Human Gene RBBP5 (ENST00000264515.11_11) from GENCODE V47lift37

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Description: RB binding protein 5, histone lysine methyltransferase complex subunit, transcript variant 1 (from RefSeq NM_005057.4)
Gencode Transcript: ENST00000264515.11_11
Gencode Gene: ENSG00000117222.14_13
Transcript (Including UTRs)
Position: hg19 chr1:205,055,270-205,091,106 Size: 35,837 Total Exon Count: 14 Strand: -
Coding Region
Position: hg19 chr1:205,057,915-205,091,001 Size: 33,087 Coding Exon Count: 14

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	CTD
Gene Alleles	RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species
GO Annotations	mRNA Descriptions	Pathways	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr1:205,055,270-205,091,106)			mRNA (may differ from genome)		Protein (538 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	Malacards	MGI	OMIM	PubMed	Reactome
UniProtKB	Wikipedia	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: RBBP5_HUMAN DESCRIPTION: RecName: Full=Retinoblastoma-binding protein 5; Short=RBBP-5; AltName: Full=Retinoblastoma-binding protein RBQ-3; FUNCTION: In embryonic stem (ES) cells, plays a crucial role in the differentiation potential, particularly along the neural lineage, regulating gene induction and H3 'Lys-4' methylation at key developmental loci, including that mediated by retinoic acid (By similarity). As part of the MLL1/MLL complex, involved in mono-, di- and trimethylation at 'Lys-4' of histone H3. Histone H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. SUBUNIT: Component of the SET1 complex, at least composed of the catalytic subunit (SETD1A or SETD1B), WDR5, WDR82, RBBP5, ASH2L/ASH2, CXXC1/CFP1, HCFC1 and DPY30. Core component of several methyltransferase-containing complexes including MLL1/MLL, MLL2/3 (also named ASCOM complex) and MLL4/WBP7. Each complex is at least composed of ASH2L, RBBP5, WDR5, DPY30, one or more specific histone methyltransferases (MLL, MLL2/ALR, MLL3 and MLL4/WBP7), and the facultative components PAGR1, C17orf49, CHD8, E2F6, HCFC1, HCFC2, HSP70, INO80C, KDM6A, KANSL1, LAS1L, MAX, MCRS1, MEN1, MGA, MYST1/MOF, NCOA6, PAXIP1/PTIP, PELP1, PHF20, PRP31, RING2, RUVB1/TIP49A, RUVB2/TIP49B, SENP3, TAF1, TAF4, TAF6, TAF7, TAF9, TEX10 and alpha- and beta-tubulin. Interacts with WDR5 and ASH2L; the interaction is direct. Interacts with WDR82 and SETD1A. INTERACTION: Q9UBL3:ASH2L; NbExp=11; IntAct=EBI-592823, EBI-540797; Q13619:CUL4A; NbExp=3; IntAct=EBI-592823, EBI-456106; Q03164:MLL; NbExp=4; IntAct=EBI-592823, EBI-591370; P61964:WDR5; NbExp=6; IntAct=EBI-592823, EBI-540834; SUBCELLULAR LOCATION: Nucleus. TISSUE SPECIFICITY: Ubiquitously expressed. PTM: Phosphorylated upon DNA damage, probably by ATM or ATR. SIMILARITY: Contains 6 WD repeats.

Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

MalaCards Disease Associations


	MalaCards Gene Search: RBBP5 Diseases sorted by gene-association score: retinoblastoma (16), kabuki syndrome 1 (5)

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D019327 Copper Sulfate D015632 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine D015655 1-Methyl-4-phenylpyridinium C009505 4,4'-diaminodiphenylmethane D000082 Acetaminophen D001564 Benzo(a)pyrene D002110 Caffeine D002994 Clofibrate D003630 Daunorubicin D008769 Methylnitronitrosoguanidine more ... click here to view the complete list

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 8.20 RPKM in Cells - EBV-transformed lymphocytes Total median expression: 218.39 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

