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Motif: AUF1_binding (RM00002)

Description: AUF1 binding site

Summary

Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam data in Wikipedia. This motif is described by a Wikipedia entry entitled HNRPD. More...

HNRNPD
Protein HNRPD PDB 1hd0.png
Available structures
PDB Ortholog search: PDBe RCSB
Identifiers
Aliases HNRNPD, AUF1, AUF1A, HNRPD, P37, hnRNPD0, heterogeneous nuclear ribonucleoprotein D
External IDs MGI: 101947 HomoloGene: 22410 GeneCards: HNRNPD
Gene location (Human)
Chromosome 4 (human)
Chr. Chromosome 4 (human)[1]
Chromosome 4 (human)
Genomic location for HNRNPD
Genomic location for HNRNPD
Band 4q21.22 Start 82,352,498 bp[1]
End 82,374,503 bp[1]
RNA expression pattern
PBB GE HNRPD 221480 at fs.png

PBB GE HNRPD 209330 s at fs.png

PBB GE HNRPD 221481 x at fs.png
More reference expression data
Orthologs
Species Human Mouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_031370
NM_001003810
NM_002138
NM_031369

NM_001077265
NM_001077266
NM_001077267
NM_007516

RefSeq (protein)

NP_001003810
NP_002129
NP_112737
NP_112738

NP_001070733
NP_001070734
NP_001070735
NP_031542

Location (UCSC) Chr 4: 82.35 – 82.37 Mb Chr 5: 99.96 – 99.98 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

Heterogeneous nuclear ribonucleoprotein D0 (HNRNPD) also known as AU-rich element RNA-binding protein 1 (AUF1) is a protein that in humans is encoded by the HNRNPD gene.[5][6] Alternative splicing of this gene results in four transcript variants.

Function

A consensus secondary structure and primary sequence for the targets of the AUF1 RNA binding protein.

This gene belongs to the subfamily of ubiquitously expressed heterogeneous nuclear ribonucleoproteins (hnRNPs). The hnRNPs are nucleic acid binding proteins and they complex with heterogeneous nuclear RNA (hnRNA). The interaction sites on the RNA are frequently biased towards particular sequence motifs.[7] These proteins are associated with pre-mRNAs in the nucleus and appear to influence pre-mRNA processing and other aspects of mRNA metabolism and transport. While all of the hnRNPs are present in the nucleus, some seem to shuttle between the nucleus and the cytoplasm. The hnRNP proteins have distinct nucleic acid binding properties. The protein encoded by this gene has two repeats of quasi-RRM domains that bind to RNAs. It localizes to both the nucleus and the cytoplasm. This protein is implicated in the regulation of mRNA stability.[6]

Interactions

HNRPD has been shown to interact with SAFB[8] and Hsp27.[9] AUF1 also has been reported to interact with mRNAs such as Mef2c mRNA.[10]

References

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000138668 - Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000000568 - Ensembl, May 2017
  3. ^ "Human PubMed Reference:". 
  4. ^ "Mouse PubMed Reference:". 
  5. ^ Dempsey LA, Li MJ, DePace A, Bray-Ward P, Maizels N (August 1998). "The human HNRPD locus maps to 4q21 and encodes a highly conserved protein". Genomics. 49 (3): 378–384. doi:10.1006/geno.1998.5237. PMID 9615222. 
  6. ^ a b "Entrez Gene: HNRPD heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding protein 1, 37kDa)". 
  7. ^ Mazan-Mamczarz K, Kuwano Y, Zhan M, White EJ, Martindale JL, Lal A, Gorospe M (Jan 2009). "Identification of a signature motif in target mRNAs of RNA-binding protein AUF1". Nucleic Acids Research. 37 (1): 204–14. doi:10.1093/nar/gkn929. PMC 2615618Freely accessible. PMID 19033365. 
  8. ^ Arao Y, Kuriyama R, Kayama F, Kato S (August 2000). "A nuclear matrix-associated factor, SAF-B, interacts with specific isoforms of AUF1/hnRNP D". Arch. Biochem. Biophys. 380 (2): 228–36. doi:10.1006/abbi.2000.1938. PMID 10933876. 
  9. ^ Sinsimer KS, Gratacós FM, Knapinska AM, Lu J, Krause CD, Wierzbowski AV, Maher LR, Scrudato S, Rivera YM, Gupta S, Turrin DK, De La Cruz MP, Pestka S, Brewer G (September 2008). "Chaperone Hsp27, a novel subunit of AUF1 protein complexes, functions in AU-rich element-mediated mRNA decay". Mol. Cell. Biol. 28 (17): 5223–37. doi:10.1128/MCB.00431-08. PMC 2519747Freely accessible. PMID 18573886. 
  10. ^ Panda AC, Abdelmohsen K, Yoon JH, Martindale JL, Yang X, Curtis J, Mercken EM, Chenette DM, Zhang Y, Schneider RJ, Becker KG, de Cabo R, Gorospe M (Aug 2014). "RNA-binding protein AUF1 promotes myogenesis by regulating MEF2C expression levels". Mol Cell Biol. 34 (16): 3106–19. doi:10.1128/MCB.00423-14. PMC 4135590Freely accessible. PMID 24891619. 

Further reading

This page is based on a wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

Alignments

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Formatting options

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Alignment format:
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Family matches

There are 2 Rfam families which match this motif.

This section shows the families which have been annotated with this motif. Users should be aware that the motifs are structural constructs and do not necessarily conform to taxonomic boundaries in the way that Rfam families do. More...

Original order Family Accession Family Description Number of Hits Fraction of Hits Sum of Bits Image
3 RF00539 Small nucleolar RNA Me28S-Cm788 4 0.800 75.2 Match Image
3 RF01267 Small nucleolar RNA snR37 3 0.333 55.2 Match Image

References

This section shows the database cross-references that we have for this Rfam motif.

Literature references

  1. Mazan-Mamczarz K, Kuwano Y, Zhan M, White EJ, Martindale JL, Lal A, Gorospe M Nucleic Acids Res. 2009;37:204-14. Identification of a signature motif in target mRNAs of RNA-binding protein AUF1. PUBMED:19033365

External database links

Curation and motif details

This section shows the detailed information about the Rfam motif. We're happy to receive updated or improved alignments for new or existing families. Submit your new alignment and we'll take a look.

Curation

Seed source Published; PMID:14981256
Structure source N/A
Type Specific Recognition Motif
Author Gardner PP
Alignment details
Alignment Number of
sequences
Average length Sequence
identity (%)
seed 8 33.88 35

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi --seed 1 CM
Gathering cutoff 16.0
Covariance model Download the Infernal CM for the motif here