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

Heterogeneous nuclear ribonucleoprotein D0

Gene

Hnrnpd

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

Functioni

Binds with high affinity to RNA molecules that contain AU-rich elements (AREs) found within the 3'-UTR of many proto-oncogenes and cytokine mRNAs. Also binds to double- and single-stranded DNA sequences in a specific manner and functions a transcription factor. Each of the RNA-binding domains specifically can bind solely to a single-stranded non-monotonous 5'-UUAG-3' sequence and also weaker to the single-stranded 5'-TTAGGG-3' telomeric DNA repeat. Binds RNA oligonucleotides with 5'-UUAGGG-3' repeats more tightly than the telomeric single-stranded DNA 5'-TTAGGG-3' repeats. Binding of RRM1 to DNA inhibits the formation of DNA quadruplex structure which may play a role in telomere elongation. May be involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. May play a role in the regulation of the rhythmic expression of circadian clock core genes. Directly binds to the 3'UTR of CRY1 mRNA and induces CRY1 rhythmic translation. May also be involved in the regulation of PER2 translation.By similarity

GO - Molecular functioni

  • AT DNA binding Source: RGD
  • chromatin binding Source: RGD
  • histone deacetylase binding Source: RGD
  • mRNA 3'-UTR AU-rich region binding Source: RGD
  • mRNA binding Source: RGD
  • nucleotide binding Source: InterPro
  • RNA binding Source: UniProtKB
  • telomeric DNA binding Source: UniProtKB
  • transcription factor binding Source: RGD

GO - Biological processi

  • 3'-UTR-mediated mRNA destabilization Source: RGD
  • brain development Source: RGD
  • cellular response to amino acid stimulus Source: RGD
  • cellular response to estradiol stimulus Source: RGD
  • cellular response to nitric oxide Source: RGD
  • cellular response to putrescine Source: RGD
  • cerebellum development Source: RGD
  • circadian regulation of translation Source: UniProtKB
  • hepatocyte dedifferentiation Source: RGD
  • liver development Source: RGD
  • mRNA stabilization Source: RGD
  • negative regulation of gene expression Source: RGD
  • nuclear-transcribed mRNA catabolic process, exonucleolytic Source: RGD
  • nucleocytoplasmic transport Source: RGD
  • positive regulation of gene expression Source: RGD
  • positive regulation of translation Source: UniProtKB
  • regulation of circadian rhythm Source: UniProtKB
  • response to calcium ion Source: RGD
  • response to electrical stimulus Source: RGD
  • response to estradiol Source: RGD
  • response to rapamycin Source: RGD
  • response to sodium phosphate Source: RGD
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein

Keywords - Biological processi

Biological rhythms

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiR-RNO-450408. AUF1 (hnRNP D0) binds and destabilizes mRNA.
R-RNO-72163. mRNA Splicing - Major Pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
Heterogeneous nuclear ribonucleoprotein D0
Short name:
hnRNP D0
Alternative name(s):
AU-rich element RNA-binding protein 1
Gene namesi
Name:Hnrnpd
Synonyms:Auf1, Hnrpd
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 14

Organism-specific databases

RGDi620365. Hnrnpd.

Subcellular locationi

  • Nucleus By similarity
  • Cytoplasm By similarity

  • Note: Localized in cytoplasmic mRNP granules containing untranslated mRNAs. Component of ribonucleosomes. Cytoplasmic localization oscillates diurnally.By similarity

