Human Gene RERE (uc001apf.3) Description and Page Index
  Description: Homo sapiens arginine-glutamic acid dipeptide (RE) repeats (RERE), transcript variant 2, mRNA.
RefSeq Summary (NM_001042681): This gene encodes a member of the atrophin family of arginine-glutamic acid (RE) dipeptide repeat-containing proteins. The encoded protein co-localizes with a transcription factor in the nucleus, and its overexpression triggers apoptosis. A similar protein in mouse associates with histone deacetylase and is thought to function as a transcriptional co-repressor during embryonic development. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr1:8,412,464-8,877,699 Size: 465,236 Total Exon Count: 23 Strand: -
Coding Region
   Position: hg19 chr1:8,415,147-8,716,356 Size: 301,210 Coding Exon Count: 22 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:8,412,464-8,877,699)mRNA (may differ from genome)Protein (1566 aa)
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Wikipedia

-  Comments and Description Text from UniProtKB
  ID: RERE_HUMAN
DESCRIPTION: RecName: Full=Arginine-glutamic acid dipeptide repeats protein; AltName: Full=Atrophin-1-like protein; AltName: Full=Atrophin-1-related protein;
FUNCTION: Plays a role as a transcriptional repressor during development. May play a role in the control of cell survival. Overexpression of RERE recruits BAX to the nucleus particularly to POD and triggers caspase-3 activation, leading to cell death.
SUBUNIT: Interacts with HDAC1 (By similarity). Interacts with ATN1. Interaction with ATN1 is improved when the poly-Gln region of ATN1 is extended. Interacts with FAT1.
INTERACTION: P54259:ATN1; NbExp=3; IntAct=EBI-948076, EBI-945980;
SUBCELLULAR LOCATION: Nucleus. Note=Localized in nuclear bodies of variables size. Colocalized with PML and BAX in nuclear PODs.
TISSUE SPECIFICITY: Widely expressed. Expressed in tumor cell lines.
DOMAIN: The interaction with ATN1 is mediated by the coiled coil domain.
DISEASE: Note=A chromosomal aberration involving RERE is found in the neuroblastoma cell line. Translocation t(1;15)(p36.2;q24).
SIMILARITY: Contains 1 BAH domain.
SIMILARITY: Contains 1 ELM2 domain.
SIMILARITY: Contains 1 GATA-type zinc finger.
SIMILARITY: Contains 1 SANT domain.
SEQUENCE CAUTION: Sequence=AAC31120.1; Type=Frameshift; Positions=588, 596; Sequence=AAD27584.1; Type=Erroneous initiation;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RERE
CDC HuGE Published Literature: RERE
Positive Disease Associations: Optic Disk , Schizophrenia , Vitiligo
Related Studies:
  1. Optic Disk
    Wishal D Ramdas et al. PLoS genetics 2010, A genome-wide association study of optic disc parameters., PLoS genetics. [PubMed 20548946]
  2. Schizophrenia
    Stephan Ripke et al. Nature genetics 2011, Genome-wide association study identifies five new schizophrenia loci., Nature genetics. [PubMed 21926974]
  3. Vitiligo
    Ying Jin et al. The New England journal of medicine 2010, Variant of TYR and autoimmunity susceptibility loci in generalized vitiligo., The New England journal of medicine. [PubMed 20410501]
    We observed associations between generalized vitiligo and markers implicating multiple genes, some associated with other autoimmune diseases and one (TYR) that may mediate target-cell specificity and indicate a mutually exclusive relationship between susceptibility to vitiligo and susceptibility to melanoma.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: RERE
Diseases sorted by gene-association score: neurodevelopmental disorder with or without anomalies of the brain, eye, or heart* (931), chromosome 1p36 deletion syndrome* (21), aortitis (7), actinomycosis (6), dextro-looped transposition of the great arteries (6), mediastinitis (5), neuroblastoma (3)
* = Manually curated disease association

-  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: 51.67 RPKM in Uterus
Total median expression: 1189.98 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
5' UTR -237.86625-0.381 Picture PostScript Text
3' UTR -877.962683-0.327 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
IPR002951 - Atrophin-like
IPR001025 - BAH_dom
IPR000949 - ELM2_dom
IPR009057 - Homeodomain-like
IPR001005 - SANT/Myb
IPR017884 - SANT_dom
IPR000679 - Znf_GATA
IPR013088 - Znf_NHR/GATA

Pfam Domains:
PF00320 - GATA zinc finger
PF01426 - BAH domain
PF01448 - ELM2 domain
PF03154 - Atrophin-1 family

SCOP Domains:
46689 - Homeodomain-like
57716 - Glucocorticoid receptor-like (DNA-binding domain)

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

2YQK
- NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q9P2R6
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 orthologGenome BrowserGenome BrowserNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details  Gene Details 
Gene SorterGene Sorter  Gene Sorter 
 RGDEnsembl WormBase 
 Protein SequenceProtein Sequence Protein Sequence 
 AlignmentAlignment Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001105 RNA polymerase II transcription coactivator activity
GO:0001106 RNA polymerase II transcription corepressor activity
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0008267 poly-glutamine tract binding
GO:0008270 zinc ion binding
GO:0043565 sequence-specific DNA binding
GO:0046872 metal ion binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006338 chromatin remodeling
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0006607 NLS-bearing protein import into nucleus
GO:0007275 multicellular organism development
GO:0021549 cerebellum development
GO:0021691 cerebellar Purkinje cell layer maturation
GO:0021930 cerebellar granule cell precursor proliferation
GO:0021942 radial glia guided migration of Purkinje cell
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048755 branching morphogenesis of a nerve
GO:0048813 dendrite morphogenesis
GO:1903507 negative regulation of nucleic acid-templated transcription

