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Aliases for RPRD1B Gene

Aliases for RPRD1B Gene

  • Regulation Of Nuclear Pre-MRNA Domain Containing 1B 2 3 5
  • Regulation Of Nuclear Pre-MRNA Domain-Containing Protein 1B 3 4
  • Cell-Cycle Related And Expression-Elevated Protein In Tumor 2 3
  • Ku70-Binding Protein 5-Hera 2 3
  • C20orf77 3 4
  • CREPT 3 4
  • Cell Cycle-Related And Expression-Elevated Protein In Tumor 4
  • Chromosome 20 Open Reading Frame 77 2
  • DJ1057B20.2 3
  • Kub5-Hera 3
  • NET60 3
  • K-H 3

External Ids for RPRD1B Gene

Previous HGNC Symbols for RPRD1B Gene

  • C20orf77

Previous GeneCards Identifiers for RPRD1B Gene

  • GC20P036096
  • GC20P036662
  • GC20P033397

Summaries for RPRD1B Gene

GeneCards Summary for RPRD1B Gene

RPRD1B (Regulation Of Nuclear Pre-MRNA Domain Containing 1B) is a Protein Coding gene. Diseases associated with RPRD1B include Retroperitoneal Leiomyosarcoma. Among its related pathways are Formation of HIV-1 elongation complex containing HIV-1 Tat and Gene Expression. Gene Ontology (GO) annotations related to this gene include RNA polymerase II complex binding. An important paralog of this gene is RPRD1A.

UniProtKB/Swiss-Prot for RPRD1B Gene

  • Interacts with phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and participates in dephosphorylation of the CTD by RPAP2. Transcriptional regulator which enhances expression of CCND1. Promotes binding of RNA polymerase II to the CCDN1 promoter and to the termination region before the poly-A site but decreases its binding after the poly-A site. Prevents RNA polymerase II from reading through the 3' end termination site and may allow it to be recruited back to the promoter through promotion of the formation of a chromatin loop. Also enhances the transcription of a number of other cell cycle-related genes including CDK2, CDK4, CDK6 and cyclin-E but not CDKN1A, CDKN1B or cyclin-A. Promotes cell proliferation.

Additional gene information for RPRD1B Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RPRD1B Gene

Genomics for RPRD1B Gene

GeneHancer (GH) Regulatory Elements for RPRD1B Gene

Promoters and enhancers for RPRD1B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20J038031 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 600.7 +0.3 273 3.7 SP1 CC2D1A ZFX ELF3 MNT SIX5 ZNF148 NKRF POLR2A CEBPG TTI1 RPRD1B SNHG17 VSTM2L SNORA71C SNORA71A RN7SKP173 RALGAPB ACTR5 RBL1
GH20J038139 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 12.2 +122.5 122503 33.6 ZNF652 ZFX CC2D1A ELF3 CTCF ZKSCAN8 MNT CBFA2T2 ZNF148 POLR2A TGM2 RALGAPB ACTR5 RN7SKP173 SNHG17 TTI1 SNORA71A SNORA71C DHX35 RPN2
GH20J038082 Enhancer 1.4 Ensembl ENCODE dbSUPER 20.4 +51.3 51257 4.8 ELF3 CBFA2T2 ZNF148 CEBPG RERE TFE3 HNF1A PPARG SP5 CREM TGM2 RPRD1B VSTM2L TTI1 GC20P038089 GC20M038052
GH20J038072 Enhancer 1.3 Ensembl ENCODE dbSUPER 20.2 +42.3 42341 6.3 CTCF CEBPG SP1 PPARG ZNF384 RAD21 KAT8 POLR2A RXRA ZNF600 VSTM2L TTI1 RPRD1B TGM2 SNORA71A ENSG00000224635 SNORA71B SNHG17 GC20P038089 GC20M038052
GH20J037983 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 14.8 -44.8 -44771 10.2 SP1 ELF3 CTCF CBFA2T2 ZNF148 CEBPG RERE ZNF384 NFIB HNF1A TGM2 VSTM2L RPRD1B TTI1 RALGAPB NNAT RN7SKP185 GC20M037976 GC20M037959
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RPRD1B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RPRD1B gene promoter:
  • CUTL1
  • E2F
  • E2F-1
  • GR
  • GR-alpha
  • GR-beta
  • Sox9

Genomic Locations for RPRD1B Gene

Genomic Locations for RPRD1B Gene
chr20:38,033,487-38,127,780
(GRCh38/hg38)
Size:
94,294 bases
Orientation:
Plus strand
chr20:36,661,948-36,720,768
(GRCh37/hg19)
Size:
58,821 bases
Orientation:
Plus strand

Genomic View for RPRD1B Gene

Genes around RPRD1B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RPRD1B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RPRD1B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RPRD1B Gene

Proteins for RPRD1B Gene

  • Protein details for RPRD1B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NQG5-RPR1B_HUMAN
    Recommended name:
    Regulation of nuclear pre-mRNA domain-containing protein 1B
    Protein Accession:
    Q9NQG5
    Secondary Accessions:
    • Q1WDE7
    • Q6PKF4