Microarray Expression Data


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mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-35.10	105	-0.334	Picture	PostScript	Text
3' UTR	-755.50	2645	-0.286	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
IPR015943 - WD40/YVTN_repeat-like_dom
IPR001680 - WD40_repeat
IPR017986 - WD40_repeat_dom

Pfam Domains:
PF00400 - WD domain, G-beta repeat

SCOP Domains:
50952 - Soluble quinoprotein glucose dehydrogenase
50956 - Thermostable phytase (3-phytase)
50960 - TolB, C-terminal domain
63825 - YWTD domain
63829 - Calcium-dependent phosphotriesterase
69304 - Tricorn protease N-terminal domain
101898 - NHL repeat
50965 - Galactose oxidase, central domain
75011 - 3-carboxy-cis,cis-mucoante lactonizing enzyme
101908 - Putative isomerase YbhE
117289 - Nucleoporin domain
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50974 - Nitrous oxide reductase, N-terminal domain
50978 - WD40 repeat-like
50993 - Peptidase/esterase 'gauge' domain
69322 - Tricorn protease domain 2
50998 - Quinoprotein alcohol dehydrogenase-like
51004 - C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
82171 - DPP6 N-terminal domain-like

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

3P4F - X-ray MuPIT

ModBase Predicted Comparative 3D Structure on Q15291


Front	Top	Side

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	Genome Browser	No ortholog
Gene Details	Gene Details		Gene Details	Gene Details
Gene Sorter	Gene Sorter		Gene Sorter	Gene Sorter
	RGD	Ensembl		WormBase
				Protein Sequence
				Alignment

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0005515 protein binding GO:0018024 histone-lysine N-methyltransferase activity GO:0035064 methylated histone binding GO:0044212 transcription regulatory region DNA binding GO:0042800 histone methyltransferase activity (H3-K4 specific) Biological Process: GO:0006325 chromatin organization GO:0006351 transcription, DNA-templated GO:0006355 regulation of transcription, DNA-templated GO:0006974 cellular response to DNA damage stimulus GO:0043627 response to estrogen GO:0043687 post-translational protein modification GO:0045652 regulation of megakaryocyte differentiation GO:0051568 histone H3-K4 methylation GO:1904837 beta-catenin-TCF complex assembly Cellular Component: GO:0005634 nucleus GO:0005654 nucleoplasm GO:0005730 nucleolus GO:0035097 histone methyltransferase complex GO:0044666 MLL3/4 complex GO:0048188 Set1C/COMPASS complex GO:0071339 MLL1 complex