GO - Cellular componenti

  • cytosol Source: RGD
  • extracellular exosome Source: Ensembl
  • intracellular ribonucleoprotein complex Source: UniProtKB
  • nucleoplasm Source: Ensembl
  • nucleus Source: RGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 353352Heterogeneous nuclear ribonucleoprotein D0PRO_0000081851Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineBy similarity
Modified residuei69 – 691PhosphoserineBy similarity
Modified residuei78 – 781PhosphoserineCombined sources
Modified residuei80 – 801PhosphoserineBy similarity
Modified residuei81 – 811PhosphoserineCombined sources
Modified residuei117 – 1171N6-methyllysineBy similarity
Modified residuei125 – 1251PhosphothreonineBy similarity
Modified residuei163 – 1631N6-acetyllysineBy similarity
Modified residuei188 – 1881PhosphoserineCombined sources
Modified residuei191 – 1911PhosphothreonineBy similarity
Modified residuei241 – 2411N6-acetyllysineBy similarity
Modified residuei249 – 2491N6-acetyllysineBy similarity
Modified residuei343 – 3431Dimethylated arginineBy similarity

Post-translational modificationi

Methylated by PRMT1, in an insulin-dependent manner. The PRMT1-mediated methylation regulates its phosphorylation.1 Publication
Arg-343 is dimethylated, probably to asymmetric dimethylarginine.By similarity

Keywords - PTMi

Acetylation, Methylation, Phosphoprotein

Proteomic databases

PaxDbiQ9JJ54.
PRIDEiQ9JJ54.

PTM databases

iPTMnetiQ9JJ54.
PhosphoSiteiQ9JJ54.

Expressioni

Gene expression databases

GenevisibleiQ9JJ54. RN.

Interactioni

Subunit structurei

Identified in a IGF2BP1-dependent mRNP granule complex containing untranslated mRNAs. Part of a complex associated with the FOS mCRD domain and consisting of PABPC1, PAIP1, CSDE1/UNR and SYNCRIP. Interacts with IGF2BP2. Interacts with GTPBP1. Interacts with EIF4G1; the interaction requires RNA. Interacts with EIF3B and RPS3.By similarity

GO - Molecular functioni

  • histone deacetylase binding Source: RGD
  • transcription factor binding Source: RGD

Protein-protein interaction databases

BioGridi249454. 1 interaction.
STRINGi10116.ENSRNOP00000046491.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini95 – 17783RRM 1PROSITE-ProRule annotationAdd
BLAST
Domaini180 – 25980RRM 2PROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi11 – 4535Ala-richAdd
BLAST
Compositional biasi268 – 34578Gly-richAdd
BLAST
Compositional biasi292 – 33039Tyr-richAdd
BLAST

Sequence similaritiesi

Contains 2 RRM (RNA recognition motif) domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0118. Eukaryota.
COG0724. LUCA.
GeneTreeiENSGT00760000118873.
HOGENOMiHOG000234441.
HOVERGENiHBG002295.
InParanoidiQ9JJ54.
KOiK13044.
OMAiTFKDEEP.
OrthoDBiEOG715Q6V.
TreeFamiTF314808.

Family and domain databases

Gene3Di3.30.70.330. 2 hits.
InterProiIPR012956. CARG-binding_factor_N.
IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF08143. CBFNT. 1 hit.
PF00076. RRM_1. 2 hits.
[Graphical view]
SMARTiSM00360. RRM. 2 hits.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 2 hits.
PROSITEiPS50102. RRM. 2 hits.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

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

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9JJ54-1) [UniParc]FASTAAdd to basket

Also known as: p45

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
MSEEQFGGDG AAAAATAAVG GSAGEQEGAM VAAAQGAAAA AGSGSGGGSA
60 70 80 90 100
PGGTEGGSTE AEGAKIDASK NEEDEGHSNS SPRHTEAATA QREEWKMFIG
110 120 130 140 150
GLSWDTTKKD LKDYFSKFGD VVDCTLKLDP ITGRSRGFGF VLFKESESVD
160 170 180 190 200
KVMDQKEHKL NGKVIDPKRA KAMKTKEPVK KIFVGGLSPD TPEEKIREYF
210 220 230 240 250
GGFGEVESIE LPMDNKTNKR RGFCFITFKE EEPVKKIMEK KYHNVGLSKC
260 270 280 290 300
EIKVAMSKEQ YQQQQQWGSR GGFAGRARGR GGGPSQNWNQ GYSNYWNQGY
310 320 330 340 350
GSYGYNSQGY GGYGGYDYTG YNSYYGYGDY SNQQSGYGKV SRRGGHQNSY

KPY
Length:353
Mass (Da):38,218
Last modified:March 4, 2015 - v2
Checksum:i7C21381A6B4A199F
GO
Isoform 2 (identifier: Q9JJ54-2) [UniParc]FASTAAdd to basket

Also known as: p42

The sequence of this isoform differs from the canonical sequence as follows:
     77-95: Missing.

