GeDiPNet: Comprehensive Gene Data - OMIM, HGNC, Ensembl, UniProt, GO, Transcription Factors & miRNA

Home
Browse
- Genes
- Diseases
- Pathways
  - Reactome
  - KEGG
Analysis
Help
Links
FAQ
Contact us

KDM2B (lysine demethylase 2B)

Gene

Lysine demethylase 2B

KDM2B

CXXC2, FBXL10, Fbl10, JHDM1B, PCCX2

12

12q24.31

This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), w

Show/Hide all(1)

SNP ID	Visualize variation	Clinical significance	Consequence
rs782304760	C>T	Likely-pathogenic	Missense variant, coding sequence variant

Show/Hide all(216)

miRTarBase ID	miRNA	Experiments	Reference
MIRT024040	hsa-miR-1-3p	Microarray	18668037
MIRT042973	hsa-miR-324-3p	CLASH	23622248
MIRT629261	hsa-miR-216a-5p	HITS-CLIP	23824327
MIRT631070	hsa-miR-5197-5p	HITS-CLIP	23824327
MIRT631069	hsa-miR-652-3p	HITS-CLIP	23824327
MIRT629260	hsa-miR-6890-3p	HITS-CLIP	23824327
MIRT629259	hsa-miR-6736-3p	HITS-CLIP	23824327
MIRT629258	hsa-miR-939-3p	HITS-CLIP	23824327
MIRT629257	hsa-miR-6852-5p	HITS-CLIP	23824327
MIRT629256	hsa-miR-6742-3p	HITS-CLIP	23824327
MIRT629255	hsa-miR-6774-3p	HITS-CLIP	23824327
MIRT629254	hsa-miR-1304-3p	HITS-CLIP	23824327
MIRT629253	hsa-miR-6787-3p	HITS-CLIP	23824327
MIRT629252	hsa-miR-3605-3p	HITS-CLIP	23824327
MIRT629251	hsa-miR-4772-3p	HITS-CLIP	23824327
MIRT631068	hsa-miR-6722-5p	HITS-CLIP	23824327
MIRT629250	hsa-miR-1343-3p	HITS-CLIP	23824327
MIRT629249	hsa-miR-6783-3p	HITS-CLIP	23824327
MIRT629261	hsa-miR-216a-5p	HITS-CLIP	23824327
MIRT629260	hsa-miR-6890-3p	HITS-CLIP	23824327
MIRT629259	hsa-miR-6736-3p	HITS-CLIP	23824327
MIRT629258	hsa-miR-939-3p	HITS-CLIP	23824327
MIRT629257	hsa-miR-6852-5p	HITS-CLIP	23824327
MIRT629256	hsa-miR-6742-3p	HITS-CLIP	23824327
MIRT629255	hsa-miR-6774-3p	HITS-CLIP	23824327
MIRT629254	hsa-miR-1304-3p	HITS-CLIP	23824327
MIRT629253	hsa-miR-6787-3p	HITS-CLIP	23824327
MIRT629252	hsa-miR-3605-3p	HITS-CLIP	23824327
MIRT629251	hsa-miR-4772-3p	HITS-CLIP	23824327
MIRT629250	hsa-miR-1343-3p	HITS-CLIP	23824327
MIRT629249	hsa-miR-6783-3p	HITS-CLIP	23824327
MIRT629261	hsa-miR-216a-5p	HITS-CLIP	23824327
MIRT631070	hsa-miR-5197-5p	HITS-CLIP	23824327
MIRT631069	hsa-miR-652-3p	HITS-CLIP	23824327
MIRT629260	hsa-miR-6890-3p	HITS-CLIP	23824327
MIRT629259	hsa-miR-6736-3p	HITS-CLIP	23824327
MIRT629258	hsa-miR-939-3p	HITS-CLIP	23824327
MIRT629257	hsa-miR-6852-5p	HITS-CLIP	23824327
MIRT629256	hsa-miR-6742-3p	HITS-CLIP	23824327
MIRT629255	hsa-miR-6774-3p	HITS-CLIP	23824327
MIRT629254	hsa-miR-1304-3p	HITS-CLIP	23824327
MIRT629253	hsa-miR-6787-3p	HITS-CLIP	23824327
MIRT629252	hsa-miR-3605-3p	HITS-CLIP	23824327
MIRT629251	hsa-miR-4772-3p	HITS-CLIP	23824327
MIRT631068	hsa-miR-6722-5p	HITS-CLIP	23824327
MIRT629250	hsa-miR-1343-3p	HITS-CLIP	23824327
MIRT629249	hsa-miR-6783-3p	HITS-CLIP	23824327
MIRT629261	hsa-miR-216a-5p	HITS-CLIP	23824327
MIRT629260	hsa-miR-6890-3p	HITS-CLIP	23824327
MIRT629259	hsa-miR-6736-3p	HITS-CLIP	23824327
