.
UniGeneiRn.144596.

Genome annotation databases

EnsembliENSRNOT00000019529; ENSRNOP00000019529; ENSRNOG00000014562.
ENSRNOT00000083843; ENSRNOP00000068652; ENSRNOG00000014562.
ENSRNOT00000091765; ENSRNOP00000069655; ENSRNOG00000014562.
GeneIDi64200.
KEGGirno:64200.
UCSCiRGD:620366. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB022209 mRNA. Translation: BAA37095.1.
BC097275 mRNA. Translation: AAH97275.1.
BC103634 mRNA. Translation: AAI03635.1.
RefSeqiNP_001032362.1. NM_001037285.1.
NP_001032363.1. NM_001037286.1.
NP_001032364.1. NM_001037287.1.
NP_071792.1. NM_022397.3.
XP_008761484.1. XM_008763262.1.
UniGeneiRn.144596.

3D structure databases

ProteinModelPortaliQ794E4.
SMRiQ794E4. Positions 1-194, 277-381.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi249006. 1 interaction.
IntActiQ794E4. 1 interaction.
STRINGi10116.ENSRNOP00000019529.

PTM databases

iPTMnetiQ794E4.
PhosphoSiteiQ794E4.

Proteomic databases

PaxDbiQ794E4.
PRIDEiQ794E4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000019529; ENSRNOP00000019529; ENSRNOG00000014562.
ENSRNOT00000083843; ENSRNOP00000068652; ENSRNOG00000014562.
ENSRNOT00000091765; ENSRNOP00000069655; ENSRNOG00000014562.
GeneIDi64200.
KEGGirno:64200.
UCSCiRGD:620366. rat.

Organism-specific databases

CTDi3185.
RGDi620366. Hnrnpf.

Phylogenomic databases

eggNOGiKOG4211. Eukaryota.
ENOG410Z6M0. LUCA.
GeneTreeiENSGT00760000119102.
HOGENOMiHOG000220896.
HOVERGENiHBG055557.
InParanoidiQ794E4.
KOiK12898.
OMAiFLSECKI.
OrthoDBiEOG7BS4BZ.
PhylomeDBiQ794E4.
TreeFamiTF316157.

Enzyme and pathway databases

ReactomeiR-RNO-72163. mRNA Splicing - Major Pathway.
R-RNO-72203. Processing of Capped Intron-Containing Pre-mRNA.

Miscellaneous databases

NextBioi612884.
PROiQ794E4.

Gene expression databases

GenevisibleiQ794E4. RN.

Family and domain databases

Gene3Di3.30.70.330. 3 hits.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
IPR012996. Znf_CHHC.
[Graphical view]
PfamiPF00076. RRM_1. 2 hits.
PF08080. zf-RNPHF. 1 hit.
[Graphical view]
SMARTiSM00360. RRM. 3 hits.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 3 hits.
PROSITEiPS50102. RRM. 3 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Association of the rat heterogeneous nuclear RNA-ribonucleoprotein F with TATA-binding protein."
    Yoshida T., Makino Y., Tamura T.
    FEBS Lett. 457:251-254(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 208-216, SUBCELLULAR LOCATION, INTERACTION WITH TBP, TISSUE SPECIFICITY.
    Tissue: Liver.
  2. "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].
    Tissue: Lung and Placenta.
  3. "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues."
    Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A., Lundby C., Olsen J.V.
    Nat. Commun. 3:876-876(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-104 AND SER-195, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiHNRPF_RAT
AccessioniPrimary (citable) accession number: Q794E4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 17, 2006
Last sequence update: January 23, 2007
Last modified: May 11, 2016
This is version 107 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. 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.