EuRBPDB

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TCGA tumor abbreviations
  • ACCAdrenocortical carcinoma
  • BLCABladder Urothelial Carcinoma
  • BRCABreast invasive carcinoma
  • CESCCervical squamous cell carcinoma and endocervical adenocarcinoma
  • CHOLCholangio carcinoma
  • COADColon adenocarcinoma
  • DLBCLymphoid Neoplasm Diffuse Large B-cell Lymphoma
  • ESCAEsophageal carcinoma
  • GBMGlioblastoma multiforme
  • HNSCHead and Neck squamous cell carcinoma
  • KICHKidney Chromophobe
  • KIRCKidney renal clear cell carcinoma
  • KIRPKidney renal papillary cell carcinoma
  • LAMLAcute Myeloid Leukemia
  • LGGBrain Lower Grade Glioma
  • LIHCLiver hepatocellular carcinoma
  • LUADLung adenocarcinoma
  • LUSCLung squamous cell carcinoma
  • MESOMesothelioma
  • OVOvarian serous cystadenocarcinoma
  • PAADPancreatic adenocarcinoma
  • PCPGPheochromocytoma and Paraganglioma
  • PRADProstate adenocarcinoma
  • READRectum adenocarcinoma
  • SARCSarcoma
  • SKCMSkin Cutaneous Melanoma
  • STADStomach adenocarcinoma
  • TGCTThyroid carcinoma
  • THCAThyroid carcinoma
  • THYMThymoma
  • UCECUterine Corpus Endometrial Carcinoma
  • UCSUterine Carcinosarcoma
  • UVMUveal Melanoma

Note: Click here to get the extension of tumor abbreviations.


  • Cancer Related Information
  • Basic Information

Cancer associated literatures
PIDTitleArticle TimeAuthorDoi
17616526RbAp48 is a critical mediator controlling the transforming activity of human papillomavirus type 16 in cervical cancer.J Biol Chem2007 Sep 7Kong L-
14966907Genes encoding Pir51, Beclin 1, RbAp48 and aldolase b are up or down-regulated in human primary hepatocellular carcinoma.World J Gastroenterol2004 Feb 15Song H-
17244783RbAp48 is a target of nuclear factor-kappaB activity in thyroid cancer.J Clin Endocrinol Metab2007 AprPacifico F-
18577416The role of retinoblastoma-associated proteins 46 and 48 in estrogen receptor alpha mediated gene expression.Mol Cell Endocrinol2008 Sep 10Creekmore ALdoi: 10.1016/j.mce.2008.05.016
29901205Overexpression of retinoblastomabinding protein 4 contributes to the radiosensitivity of AGS gastric cancer cells via phosphoinositide3kinase/protein kinase B pathway suppression.Mol Med Rep2018 AugJin Xdoi: 10.3892/mmr.2018.9153