MIRT629258	hsa-miR-939-3p	HITS-CLIP	23824327
MIRT629257	hsa-miR-6852-5p	HITS-CLIP	23824327
MIRT629256	hsa-miR-6742-3p	HITS-CLIP	23824327
MIRT629255	hsa-miR-6774-3p	HITS-CLIP	23824327
MIRT629254	hsa-miR-1304-3p	HITS-CLIP	23824327
MIRT629253	hsa-miR-6787-3p	HITS-CLIP	23824327
MIRT629252	hsa-miR-3605-3p	HITS-CLIP	23824327
MIRT629251	hsa-miR-4772-3p	HITS-CLIP	23824327
MIRT629250	hsa-miR-1343-3p	HITS-CLIP	23824327
MIRT629249	hsa-miR-6783-3p	HITS-CLIP	23824327
MIRT1084278	hsa-miR-1200	CLIP-seq
MIRT1084279	hsa-miR-1287	CLIP-seq
MIRT1084280	hsa-miR-130a	CLIP-seq
MIRT1084281	hsa-miR-130b	CLIP-seq
MIRT1084282	hsa-miR-1323	CLIP-seq
MIRT1084283	hsa-miR-139-5p	CLIP-seq
MIRT1084284	hsa-miR-148a	CLIP-seq
MIRT1084285	hsa-miR-148b	CLIP-seq
MIRT1084286	hsa-miR-152	CLIP-seq
MIRT1084287	hsa-miR-182	CLIP-seq
MIRT1084288	hsa-miR-198	CLIP-seq
MIRT1084289	hsa-miR-19a	CLIP-seq
MIRT1084290	hsa-miR-19b	CLIP-seq
MIRT1084291	hsa-miR-216a	CLIP-seq
MIRT1084292	hsa-miR-301a	CLIP-seq
MIRT1084293	hsa-miR-301b	CLIP-seq
MIRT1084294	hsa-miR-3125	CLIP-seq
MIRT1084295	hsa-miR-3135b	CLIP-seq
MIRT1084296	hsa-miR-3150a-5p	CLIP-seq
MIRT1084297	hsa-miR-3150b-5p	CLIP-seq
MIRT1084298	hsa-miR-3591-3p	CLIP-seq
MIRT1084299	hsa-miR-3609	CLIP-seq
MIRT1084300	hsa-miR-3616-5p	CLIP-seq
MIRT1084301	hsa-miR-3647-3p	CLIP-seq
MIRT1084302	hsa-miR-3647-5p	CLIP-seq
MIRT1084303	hsa-miR-3666	CLIP-seq
MIRT1084304	hsa-miR-371-5p	CLIP-seq
MIRT1084305	hsa-miR-371b-5p	CLIP-seq
MIRT1084306	hsa-miR-3916	CLIP-seq
MIRT1084307	hsa-miR-3929	CLIP-seq
MIRT1084308	hsa-miR-4295	CLIP-seq
MIRT1084309	hsa-miR-4324	CLIP-seq
MIRT1084310	hsa-miR-4419b	CLIP-seq
MIRT1084311	hsa-miR-4452	CLIP-seq
MIRT1084312	hsa-miR-4468	CLIP-seq
MIRT1084313	hsa-miR-4477b	CLIP-seq
MIRT1084314	hsa-miR-4478	CLIP-seq
MIRT1084315	hsa-miR-4496	CLIP-seq
MIRT1084316	hsa-miR-4519	CLIP-seq
MIRT1084317	hsa-miR-454	CLIP-seq
MIRT1084318	hsa-miR-4667-3p	CLIP-seq
MIRT1084319	hsa-miR-4671-5p	CLIP-seq
MIRT1084320	hsa-miR-4684-3p	CLIP-seq
MIRT1084321	hsa-miR-4684-5p	CLIP-seq
MIRT1084322	hsa-miR-4708-3p	CLIP-seq
MIRT1084323	hsa-miR-4768-5p	CLIP-seq
MIRT1084324	hsa-miR-4795-5p	CLIP-seq
MIRT1084325	hsa-miR-4797-5p	CLIP-seq
MIRT1084326	hsa-miR-518a-5p	CLIP-seq
MIRT1084327	hsa-miR-522	CLIP-seq
MIRT1084328	hsa-miR-527	CLIP-seq
MIRT1084329	hsa-miR-544b	CLIP-seq
MIRT1084330	hsa-miR-548ah	CLIP-seq
MIRT1084331	hsa-miR-548o	CLIP-seq
MIRT1084332	hsa-miR-548t	CLIP-seq
MIRT1084333	hsa-miR-573	CLIP-seq
MIRT1084334	hsa-miR-873	CLIP-seq
MIRT1084335	hsa-miR-935	CLIP-seq
MIRT1084284	hsa-miR-148a	CLIP-seq
MIRT1084285	hsa-miR-148b	CLIP-seq
MIRT1084286	hsa-miR-152	CLIP-seq
MIRT1084336	hsa-miR-183	CLIP-seq
MIRT1084337	hsa-miR-340	CLIP-seq
MIRT1084335	hsa-miR-935	CLIP-seq
MIRT2021395	hsa-miR-1285	CLIP-seq
MIRT1084282	hsa-miR-1323	CLIP-seq
MIRT1084284	hsa-miR-148a	CLIP-seq
MIRT1084285	hsa-miR-148b	CLIP-seq
MIRT1084286	hsa-miR-152	CLIP-seq
MIRT1084288	hsa-miR-198	CLIP-seq
MIRT2021396	hsa-miR-3187-5p	CLIP-seq