Descriptions from all associated GenBank mRNAs


	BC037284 - Homo sapiens retinoblastoma binding protein 5, mRNA (cDNA clone MGC:33095 IMAGE:5266066), complete cds. JD087767 - Sequence 68791 from Patent EP1572962. JD440966 - Sequence 421990 from Patent EP1572962. JD481437 - Sequence 462461 from Patent EP1572962. JD512705 - Sequence 493729 from Patent EP1572962. JD412749 - Sequence 393773 from Patent EP1572962. JD212394 - Sequence 193418 from Patent EP1572962. DQ594320 - Homo sapiens piRNA piR-60432, complete sequence. X85134 - H.sapiens RBQ-3 mRNA. BC053856 - Homo sapiens retinoblastoma binding protein 5, mRNA (cDNA clone MGC:61473 IMAGE:5576406), complete cds. JD221364 - Sequence 202388 from Patent EP1572962. JD517197 - Sequence 498221 from Patent EP1572962. JD318906 - Sequence 299930 from Patent EP1572962. JD447279 - Sequence 428303 from Patent EP1572962. JD144398 - Sequence 125422 from Patent EP1572962. JD058373 - Sequence 39397 from Patent EP1572962. JD430551 - Sequence 411575 from Patent EP1572962. JD430550 - Sequence 411574 from Patent EP1572962. JD257069 - Sequence 238093 from Patent EP1572962. JD514978 - Sequence 496002 from Patent EP1572962. JD060426 - Sequence 41450 from Patent EP1572962. JD316295 - Sequence 297319 from Patent EP1572962. JD238305 - Sequence 219329 from Patent EP1572962. JD135714 - Sequence 116738 from Patent EP1572962. JD378217 - Sequence 359241 from Patent EP1572962. JD052720 - Sequence 33744 from Patent EP1572962. JD486285 - Sequence 467309 from Patent EP1572962. JD545434 - Sequence 526458 from Patent EP1572962. JD524215 - Sequence 505239 from Patent EP1572962. JD510502 - Sequence 491526 from Patent EP1572962. JD281022 - Sequence 262046 from Patent EP1572962. JD160591 - Sequence 141615 from Patent EP1572962. JD208871 - Sequence 189895 from Patent EP1572962. JD159057 - Sequence 140081 from Patent EP1572962. JD511534 - Sequence 492558 from Patent EP1572962. JD286694 - Sequence 267718 from Patent EP1572962. JD144702 - Sequence 125726 from Patent EP1572962. JD395784 - Sequence 376808 from Patent EP1572962. JD231963 - Sequence 212987 from Patent EP1572962. JD315425 - Sequence 296449 from Patent EP1572962. JD172385 - Sequence 153409 from Patent EP1572962. JD299752 - Sequence 280776 from Patent EP1572962. JD252838 - Sequence 233862 from Patent EP1572962. JD061319 - Sequence 42343 from Patent EP1572962. JD375135 - Sequence 356159 from Patent EP1572962. JD320223 - Sequence 301247 from Patent EP1572962. JD434220 - Sequence 415244 from Patent EP1572962. JD559747 - Sequence 540771 from Patent EP1572962. JD114380 - Sequence 95404 from Patent EP1572962. JD042723 - Sequence 23747 from Patent EP1572962. JD297802 - Sequence 278826 from Patent EP1572962. JD438668 - Sequence 419692 from Patent EP1572962. JD336949 - Sequence 317973 from Patent EP1572962. AK290137 - Homo sapiens cDNA FLJ75510 complete cds, highly similar to Homo sapiens retinoblastoma binding protein 5, mRNA. AK296978 - Homo sapiens cDNA FLJ60295 complete cds, highly similar to Retinoblastoma-binding protein 5. JD440036 - Sequence 421060 from Patent EP1572962. JD174100 - Sequence 155124 from Patent EP1572962. AK297540 - Homo sapiens cDNA FLJ59722 complete cds, highly similar to Retinoblastoma-binding protein 5. JD301550 - Sequence 282574 from Patent EP1572962. JD111252 - Sequence 92276 from Patent EP1572962. JD101788 - Sequence 82812 from Patent EP1572962. JD528717 - Sequence 509741 from Patent EP1572962. BC075059 - Homo sapiens retinoblastoma binding protein 5, mRNA (cDNA clone MGC:104129 IMAGE:30915584), complete cds. BC075060 - Homo sapiens retinoblastoma binding protein 5, mRNA (cDNA clone MGC:103967 IMAGE:30915368), complete cds. DQ891205 - Synthetic construct clone IMAGE:100003835; FLH170144.01X; RZPDo839C0398D retinoblastoma binding protein 5 (RBBP5) gene, encodes complete protein. DQ894388 - Synthetic construct Homo sapiens clone IMAGE:100008848; FLH170140.01L; RZPDo839C0397D retinoblastoma binding protein 5 (RBBP5) gene, encodes complete protein. KJ897454 - Synthetic construct Homo sapiens clone ccsbBroadEn_06848 RBBP5 gene, encodes complete protein. AB527310 - Synthetic construct DNA, clone: pF1KB9771, Homo sapiens RBBP5 gene for retinoblastoma binding protein 5, without stop codon, in Flexi system. CU691040 - Synthetic construct Homo sapiens gateway clone IMAGE:100021743 5' read RBBP5 mRNA. JD476332 - Sequence 457356 from Patent EP1572962.