    Protein attributes for RPRD1B Gene

    Size:
    326 amino acids
    Molecular mass:
    36900 Da
    Quaternary structure:
    • Homodimer (PubMed:24997600). May form a heterodimer with RPRD1A (PubMed:24997600). Associates with RPAP2 (PubMed:24997600). Associates with the RNA polymerase II complex (PubMed:22231121, PubMed:24399136, PubMed:24997600).
    SequenceCaution:
    • Sequence=AAH01696.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for RPRD1B Gene

neXtProt entry for RPRD1B Gene

Post-translational modifications for RPRD1B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RPRD1B Gene

Domains & Families for RPRD1B Gene

Gene Families for RPRD1B Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RPRD1B Gene

Suggested Antigen Peptide Sequences for RPRD1B Gene

GenScript: Design optimal peptide antigens:
  • Cell cycle-related and expression-elevated protein in tumor (RPR1B_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NQG5

UniProtKB/Swiss-Prot:

RPR1B_HUMAN :
  • Belongs to the UPF0400 (RTT103) family.
Family:
  • Belongs to the UPF0400 (RTT103) family.
genes like me logo Genes that share domains with RPRD1B: view

Function for RPRD1B Gene

Molecular function for RPRD1B Gene

UniProtKB/Swiss-Prot Function:
Interacts with phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and participates in dephosphorylation of the CTD by RPAP2. Transcriptional regulator which enhances expression of CCND1. Promotes binding of RNA polymerase II to the CCDN1 promoter and to the termination region before the poly-A site but decreases its binding after the poly-A site. Prevents RNA polymerase II from reading through the 3' end termination site and may allow it to be recruited back to the promoter through promotion of the formation of a chromatin loop. Also enhances the transcription of a number of other cell cycle-related genes including CDK2, CDK4, CDK6 and cyclin-E but not CDKN1A, CDKN1B or cyclin-A. Promotes cell proliferation.

Phenotypes From GWAS Catalog for RPRD1B Gene

Gene Ontology (GO) - Molecular Function for RPRD1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000993 RNA polymerase II complex binding IDA 22264791
GO:0005515 protein binding IPI 22264791
GO:0042802 identical protein binding IPI 24997600
genes like me logo Genes that share ontologies with RPRD1B: view
genes like me logo Genes that share phenotypes with RPRD1B: view

Animal Models for RPRD1B Gene

MGI Knock Outs for RPRD1B:
  • Rprd1b Rprd1b<tm1a(EUCOMM)Hmgu>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RPRD1B

Clone Products

  • Applied Biological Materials (abm): Clones for RPRD1B - Now 50% OFF >
  • * RPRD1B as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * RPRD1B tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RPRD1B Gene

Localization for RPRD1B Gene

Subcellular locations from UniProtKB/Swiss-Prot for RPRD1B Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RPRD1B gene
Compartment Confidence
nucleus 5
cytoskeleton 4
cytosol 4
plasma membrane 0
mitochondrion 0
endoplasmic reticulum 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Centrosome (2)
  • Cytosol (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RPRD1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 22264791
GO:0005654 nucleoplasm TAS --
GO:0005813 centrosome IDA --
GO:0005829 cytosol IDA --
GO:0016591 RNA polymerase II, holoenzyme IBA,IDA 22231121
genes like me logo Genes that share ontologies with RPRD1B: view

Pathways & Interactions for RPRD1B Gene

genes like me logo Genes that share pathways with RPRD1B: view

Pathways by source for RPRD1B Gene

2 Reactome pathways for RPRD1B Gene

Gene Ontology (GO) - Biological Process for RPRD1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008284 positive regulation of cell proliferation IDA 22264791
GO:0010564 regulation of cell cycle process IDA 22264791
GO:0031124 mRNA 3'-end processing IBA 21873635
GO:0042795 snRNA transcription by RNA polymerase II TAS --
GO:0045944 positive regulation of transcription by RNA polymerase II IDA 22264791
genes like me logo Genes that share ontologies with RPRD1B: view

No data available for SIGNOR curated interactions for RPRD1B Gene

Drugs & Compounds for RPRD1B Gene

No Compound Related Data Available

Transcripts for RPRD1B Gene

mRNA/cDNA for RPRD1B Gene

Unigene Clusters for RPRD1B Gene

Regulation of nuclear pre-mRNA domain containing 1B:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RPRD1B

Clone Products

  • Applied Biological Materials (abm): Clones for RPRD1B - Now 50% OFF >
  • * RPRD1B as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * RPRD1B tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

Alternative Splicing Database (ASD) splice patterns (SP) for RPRD1B Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11a · 11b · 11c
SP1: - - - - -
SP2: - - - -
SP3: - -
SP4: - -
SP5: -
SP6:
SP7:

Relevant External Links for RPRD1B Gene

GeneLoc Exon Structure for
RPRD1B
ECgene alternative splicing isoforms for
RPRD1B

Expression for RPRD1B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RPRD1B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RPRD1B Gene

This gene is overexpressed in Liver (x6.1).