MIRT2021397	hsa-miR-326	CLIP-seq
MIRT2021398	hsa-miR-330-5p	CLIP-seq
MIRT2021399	hsa-miR-345	CLIP-seq
MIRT2021400	hsa-miR-378g	CLIP-seq
MIRT2021401	hsa-miR-4484	CLIP-seq
MIRT2021402	hsa-miR-4486	CLIP-seq
MIRT1084315	hsa-miR-4496	CLIP-seq
MIRT1084316	hsa-miR-4519	CLIP-seq
MIRT2021403	hsa-miR-4522	CLIP-seq
MIRT2021404	hsa-miR-4778-3p	CLIP-seq
MIRT1084327	hsa-miR-522	CLIP-seq
MIRT2021405	hsa-miR-548an	CLIP-seq
MIRT1084331	hsa-miR-548o	CLIP-seq
MIRT2021406	hsa-miR-550b	CLIP-seq
MIRT2021407	hsa-miR-578	CLIP-seq
MIRT2021408	hsa-miR-612	CLIP-seq
MIRT2021409	hsa-miR-643	CLIP-seq
MIRT1084335	hsa-miR-935	CLIP-seq
MIRT2252859	hsa-miR-1208	CLIP-seq
MIRT1084337	hsa-miR-340	CLIP-seq
MIRT1084298	hsa-miR-3591-3p	CLIP-seq
MIRT2252860	hsa-miR-3680	CLIP-seq
MIRT2252861	hsa-miR-4261	CLIP-seq
MIRT2021401	hsa-miR-4484	CLIP-seq
MIRT1084315	hsa-miR-4496	CLIP-seq
MIRT1084318	hsa-miR-4667-3p	CLIP-seq
MIRT2252862	hsa-miR-4729	CLIP-seq
MIRT1084327	hsa-miR-522	CLIP-seq
MIRT2021405	hsa-miR-548an	CLIP-seq
MIRT2021406	hsa-miR-550b	CLIP-seq
MIRT2252863	hsa-miR-568	CLIP-seq
MIRT2252864	hsa-miR-580	CLIP-seq
MIRT2389704	hsa-miR-300	CLIP-seq
MIRT2389705	hsa-miR-3065-5p	CLIP-seq
MIRT2389706	hsa-miR-381	CLIP-seq
MIRT2389707	hsa-miR-421	CLIP-seq
MIRT2389708	hsa-miR-4272	CLIP-seq
MIRT2389709	hsa-miR-4666-3p	CLIP-seq
MIRT2389710	hsa-miR-4789-5p	CLIP-seq
MIRT2389711	hsa-miR-548m	CLIP-seq
MIRT1084278	hsa-miR-1200	CLIP-seq
MIRT2252859	hsa-miR-1208	CLIP-seq
MIRT1084279	hsa-miR-1287	CLIP-seq
MIRT1084280	hsa-miR-130a	CLIP-seq
MIRT1084281	hsa-miR-130b	CLIP-seq
MIRT2555885	hsa-miR-185	CLIP-seq
MIRT1084289	hsa-miR-19a	CLIP-seq
MIRT1084290	hsa-miR-19b	CLIP-seq
MIRT2555886	hsa-miR-299-3p	CLIP-seq
MIRT1084292	hsa-miR-301a	CLIP-seq
MIRT1084293	hsa-miR-301b	CLIP-seq
MIRT1084295	hsa-miR-3135b	CLIP-seq
MIRT2555887	hsa-miR-3150b-3p	CLIP-seq
MIRT2555888	hsa-miR-335	CLIP-seq
MIRT1084303	hsa-miR-3666	CLIP-seq
MIRT2555889	hsa-miR-3670	CLIP-seq
MIRT2252860	hsa-miR-3680	CLIP-seq
MIRT2555890	hsa-miR-380	CLIP-seq
MIRT1084307	hsa-miR-3929	CLIP-seq
MIRT2555891	hsa-miR-4257	CLIP-seq
MIRT1084308	hsa-miR-4295	CLIP-seq
MIRT2555892	hsa-miR-4300	CLIP-seq
MIRT2555893	hsa-miR-4306	CLIP-seq
MIRT1084309	hsa-miR-4324	CLIP-seq
MIRT1084310	hsa-miR-4419b	CLIP-seq
MIRT1084312	hsa-miR-4468	CLIP-seq
MIRT1084314	hsa-miR-4478	CLIP-seq
MIRT2555894	hsa-miR-4491	CLIP-seq
MIRT2555895	hsa-miR-4495	CLIP-seq
MIRT1084317	hsa-miR-454	CLIP-seq
MIRT2555896	hsa-miR-4644	CLIP-seq
MIRT2555897	hsa-miR-4648	CLIP-seq
MIRT2555898	hsa-miR-4654	CLIP-seq
MIRT2555899	hsa-miR-4657	CLIP-seq
MIRT2252862	hsa-miR-4729	CLIP-seq
MIRT2555900	hsa-miR-4769-5p	CLIP-seq
MIRT2555901	hsa-miR-4784	CLIP-seq
MIRT1084326	hsa-miR-518a-5p	CLIP-seq
MIRT1084328	hsa-miR-527	CLIP-seq
MIRT1084329	hsa-miR-544b	CLIP-seq
MIRT2555902	hsa-miR-548p	CLIP-seq
MIRT2252863	hsa-miR-568	CLIP-seq
MIRT2555903	hsa-miR-920	CLIP-seq
MIRT1084288	hsa-miR-198	CLIP-seq
MIRT1084327	hsa-miR-522	CLIP-seq