Biochemical and Signaling Pathways


	Reactome (by CSHL, EBI, and GO) Protein Q15291 (Reactome details) participates in the following event(s): R-HSA-3364014 Recruitment of SET1 methyltransferase complex R-HSA-8935740 RUNX1 and GATA1 bind the promoter of the ITGA2B gene R-HSA-8936616 RUNX1 and GATA1 bind the promoter of the GP1BA gene R-HSA-8936979 RUNX1 and GATA1 bind the promoter of the THBS1 gene R-HSA-8937037 RUNX1 and GATA1 bind the promoter of the MIR27A gene R-HSA-3364026 SET1 complex trimethylates H3K4 at the MYC gene R-HSA-8955245 CAND1 binds CRL4 E3 ubiquitin ligase in the nucleus R-HSA-8936481 Core MLL complex methylates H3K4Me2-Nucleosome at the ITGA2B gene promoter R-HSA-8936621 Core MLL complex methylates H3K4Me2-Nucleosome at the GP1BA gene promoter R-HSA-8937016 Core MLL complex methylates H3K4Me2-Nucleosome at the THBS1 gene promoter R-HSA-8937050 Core MLL complex methylates H3K4Me2-Nucleosome at the MIR27A gene promoter R-HSA-5159245 SETD3, SETD7 (KMT7), WHSC1L1 (KMT3F), Core MLL complex methylate lysine-5 of histone H3 (H3K4) R-HSA-5244692 Core MLL complex, SMYD3, PRDM9 methylate dimethyl-lysine-5 of histone H3 (H3K4) R-HSA-5637686 WHSC1L1 (KMT3F), Core MLL complex, SMYD3 (KMT3E) methylate methyl-lysine-5 of histone H3 (H3K4) R-HSA-8955285 COMMDs displace CAND1 from CRL4 E3 ubiquitin ligase complex R-HSA-8952639 NEDD8:AcM-UBE2M binds CRL4 E3 ubiquitin ligase complex R-HSA-8956045 COP9 signalosome deneddylates nuclear CRL4 E3 ubiquitin ligase complex R-HSA-8952638 AcM-UBE2M transfers NEDD8 to CRL4 E3 ubiquitin ligase complex R-HSA-201722 Formation of the beta-catenin:TCF transactivating complex R-HSA-3769402 Deactivation of the beta-catenin transactivating complex R-HSA-8936459 RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function R-HSA-5617472 Activation of anterior HOX genes in hindbrain development during early embryogenesis R-HSA-201681 TCF dependent signaling in response to WNT R-HSA-8878171 Transcriptional regulation by RUNX1 R-HSA-5619507 Activation of HOX genes during differentiation R-HSA-8951664 Neddylation R-HSA-195721 Signaling by WNT R-HSA-3214841 PKMTs methylate histone lysines R-HSA-212436 Generic Transcription Pathway R-HSA-1266738 Developmental Biology R-HSA-597592 Post-translational protein modification R-HSA-162582 Signal Transduction R-HSA-3247509 Chromatin modifying enzymes R-HSA-73857 RNA Polymerase II Transcription R-HSA-392499 Metabolism of proteins R-HSA-4839726 Chromatin organization R-HSA-74160 Gene expression (Transcription)

Other Names for This Gene


	Alternate Gene Symbols: A8K272, ENST00000264515.1, ENST00000264515.10, ENST00000264515.2, ENST00000264515.3, ENST00000264515.4, ENST00000264515.5, ENST00000264515.6, ENST00000264515.7, ENST00000264515.8, ENST00000264515.9, NM_005057, Q15291, Q7Z6D8, Q8NDZ7, RBBP5_HUMAN, RBQ3, uc317hta.1, uc317hta.2 UCSC ID: ENST00000264515.11_11 RefSeq Accession: NM_005057.4 Protein: Q15291 (aka RBBP5_HUMAN or RBB5_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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