Expression in 33 cancers

Mutations
CancerChrPosition Mutation TypedbSNPProtein-change Allele FreqRBD
BLCAchr132668778Missense_MutationnovelG175E0.41
BLCAchr132668845SilentnovelS197S0.24
BLCAchr132669088SilentNAH239H0.42
BLCAchr1326842313'UTRrs7493317230.18
BLCAchr132652005Missense_MutationnovelM36I0.06
BLCAchr132672498Missense_MutationNAD339N0.4
BLCAchr1326838533'UTRnovel0.15
BLCAchr132672829SilentNAF380F0.14
BLCAchr132672691Missense_MutationnovelE365K0.29
BLCAchr132679705Nonstop_Mutationnovel*426Yext*70.14
BRCAchr132657469SilentNAG69G0.16
BRCAchr132651948SilentNAI17I0.19
BRCAchr1326797963'UTRnovel0.18
BRCAchr1326797983'UTRnovel0.16
BRCAchr1326809073'UTRnovel0.32
BRCAchr1326803263'UTRnovel0.28
BRCAchr132672883SilentNAI398I0.32
BRCAchr1326819673'UTRnovel0.08
BRCAchr132651948SilentNAI17I0.2
BRCAchr1326843913'UTRnovel0.28
BRCAchr132669492Missense_MutationnovelA299S0.04
CESCchr1326816863'UTRnovel0.45
CESCchr1326811903'UTRnovel0.39
CESCchr1326819013'UTRnovel0.21
CESCchr1326810993'UTRnovel0.08
CESCchr1326808763'UTRnovel0.13
CESCchr1326819933'UTRnovel0.23
CESCchr132679658Missense_MutationNAD411H0.42
CESCchr1326816393'UTRnovel0.24
CHOLchr1326805643'UTRnovel0.29
COADchr1326845513'UTRnovel0.54
COADchr132679678SilentnovelS417S0.35
COADchr1326844583'UTRnovel0.24
COADchr1326805133'UTRnovel0.2
COADchr132672654Missense_MutationNAE352D0.3
COADchr132651988Missense_MutationnovelL31I0.07
COADchr132679645Missense_MutationnovelE406D0.06
COADchr132672797Missense_MutationNAH370N0.35
COADchr1326807593'UTRnovel0.11
COADchr1326807613'UTRnovel0.1
COADchr1326512555'UTRnovel0.7
COADchr132657546Missense_Mutationrs773549765A95V0.32
ESCAchr132672468Missense_MutationnovelN329Y0.17
ESCAchr132668997Missense_MutationnovelA209V0.25
ESCAchr1326805133'UTRnovel0.41
GBMchr132669232Missense_MutationNAW255G0.35
GBMchr1326841013'UTRnovel0.21
HNSCchr132672682Missense_MutationnovelG362R0.12
HNSCchr1326838163'UTRnovel0.12
HNSCchr1326844453'UTRnovel0.73
HNSCchr132679658Missense_MutationnovelD411N0.38
HNSCchr1326816503'UTRnovel0.33
KICHchr1326805133'UTRnovel0.04
KIRCchr1326819013'UTRnovel0.47
KIRCchr132672832SilentnovelS381S0.12
KIRCchr1326819853'UTRnovel0.07
KIRPchr1326844593'UTRnovel0.29
LAMLchr132672471Missense_Mutationrs766075227E330K0.42
LAMLchr132672471Missense_Mutationrs766075227E330K0.16
LGGchr132668233Missense_MutationnovelG107C0.24
LGGchr132679705Nonstop_Mutationnovel*426Yext*70.41
LIHCchr132668834Missense_MutationnovelL194F0.22
LUADchr1326841413'UTRnovel0.25
LUADchr1326844843'UTRnovel0.75
LUADchr132672666SilentnovelP356P0.13
LUADchr132668271SilentNAI119I0.17
LUADchr1326838193'UTRnovel0.2
LUADchr1326797733'UTRnovel0.15
LUADchr1326819853'UTRnovel0.38
LUSCchr132669316Missense_MutationNAP283S0.31
LUSCchr132672525Missense_MutationnovelS348C0.25
OVchr1326841463'UTRnovel0.05
OVchr132669337Missense_MutationnovelA290T0.28
OVchr132651419Intronnovel0.07
OVchr1326819413'UTRnovel0.4
OVchr132657507Missense_MutationNAA82D0.5
PAADchr1326819203'UTRnovel0.16
PAADchr1326839353'UTRnovel0.21
PRADchr132657546Missense_Mutationrs773549765A95V0.4