Protein differential expression in normal tissues from HIPED for RPRD1B Gene

This gene is overexpressed in Peripheral blood mononuclear cells (8.7) and Lymph node (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RPRD1B Gene



Protein tissue co-expression partners for RPRD1B Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RPRD1B Gene:

RPRD1B

SOURCE GeneReport for Unigene cluster for RPRD1B Gene:

Hs.278839

mRNA Expression by UniProt/SwissProt for RPRD1B Gene:

Q9NQG5-RPR1B_HUMAN
Tissue specificity: Preferentially expressed in a range of tumor tissues including colon, lung, liver, breast, prostate, stomach, uterine endometrium and cervical cancers with higher levels in tumors than in adjacent non-tumor tissue (at protein level).

Evidence on tissue expression from TISSUES for RPRD1B Gene

  • Nervous system(4.8)
  • Liver(4.3)
genes like me logo Genes that share expression patterns with RPRD1B: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for RPRD1B Gene

Orthologs for RPRD1B Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for RPRD1B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RPRD1B 35 34
  • 99.9 (n)
OneToOne
dog
(Canis familiaris)
Mammalia RPRD1B 35 34
  • 94.89 (n)
OneToOne
cow
(Bos Taurus)
Mammalia RPRD1B 35 34
  • 93.66 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rprd1b 34
  • 93.46 (n)
mouse
(Mus musculus)
Mammalia Rprd1b 17 35 34
  • 92.41 (n)
oppossum
(Monodelphis domestica)
Mammalia RPRD1B 35
  • 87 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 42 (a)
OneToMany
-- 35
  • 42 (a)
OneToMany
chicken
(Gallus gallus)
Aves RPRD1B 34
  • 83.69 (n)
CREPT 35
  • 80 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RPRD1B 35
  • 95 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rprd1a 34
  • 74.36 (n)
Str.4805 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.29308 34
zebrafish
(Danio rerio)
Actinopterygii rprd1b 35 34
  • 71.37 (n)
OneToOne
wufb23h08 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005331 34
  • 53.21 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG9018 35 34
  • 52.92 (n)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea cids-1 35
  • 23 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RTT103 37 35
  • 15 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4640 35
  • 54 (a)
OneToMany
Species where no ortholog for RPRD1B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for RPRD1B Gene

ENSEMBL:
Gene Tree for RPRD1B (if available)
TreeFam:
Gene Tree for RPRD1B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RPRD1B: view image

Paralogs for RPRD1B Gene

Paralogs for RPRD1B Gene

(1) SIMAP similar genes for RPRD1B Gene using alignment to 4 proteins:

  • RPR1B_HUMAN
  • A2A2M0_HUMAN
  • E9PIQ9_HUMAN
  • E9PQF3_HUMAN

Pseudogenes.org Pseudogenes for RPRD1B Gene

genes like me logo Genes that share paralogs with RPRD1B: view

Variants for RPRD1B Gene

Sequence variations from dbSNP and Humsavar for RPRD1B Gene

SNP ID Clin Chr 20 pos Variation AA Info Type
rs1000007465 -- 38,052,492(+) C/T intron_variant
rs1000021589 -- 38,048,264(+) TTTCTTTT/TTT intron_variant
rs1000022581 -- 38,074,259(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000025020 -- 38,089,229(+) G/A 3_prime_UTR_variant, genic_downstream_transcript_variant, intron_variant
rs1000161416 -- 38,071,877(+) C/G genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for RPRD1B Gene

Variant ID Type Subtype PubMed ID
dgv4308n100 CNV gain 25217958
esv2670839 CNV deletion 23128226
esv2763659 CNV gain 21179565
esv3645771 CNV loss 21293372
nsv1057334 CNV loss 25217958
nsv585963 CNV gain 21841781
nsv833971 CNV gain 17160897
nsv833972 CNV loss 17160897

Variation tolerance for RPRD1B Gene

Residual Variation Intolerance Score: 24.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.89; 18.58% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RPRD1B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RPRD1B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RPRD1B Gene

Disorders for RPRD1B Gene

MalaCards: The human disease database

(1) MalaCards diseases for RPRD1B Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
retroperitoneal leiomyosarcoma
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for RPRD1B

genes like me logo Genes that share disorders with RPRD1B: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RPRD1B Gene

Publications for RPRD1B Gene

  1. Control of the RNA polymerase II phosphorylation state in promoter regions by CTD interaction domain-containing proteins RPRD1A and RPRD1B. (PMID: 22231121) Ni Z … Greenblatt JF (Transcription 2011) 2 3 4 58
  2. RPRD1A and RPRD1B are human RNA polymerase II C-terminal domain scaffolds for Ser5 dephosphorylation. (PMID: 24997600) Ni Z … Greenblatt JF (Nature structural & molecular biology 2014) 3 4 58
  3. CREPT accelerates tumorigenesis by regulating the transcription of cell-cycle-related genes. (PMID: 22264791) Lu D … Chang Z (Cancer cell 2012) 3 4 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for RPRD1B Gene

Sources for RPRD1B Gene

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