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KDM5B (lysine demethylase 5B)

Gene
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.
10765
Gene nameGene Name - the full gene name approved by the HGNC.
Lysine demethylase 5B
Gene symbolGene Symbol - the official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name.
KDM5B
SynonymsGene synonyms aliases
CT31, JARID1B, MRT65, PLU-1, PLU1, PPP1R98, PUT1, RBBP2H1A, RBP2-H1
ChromosomeChromosome number
1
Chromosome locationChromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
1q32.1
SummarySummary of gene provided in NCBI Entrez Gene.
This gene encodes a lysine-specific histone demethylase that belongs to the jumonji/ARID domain-containing family of histone demethylases. The encoded protein is capable of demethylating tri-, di- and monomethylated lysine 4 of histone H3. This protein pl
SNPsSNP information provided by dbSNP.
SNP ID Visualize variation Clinical significance Consequence
rs375695605 G>A,C Pathogenic Coding sequence variant, missense variant
rs755833290 AA>-,AAA Likely-pathogenic Frameshift variant, coding sequence variant
rs1558478047 A>C Likely-pathogenic Stop gained, coding sequence variant
rs1558479778 G>- Pathogenic Frameshift variant, coding sequence variant
rs1558498928 G>A Likely-pathogenic Stop gained, coding sequence variant
miRNAmiRNA information provided by mirtarbase database.
miRTarBase ID miRNA Experiments Reference
MIRT016728 hsa-miR-335-5p Microarray 18185580
MIRT020412 hsa-miR-29c-3p Sequencing 20371350
MIRT046553 hsa-let-7i-5p CLASH 23622248
MIRT038506 hsa-miR-296-3p CLASH 23622248
MIRT656976 hsa-miR-766-3p HITS-CLIP 23824327
Gene ontology (GO)Gene ontology information of associated ontologies with gene provided by GO database.
GO ID Ontology Definition Evidence Reference
GO:0003677 Function DNA binding IDA 15640446
GO:0003714 Function Transcription corepressor activity IDA 12657635
GO:0005515 Function Protein binding IPI 12657635, 24937458
GO:0005634 Component Nucleus IBA 21873635
GO:0005634 Component Nucleus IDA 20403335
Other IDsOther ids provides unique ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
MIM
HGNC
e!Ensembl
Protein
UniProt ID Q9UGL1
Protein name Lysine-specific demethylase 5B (EC 1.14.11.67) (Cancer/testis antigen 31) (CT31) (Histone demethylase JARID1B) (Jumonji/ARID domain-containing protein 1B) (PLU-1) (Retinoblastoma-binding protein 2 homolog 1) (RBP2-H1) ([histone H3]-trimethyl-L-lysine(4) d
Protein function Histone demethylase that demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code (PubMed:24952722, PubMed:27214403, PubMed:28262558). Does not demethylate histone H3 'Lys-9' or H3 'Lys-27'. Demethylates trimethylated,
PDB 2MA5 , 2MNY , 2MNZ , 5A1F , 5A3N , 5A3P , 5A3T , 5A3W , 5FPL , 5FPU , 5FUN , 5FUP , 5FV3 , 5FY4 , 5FY5 , 5FY9 , 5FYB , 5FYS , 5FYT , 5FYU , 5FYV , 5FYY , 5FYZ , 5FZ0 , 5FZ1 , 5FZ3 , 5FZ4 , 5FZ6 , 5FZ7 , 5FZ8 , 5FZ9 , 5FZA , 5FZB , 5FZC , 5FZD , 5FZE , 5FZF , 5FZG , 5FZH , 5FZI , 5FZK , 5FZL , 5FZM , 5LW9 , 5LWB , 6EIN , 6EIU , 6EIY , 6EJ0 , 6EJ1 , 6EK6
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF02375 JmjN
33 66
jmjN domain
Family
PF01388 ARID
99 183
ARID/BRIGHT DNA binding domain
Domain
PF00628 PHD
311 359
PHD-finger
Domain
PF02373 JmjC
486 602
JmjC domain, hydroxylase
Domain
PF02928 zf-C5HC2
692 744
C5HC2 zinc finger
Domain
PF08429 PLU-1
757 1088
PLU-1-like protein
Family
PF00628 PHD
1178 1224
PHD-finger
Domain
PF00628 PHD
1486 1538
PHD-finger
Domain
Sequence
MEAATTLHPGPRPALPLGGPGPLGEFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTG
ICKVRP
PPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKLNFLDQIAKYWELQGSTLKI
PHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGKAVGSHIRGHYERILN
PYN
LFLSGDSLRCLQKPNLTTDTKDKEYKPHDIPQRQSVQPSETCPPARRAKRMRAEAMN
IKIEPEETTEARTHNLRRRMGCPTPKCENEKEMKSSIKQEPIERKDYIVENEKEKPKSRS
KKATNAVDLYVCLLCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKCLAQE
CSKPQEAFGFEQAARDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEED
VTVEYGADIASKEFGSGFPVRDGKIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADIC
GMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPE
LFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAV
NF
CTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIE
DEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVK
ELCSCPPYKYKLRYRYTLDDLYPM
MNALKLRAESYNEWALNVNEALEAKINKKKSLVSFK
ALIEESEMKKFPDNDLLRHLRLVTQDAEKCASVAQQLLNGKRQTRYRSGGGKSQNQLTVN
ELRQFVTQLYALPCVLSQTPLLKDLLNRVEDFQQHSQKLLSEETPSAAELQDLLDVSFEF
DVELPQLAEMRIRLEQARWLEEVQQACLDPSSLTLDDMRRLIDLGVGLAPYSAVEKAMAR
LQELLTVSEHWDDKAKSLLKARPRHSLNSLATAVKEIEEIPAYLPNGAALKDSVQRARDW
LQDVEGLQAGGRVPVLDTLIELVTRGRSIPVHLNSLPRLETLVAEVQAWKECAVNTFLTE
NSPYSLLE
VLCPRCDIGLLGLKRKQRKLKEPLPNGKKKSTKLESLSDLERALTESKETAS
AMATLGEARLREMEALQSLRLANEGKLLSPLQDVDIKICLCQKAPAAPMIQCELCRDAFH
TSCVAVPSISQGLRIWLCPHCRRS
EKPPLEKILPLLASLQRIRVRLPEGDALRYMIERTV
NWQHRAQQLLSSGNLKFVQDRVGSGLLYSRWQASAGQVSDTNKVSQPPGTTSFSLPDDWD
NRTSYLHSPFSTGRSCIPLHGVSPEVNELLMEAQLLQVSLPEIQELYQTLLAKPSPAQQT
DRSSPVRPSSEKNDCCRGKRDGINSLERKLKRRLEREGLSSERWERVKKMRTPKKKKIKL
SHPKDMNNFKLERERSYELVRSAETHSLPSDTSYSEQEDSEDEDAICPAVSCLQPEGDEV
DWVQCDGSCNQWFHQVCVGVSPEMAEKEDYICVRCTVK
DAPSRK
Sequence length 1544
Interactions View interactions
PathwaysPathway information has different metabolic/signaling pathways associated with genes. Each record is hyperlinked to a complete information page which also includes links to the KEGG/Reactome pathway database.
 