Show »
Length:334
Mass (Da):36,042
Checksum:iE391A9B5F116AC60
GO
Isoform 3 (identifier: Q9JJ54-3) [UniParc]FASTAAdd to basket

Also known as: p40

The sequence of this isoform differs from the canonical sequence as follows:
     283-332: GPSQNWNQGYSNYWNQGYGSYGYNSQGYGGYGGYDYTGYNSYYGYGDYSN → D

Show »
Length:304
Mass (Da):32,672
Checksum:i6991CEF5913C56AF
GO
Isoform 4 (identifier: Q9JJ54-4) [UniParc]FASTAAdd to basket

Also known as: p37

The sequence of this isoform differs from the canonical sequence as follows:
     77-95: Missing.
     283-332: GPSQNWNQGYSNYWNQGYGSYGYNSQGYGGYGGYDYTGYNSYYGYGDYSN → D

Show »
Length:285
Mass (Da):30,496
Checksum:iBF3BCA2717A2FC58
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti51 – 511P → A in BAB03465 (Ref. 1) Curated
Sequence conflicti51 – 511P → A in BAB03466 (Ref. 1) Curated
Sequence conflicti51 – 511P → A in BAB03467 (Ref. 1) Curated
Sequence conflicti51 – 511P → A in BAB03468 (Ref. 1) Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei77 – 9519Missing in isoform 2 and isoform 4. 1 PublicationVSP_005836Add
BLAST
Alternative sequencei283 – 33250GPSQN…GDYSN → D in isoform 3 and isoform 4. 1 PublicationVSP_005837Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB046615 mRNA. Translation: BAB03465.1.
AB046616 mRNA. Translation: BAB03466.1.
AB046617 mRNA. Translation: BAB03467.1.
AB046618 mRNA. Translation: BAB03468.1.
AABR06077578 Genomic DNA. No translation available.
CH474022 Genomic DNA. Translation: EDL99590.1.
X16933 mRNA. Translation: CAA34808.1.
PIRiS09017.
RefSeqiNP_001076008.1. NM_001082539.1. [Q9JJ54-2]
NP_001076009.1. NM_001082540.1. [Q9JJ54-3]
NP_001076010.1. NM_001082541.1. [Q9JJ54-4]
NP_077380.2. NM_024404.2. [Q9JJ54-1]
UniGeneiRn.101929.
Rn.94022.

Genome annotation databases

EnsembliENSRNOT00000003158; ENSRNOP00000003158; ENSRNOG00000002292. [Q9JJ54-3]
ENSRNOT00000003173; ENSRNOP00000003173; ENSRNOG00000002292. [Q9JJ54-2]
ENSRNOT00000047840; ENSRNOP00000046491; ENSRNOG00000002292. [Q9JJ54-1]
GeneIDi79256.
KEGGirno:79256.
UCSCiRGD:620365. rat. [Q9JJ54-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB046615 mRNA. Translation: BAB03465.1.
AB046616 mRNA. Translation: BAB03466.1.
AB046617 mRNA. Translation: BAB03467.1.
AB046618 mRNA. Translation: BAB03468.1.
AABR06077578 Genomic DNA. No translation available.
CH474022 Genomic DNA. Translation: EDL99590.1.
X16933 mRNA. Translation: CAA34808.1.
PIRiS09017.
RefSeqiNP_001076008.1. NM_001082539.1. [Q9JJ54-2]
NP_001076009.1. NM_001082540.1. [Q9JJ54-3]
NP_001076010.1. NM_001082541.1. [Q9JJ54-4]
NP_077380.2. NM_024404.2. [Q9JJ54-1]
UniGeneiRn.101929.
Rn.94022.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi249454. 1 interaction.
STRINGi10116.ENSRNOP00000046491.