READchr1326817643'UTRnovel0.37
SARCchr132669117Missense_MutationnovelD249V0.89
SARCchr1326810533'UTRnovel0.15
SKCMchr132652040Missense_MutationNAQ48R0.23
SKCMchr132669533SilentNAS312S0.93
SKCMchr132668851SilentNAD199D0.07
SKCMchr132669085SilentNAL238L0.17
SKCMchr132672891Missense_MutationNAV401A0.17
SKCMchr132672501Missense_MutationNAR340C0.78
SKCMchr132672834Nonsense_MutationNAW382*0.34
SKCMchr1326841443'UTRnovel0.21
STADchr132668826Missense_MutationNAG191V0.11
STADchr132669133Splice_SitenovelX254_splice0.05
STADchr132668332Missense_MutationNAI140V0.23
STADchr132668799Missense_MutationNAG182E0.28
STADchr132669015Missense_Mutationrs77147900K215R0.13
STADchr132668850Missense_MutationNAD199G0.31
STADchr1326819963'UTRnovel0.29
STADchr1326839293'UTRrs7527841020.22
STADchr132652006Missense_MutationNAT37A0.23
STADchr1326817803'UTRnovel0.34
STADchr1326845833'UTRnovel0.67
TGCTchr1326512465'UTRrs3708250900.19
THCAchr132657431Missense_MutationNAE57K0.06
THCAchr1326819853'UTRnovel0.17
UCECchr132669111Missense_MutationNAA247V0.36
UCECchr1326818833'UTRnovel0.34
UCECchr1326801403'UTRnovel0.16
UCECchr1326805493'UTRnovel0.45
UCECchr132657550SilentnovelS96S0.15
UCECchr1326845343'UTRnovel0.19
UCECchr1326841853'UTRnovel0.16
UCECchr1326797123'UTRnovel0.4
UCECchr132672864Missense_MutationNAS392F0.21
UCECchr132669111Missense_MutationNAA247D0.35
UCECchr132668834Missense_MutationnovelL194I0.17
UCECchr132679702SilentnovelS425S0.19
UCECchr1326803303'UTRnovel0.32
UCECchr132679678SilentnovelS417S0.07
UCECchr1326845523'UTRnovel0.15
UCECchr132669508Missense_MutationnovelR304I0.2
UCECchr1326802233'UTRnovel0.38
UCECchr132672514Missense_MutationnovelV344G0.56
UCECchr1326816863'UTRnovel0.54
UCECchr1326810203'UTRnovel0.58
UCECchr132668386Missense_MutationnovelP158S0.27
UCECchr132672654Missense_MutationNAE352D0.25
UCECchr1326806973'UTRnovel0.23
UCECchr1326818813'UTRnovel0.26
UCECchr1326807663'UTRnovel0.41
UCECchr132657455Nonsense_MutationnovelR65*0.45
UCECchr1326811243'UTRnovel0.53
UCECchr1326797863'UTRnovel0.08
UCECchr1326818903'UTRnovel0.06
UCECchr132651930SilentNAA11A0.39
UCECchr1326803393'UTRnovel0.6
UCECchr1326797993'UTRnovel0.44
UCECchr1326841113'UTRnovel0.4
UCECchr1326811033'UTRnovel0.26
UCECchr1326819483'UTRnovel0.4
UCECchr132679657In_Frame_InsnovelD411_E421dup0.29
UCECchr132651954Missense_MutationnovelE19D0.21
UCECchr132657481Silentrs768938293S73S0.1
UCECchr1326838683'UTRnovel0.19
UCECchr132668738Splice_SitenovelX162_splice0.43
UCECchr132657570Missense_MutationnovelG103E0.24
UCECchr132672822Missense_MutationnovelS378Y0.18
UCECchr1326819553'UTRnovel0.24
UCECchr1326838223'UTRnovel0.5
UCECchr1326838633'UTRnovel0.13
UCECchr1326838653'UTRnovel0.21
UCECchr1326841983'UTRnovel0.03
UCECchr132669027Missense_MutationnovelA219V0.25
UCECchr1326798723'UTRnovel0.43
UCECchr1326803393'UTRnovel0.7
UCECchr132668832Nonsense_MutationnovelL193*0.1
UCECchr132668768Missense_MutationnovelR172C0.27
UCECchr1326818993'UTRnovel0.54
UCECchr132672682Missense_MutationnovelG362R0.38
UCECchr1326805433'UTRnovel0.32
UCECchr1326810773'UTRnovel0.43