Show/Hide all(34)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	ISS
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA
GO:0003677	Function	DNA binding	NAS
GO:0003712	Function	Transcription coregulator activity	IBA	21873635
GO:0005515	Function	Protein binding	IPI	16943429, 24981860, 26496610, 27505670, 27705803
GO:0005634	Component	Nucleus	IDA	26237645
GO:0005634	Component	Nucleus	NAS
GO:0005654	Component	Nucleoplasm	TAS
GO:0005730	Component	Nucleolus	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA	21873635
GO:0006482	Process	Protein demethylation	IBA	21873635
GO:0007283	Process	Spermatogenesis	ISS
GO:0008270	Function	Zinc ion binding	IDA	29276034
GO:0019843	Function	RRNA binding	IEA
GO:0021555	Process	Midbrain-hindbrain boundary morphogenesis	ISS
GO:0021592	Process	Fourth ventricle development	ISS
GO:0021670	Process	Lateral ventricle development	ISS
GO:0021678	Process	Third ventricle development	ISS
GO:0021993	Process	Initiation of neural tube closure	ISS
GO:0030307	Process	Positive regulation of cell growth	IEA
GO:0030900	Process	Forebrain development	ISS
GO:0030901	Process	Midbrain development	ISS
GO:0030902	Process	Hindbrain development	ISS
GO:0031519	Component	PcG protein complex	IDA	16943429
GO:0032452	Function	Histone demethylase activity	IBA	21873635
GO:0032452	Function	Histone demethylase activity	TAS	21220025
GO:0035518	Process	Histone H2A monoubiquitination	IDA	16943429
GO:0043524	Process	Negative regulation of neuron apoptotic process	ISS
GO:0045322	Function	Unmethylated CpG binding	IDA	29276034
GO:0048596	Process	Embryonic camera-type eye morphogenesis	ISS
GO:0051864	Function	Histone demethylase activity (H3-K36 specific)	IDA	26237645
GO:0070544	Process	Histone H3-K36 demethylation	IDA	26237645
GO:1902459	Process	Positive regulation of stem cell population maintenance	IEA
GO:2000178	Process	Negative regulation of neural precursor cell proliferation	ISS