Reactome
    HDMs demethylate histones
TFAP2 (AP-2) family regulates transcription of cell cycle factors
Associated diseases
Causal
Disease name Disease term dbSNP ID References
Atrial septal defect Atrial Septal Defects rs137852951, rs137852953, rs137852955, rs267607106, rs104893900, rs104893901, rs104893903, rs606231358, rs606231359, rs137852683, rs606231360, rs104893907, rs104894073, rs1585703301, rs104894074, rs267606903, rs121912677, rs387906585, rs387906773, rs72554028, rs587782928, rs587782929, rs587782930, rs587784067, rs1555226315, rs879253754, rs1114167356, rs773922431, rs1554093487, rs1554093433, rs1554093461, rs1561621507, rs1561619801, rs766692577, rs1581108237, rs1581111034, rs1579663872, rs1583066622, rs1456289029, rs1761430125
Autism Autistic Disorder, Autistic behavior rs121964908, rs121912597, rs2710102, rs7794745, rs142990298, rs62643608, rs181327458, rs797046134, rs869312704, rs1555013332, rs876657679, rs1057518999, rs1057518658, rs771827120, rs1555187899, rs773080572, rs753871454, rs1684130791, rs1684180699, rs1553510219, rs1684182454, rs1559060428, rs1553510677, rs1576352885, rs1574152522, rs1574152672, rs1696658542, rs1751123722, rs1750373491, rs1751075634 24307393
Colonic neoplasms Malignant tumor of colon, Colonic Neoplasms rs267607789, rs774277300, rs781222233, rs1060502734, rs1060503333, rs1339238483 25043185
Cryptorchidism Cryptorchidism rs121912555, rs104894697, rs104894698, rs398122886
Unknown
Disease name Disease term dbSNP ID References
Absence of septum pellucidum Absence of septum pellucidum
Astigmatism Astigmatism
Central visual impairment Central visual impairment
Cerebral atrophy Cerebral atrophy

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