Copy Number Variations (CNVs)
CancerTypeFreq Q-value
DLBCDEL0.1250.011841
LIHCDEL0.31891.6679e-20
TGCTDEL0.140.00046313

Survival Analysis
CancerP-value Q-value
THYM0.0056

Kaplan-Meier Survival Analysis

STAD0.0043

Kaplan-Meier Survival Analysis

SARC0.00027

Kaplan-Meier Survival Analysis

MESO0.031

Kaplan-Meier Survival Analysis

ACC0.00088

Kaplan-Meier Survival Analysis

BRCA0.009

Kaplan-Meier Survival Analysis

KIRP0.031

Kaplan-Meier Survival Analysis

COAD0.042

Kaplan-Meier Survival Analysis

BLCA0.015

Kaplan-Meier Survival Analysis

CESC0.0024

Kaplan-Meier Survival Analysis

KICH0.043

Kaplan-Meier Survival Analysis

GBM0.02

Kaplan-Meier Survival Analysis

LIHC0.0001

Kaplan-Meier Survival Analysis

LGG0.00011

Kaplan-Meier Survival Analysis

LUAD0.0054

Kaplan-Meier Survival Analysis

Drugs

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Eesembl ID



Cell lines and drugs in GSE70138 or GSE92742

  • Description
  • RBPome
  • Expression
  • Transcripts
  • Gene Model
  • Pathways
  • Phenotypes
  • PPI
  • Gene Ontology
Description
Ensembl ID
ENSG00000162521 (Gene tree)
Gene ID
5928
Gene Symbol
RBBP4
Alias
RbAp48|NURF55|lin-53
Full Name
RB binding protein 4, chromatin remodeling factor
Gene Type
protein_coding
Species
Homo_sapiens
Status
putative
Strand
Plus strand
Length
35,070 bases
Position
chr1:32,651,142-32,686,211
Accession
9887
RBP type
non-canonical RBP
Summary
This gene encodes a ubiquitously expressed nuclear protein which belongs to a highly conserved subfamily of WD-repeat proteins. It is present in protein complexes involved in histone acetylation and chromatin assembly. It is part of the Mi-2 complex which has been implicated in chromatin remodeling and transcriptional repression associated with histone deacetylation. This encoded protein is also part of co-repressor complexes, which is an integral component of transcriptional silencing. It is found among several cellular proteins that bind directly to retinoblastoma protein to regulate cell proliferation. This protein also seems to be involved in transcriptional repression of E2F-responsive genes. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2008]
RNA binding proteome (RBPome)
PIDTitleMethod TimeAuthorDoi
30607034Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)OOPS & HEK2932019 Jan 3Queiroz RMLDOI: 10.1038/s41587-018-0001-2
30607034Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)OOPS & MCF10A2019 Jan 3Queiroz RMLDOI: 10.1038/s41587-018-0001-2
30607034Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)OOPS & U2OS2019 Jan 3Queiroz RMLDOI: 10.1038/s41587-018-0001-2
30352994Discovery of RNA-binding proteins and characterization of their dynamic responses by enhanced RNA interactome captureRIC & Jurkat2018 Oct 23Perez-Perri JIDOI:10.1038/s41467-018-06557-8
Expression
Transcripts
Transcript IDNameLengthRefSeq ID Protein IDLengthRefSeq IDUniportKB ID
ENST00000477563RBBP4-211544-ENSP00000432774104 (aa)-E9PNS6
ENST00000492348RBBP4-2141547-ENSP0000043666387 (aa)-E9PIC4
ENST00000401893RBBP4-203762--- (aa)--
ENST00000527118RBBP4-218700-ENSP0000043278062 (aa)-E9PNS2
ENST00000458695RBBP4-2061674-ENSP00000396057390 (aa)-Q09028
ENST00000490500RBBP4-213632-ENSP0000043721068 (aa)-E9PND5
ENST00000414241RBBP4-2041788-ENSP00000398242424 (aa)-Q09028
ENST00000373485RBBP4-2011417-ENSP00000362584410 (aa)-Q09028
ENST00000463378RBBP4-208882-ENSP00000433805262 (aa)-H0YDK2
ENST00000482190RBBP4-212616-ENSP00000436565167 (aa)-H0YEU5
ENST00000373493RBBP4-2027943-ENSP00000362592425 (aa)-Q09028
ENST00000526193RBBP4-217568-ENSP0000043492587 (aa)-E9PIC4
ENST00000525506RBBP4-216501--- (aa)--
ENST00000475321RBBP4-210619-ENSP00000436986207 (aa)-H0YF10
ENST00000460669RBBP4-207783-ENSP00000432298180 (aa)-H0YCT5
ENST00000445722RBBP4-205580-ENSP0000038943787 (aa)-C9JPP3
ENST00000524393RBBP4-215583--- (aa)--
ENST00000531983RBBP4-219473--- (aa)--
ENST00000465780RBBP4-209690--- (aa)--
Gene Model
Click here to download ENSG00000162521's gene model file
Pathways
Pathway IDPathway NameSource
hsa04218Cellular senescenceKEGG
Phenotypes
ensgIDTraitpValuePubmed ID
ENSG00000162521Coronary Disease2.2710000E-005-
Protein-Protein Interaction (PPI)