Cellular Component:
GO:0000118 histone deacetylase complex
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AB036737 - Homo sapiens mRNA for RERE, complete cds.
AB007927 - Homo sapiens mRNA for KIAA0458 protein, partial cds.
BC062342 - Homo sapiens cDNA clone IMAGE:6379220, containing frame-shift errors.
BC167857 - Synthetic construct Homo sapiens clone IMAGE:100068247, MGC:195864 arginine-glutamic acid dipeptide (RE) repeats (RERE) mRNA, encodes complete protein.
AB384483 - Synthetic construct DNA, clone: pF1KA0458, Homo sapiens RERE gene for arginine-glutamic acid dipeptide repeats protein, complete cds, without stop codon, in Flexi system.
AK096094 - Homo sapiens cDNA FLJ38775 fis, clone KIDNE2018269, highly similar to Homo sapiens mRNA for RERE.
BC009619 - Homo sapiens, clone IMAGE:3892190, mRNA.
AL050176 - Homo sapiens mRNA; cDNA DKFZp586H2022 (from clone DKFZp586H2022).
AK074834 - Homo sapiens cDNA FLJ90353 fis, clone NT2RP2003383.
JD291276 - Sequence 272300 from Patent EP1572962.
JD168235 - Sequence 149259 from Patent EP1572962.
JD180378 - Sequence 161402 from Patent EP1572962.
JD474844 - Sequence 455868 from Patent EP1572962.
JD490341 - Sequence 471365 from Patent EP1572962.
JD164371 - Sequence 145395 from Patent EP1572962.
JD075793 - Sequence 56817 from Patent EP1572962.
JD036916 - Sequence 17940 from Patent EP1572962.
JD559790 - Sequence 540814 from Patent EP1572962.
JD037779 - Sequence 18803 from Patent EP1572962.
JD275396 - Sequence 256420 from Patent EP1572962.
JD460851 - Sequence 441875 from Patent EP1572962.
JD261369 - Sequence 242393 from Patent EP1572962.
JD318160 - Sequence 299184 from Patent EP1572962.
JD215461 - Sequence 196485 from Patent EP1572962.
JD566163 - Sequence 547187 from Patent EP1572962.
JD287214 - Sequence 268238 from Patent EP1572962.
JD379108 - Sequence 360132 from Patent EP1572962.
JD352231 - Sequence 333255 from Patent EP1572962.
JD140004 - Sequence 121028 from Patent EP1572962.
JD075869 - Sequence 56893 from Patent EP1572962.
JD118938 - Sequence 99962 from Patent EP1572962.
JD372716 - Sequence 353740 from Patent EP1572962.
JD078797 - Sequence 59821 from Patent EP1572962.
JD446592 - Sequence 427616 from Patent EP1572962.
JD157496 - Sequence 138520 from Patent EP1572962.
JD101754 - Sequence 82778 from Patent EP1572962.
JD459210 - Sequence 440234 from Patent EP1572962.
JD143268 - Sequence 124292 from Patent EP1572962.
JD233248 - Sequence 214272 from Patent EP1572962.
JD121429 - Sequence 102453 from Patent EP1572962.
JD528696 - Sequence 509720 from Patent EP1572962.
JD153861 - Sequence 134885 from Patent EP1572962.
JD261826 - Sequence 242850 from Patent EP1572962.
JD195414 - Sequence 176438 from Patent EP1572962.
JD357879 - Sequence 338903 from Patent EP1572962.
DQ570251 - Homo sapiens piRNA piR-30363, complete sequence.
AF016005 - Homo sapiens chromosome 1 atrophin-1 related protein (DRPLA) mRNA, complete cds.
JD528768 - Sequence 509792 from Patent EP1572962.
JD328835 - Sequence 309859 from Patent EP1572962.
JD383082 - Sequence 364106 from Patent EP1572962.
JD423638 - Sequence 404662 from Patent EP1572962.
JD549415 - Sequence 530439 from Patent EP1572962.
JD464065 - Sequence 445089 from Patent EP1572962.
JD251287 - Sequence 232311 from Patent EP1572962.
JD111346 - Sequence 92370 from Patent EP1572962.
JD266748 - Sequence 247772 from Patent EP1572962.
JD525602 - Sequence 506626 from Patent EP1572962.
JD566153 - Sequence 547177 from Patent EP1572962.
JD243758 - Sequence 224782 from Patent EP1572962.
JD093272 - Sequence 74296 from Patent EP1572962.
JD302148 - Sequence 283172 from Patent EP1572962.
JD304573 - Sequence 285597 from Patent EP1572962.
AF118275 - Homo sapiens atrophin-related protein ARP mRNA, complete cds.
JD476947 - Sequence 457971 from Patent EP1572962.
JD460317 - Sequence 441341 from Patent EP1572962.
JD108271 - Sequence 89295 from Patent EP1572962.
JD157385 - Sequence 138409 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ARG, ARP, ATN1L, KIAA0458, NM_001042681, NP_036234, O43393, O75046, O75359, Q5VXL9, Q6P6B9, Q9P2R6, Q9Y2W4, RERE_HUMAN
UCSC ID: uc001apf.3
RefSeq Accession: NM_001042681
Protein: Q9P2R6 (aka RERE_HUMAN)
CCDS: CCDS95.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene RERE:
rere-dis (RERE-Related Disorders)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001042681.1
exon count: 23CDS single in 3' UTR: no RNA size: 8022
ORF size: 4701CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 9569.00frame shift in genome: no % Coverage: 99.84
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.