PTM databases

iPTMnetiQ9JJ54.
PhosphoSiteiQ9JJ54.

Proteomic databases

PaxDbiQ9JJ54.
PRIDEiQ9JJ54.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000003158; ENSRNOP00000003158; ENSRNOG00000002292. [Q9JJ54-3]
ENSRNOT00000003173; ENSRNOP00000003173; ENSRNOG00000002292. [Q9JJ54-2]
ENSRNOT00000047840; ENSRNOP00000046491; ENSRNOG00000002292. [Q9JJ54-1]
GeneIDi79256.
KEGGirno:79256.
UCSCiRGD:620365. rat. [Q9JJ54-1]

Organism-specific databases

CTDi3184.
RGDi620365. Hnrnpd.

Phylogenomic databases

eggNOGiKOG0118. Eukaryota.
COG0724. LUCA.
GeneTreeiENSGT00760000118873.
HOGENOMiHOG000234441.
HOVERGENiHBG002295.
InParanoidiQ9JJ54.
KOiK13044.
OMAiTFKDEEP.
OrthoDBiEOG715Q6V.
TreeFamiTF314808.

Enzyme and pathway databases

ReactomeiR-RNO-450408. AUF1 (hnRNP D0) binds and destabilizes mRNA.
R-RNO-72163. mRNA Splicing - Major Pathway.

Miscellaneous databases

PROiQ9JJ54.

Gene expression databases

GenevisibleiQ9JJ54. RN.

Family and domain databases

Gene3Di3.30.70.330. 2 hits.
InterProiIPR012956. CARG-binding_factor_N.
IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF08143. CBFNT. 1 hit.
PF00076. RRM_1. 2 hits.
[Graphical view]
SMARTiSM00360. RRM. 2 hits.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 2 hits.
PROSITEiPS50102. RRM. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Differential expression of AUF1 isoforms in rat tissues."
    Arao Y., Kikuchi A.
    Submitted (JUL-2000) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 2; 3 AND 4).
    Tissue: Kidney.
  2. "Genome sequence of the Brown Norway rat yields insights into mammalian evolution."
    Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J., Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G., Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G., Morgan M.
    , Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G., Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S., Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T., Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D., Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L., Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D., Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M., Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C., Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J., Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H., Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X., Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q., Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P., Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A., Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C., Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J., Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J., Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F., Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A., Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A., Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J., Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E., Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M., Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C., Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L., Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W., Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y., Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V., Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M., Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S., Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B., Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R., Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J., Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D., Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S., Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S., Mockrin S., Collins F.S.
    Nature 428:493-521(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Brown Norway.
  3. Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
    Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Brown Norway.
  4. "Cloning of the nucleic acid-binding domain of the rat HnRNP C-type protein."
    Sharp Z.D., Smith K.P., Cao Z., Helsel S.
    Biochim. Biophys. Acta 1048:306-309(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 147-304 (ISOFORMS 3/4).
    Tissue: Pituitary.
  5. "Phosphoproteomic analysis of rat liver by high capacity IMAC and LC-MS/MS."
    Moser K., White F.M.
    J. Proteome Res. 5:98-104(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  6. "Involvement of PRMT1 in hnRNPQ activation and internalization of insulin receptor."
    Iwasaki H.
    Biochem. Biophys. Res. Commun. 372:314-319(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: METHYLATION.
  7. "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-78; SER-81 AND SER-188, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiHNRPD_RAT
AccessioniPrimary (citable) accession number: Q9JJ54
Secondary accession number(s): G3V9G2
, P17132, Q9JJ51, Q9JJ52, Q9JJ53
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 21, 2001
Last sequence update: March 4, 2015
Last modified: June 8, 2016
This is version 118 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, 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.