Clik here to download ENSG00000162521's network

* RBP PPI network refers to all genes directly bind to RBP
Gene Ontology
Go IDGo_termPubmedIDEvidenceCategory
GO:0000790nuclear chromatin16217013.HDAComponent
GO:0000790nuclear chromatin14718166.IDAComponent
GO:0000978RNA polymerase II proximal promoter sequence-specific DNA binding16217013.HDAFunction
GO:0000980RNA polymerase II distal enhancer sequence-specific DNA binding16217013.HDAFunction
GO:0005515protein binding7503932.9150135.10220385.14609955.19703393.20127688.21047798.21258344.22720776.23752268.25416956.27705803.IPIFunction
GO:0005634nucleus14609955.IDAComponent
GO:0005654nucleoplasm22720776.IDAComponent
GO:0005654nucleoplasm-TASComponent
GO:0005829cytosol-IDAComponent
GO:0006260DNA replication-IEAProcess
GO:0006335DNA replication-dependent nucleosome assembly14718166.IDAProcess
GO:0006336DNA replication-independent nucleosome assembly14718166.IDAProcess
GO:0006338chromatin remodeling14609955.IDAProcess
GO:0007049cell cycle-IEAProcess
GO:0008094DNA-dependent ATPase activity14609955.IDAFunction
GO:0008285negative regulation of cell proliferation8350924.TASProcess
GO:0016580Sin3 complex17827154.NASComponent
GO:0016581NuRD complex19644445.22926524.IDAComponent
GO:0016581NuRD complex17827154.NASComponent
GO:0016589NURF complex20850016.IDAComponent
GO:0031492nucleosomal DNA binding16217013.HDAFunction
GO:0031497chromatin assembly8858152.IDAProcess
GO:0032991protein-containing complex16217013.HDAComponent
GO:0032991protein-containing complex14718166.IDAComponent
GO:0033186CAF-1 complex8858152.IDAComponent
GO:0034080CENP-A containing nucleosome assembly-TASProcess
GO:0035098ESC/E(Z) complex20075857.23104054.23273982.IDAComponent
GO:0042393histone binding17827154.NASFunction
GO:0042826histone deacetylase binding17827154.IPIFunction
GO:0043044ATP-dependent chromatin remodeling16217013.HDAProcess
GO:0045814negative regulation of gene expression, epigenetic-TASProcess
GO:0051726regulation of cell cycle-TASProcess
GO:0060416response to growth hormone-IEAProcess
GO:0070317negative regulation of G0 to G1 transition-TASProcess
GO:1901796regulation of signal transduction by p53 class mediator-TASProcess
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