MIM	HGNC	e!Ensembl
609078	13610	ENSG00000089094

Protein

UniProt ID

Protein name

Lysine-specific demethylase 2B (EC 1.14.11.27) (CXXC-type zinc finger protein 2) (F-box and leucine-rich repeat protein 10) (F-box protein FBL10) (F-box/LRR-repeat protein 10) (JmjC domain-containing histone demethylation protein 1B) (Jumonji domain-conta

Protein function

Histone demethylase that demethylates 'Lys-4' and 'Lys-36' of histone H3, thereby playing a central role in histone code (PubMed:16362057, PubMed:17994099, PubMed:26237645). Preferentially demethylates trimethylated H3 'Lys-4' and dimethylated H

PDB

4O64 , 5JH5 , 6BVA , 8HCU

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF13621	Cupin_8	23 → 336	Cupin-like domain	Domain
PF17811	JHD	333 → 418	Jumonji helical domain	Domain
PF02008	zf-CXXC	605 → 651	CXXC zinc finger domain	Domain
PF16866	PHD_4	656 → 723	PHD-finger	Domain
PF00646	F-box	1050 → 1107	F-box domain	Domain

Sequence

MAGPQMGGSAEDHPPRKRHAAEKQKKKTVIYTKCFEFESATQRPIDRQRYDENEDLSDVE
EIVSVRGFSLEEKLRSQLYQGDFVHAMEGKDFNYEYVQREALRVPLIFREKDGLGIKMPD
PDFTVRDVKLLVGSRRLVDVMDVNTQKGTEMSMSQFVRYYETPEAQRDKLYNVISLEFSH
TKLEHLVKRPTVVDLVDWVDNMWPQHLKEKQTEATNAIAEMKYPKVKKYCLMSVKGCFTD
FHIDFGGTSVWYHVFRGGKIFWLIPPTLHNLALYEEWVLSGKQSDIFLGDRVERCQRIEL
KQGYTFFIPSGWIHAVYTPVDSLVFGGNILHSFNVPMQLRIYEIEDRTRVQPKFRYPFYY
EMCWYVLERYVYCVTQRSHLTQEYQRESMLIDAPRKPSIDGFSSDSWLEMEEEACDQQPQ
EEEEKDEEGEGRDRAPKPPTDGSTSPTSTPSEDQEALGKKPKAPALRFLKRTLSNESEES
VKSTTLAVDYPKTPTGSPATEVSAKWTHLTEFELKGLKALVEKLESLPENKKCVPEGIED
PQALLEGVKNVLKEHADDDPSLAITGVPVVTWPKKTPKNRAVGRPKGKLGPASAVKLAAN
RTTAGARRRRTRCRKCEACLRTECGECHFCKDMKKFGGPGRMKQSCIMRQCIAPVLPHTA
VCLVCGEAGKEDTVEEEEGKFNLMLMECSICNEIIHPGCLKIKESEGVVNDELPNCWECP
KCNHAGKTGKQKRGPGFKYASNLPGSLLKEQKMNRDNKEGQEPAKRRSECEEAPRRRSDE
HSKKVPPDGLLRRKSDDVHLRKKRKYEKPQELSGRKRASSLQTSPGSSSHLSPRPPLGSS
LSPWWRSSLTYFQQQLKPGKEDKLFRKKRRSWKNAEDRMALANKPLRRFKQEPEDELPEA
PPKTRESDHSRSSSPTAGPSTEGAEGPEEKKKVKMRRKRRLPNKELSRELSKELNHEIQR
TENSLANENQQPIKSEPESEGEEPKRPPGICERPHRFSKGLNGTPRELRHQLGPSLRSPP
RVISRPPPSVSPPKCIQMERHVIRPPPISPPPDSLPLDDGAAHVMHREVWMAVFSYLSHQ
DLCVCMRVCRTWNRWCCDKRLWTRIDLNHCKSITPLMLSGIIRRQPVSLDLSWTNISKKQ
LSWLINRLPGLRDLVLSGCSWIAVSALCSSSCPLLRTLDVQWVEGLKDAQMRDLLSPPTD
NRPGQMDNRSKLRNIVELRLAGLDITDASLRLIIRHMPLLSKLHLSYCNHVTDQSINLLT
AVGTTTRDSLTEINLSDCNKVTDQCLSFFKRCGNICHIDLRYCKQVTKEGCEQFIAEMSV
SVQFGQVEEKLLQKLS

Sequence length

1336

Interactions

View interactions

	KEGG		Reactome
	Polycomb repressive complex		HDMs demethylate histones

Associated diseases

Show/Hide Causal Diseases (3)

Causal
Disease name	Disease term	dbSNP ID	References
Developmental delay	Global developmental delay	rs28941770, rs199469464, rs281865469, rs143747297, rs398123009, rs587777428, rs786205133, rs606231459, rs797044854, rs797045027, rs864309504, rs878853160, rs886039902, rs886042046, rs886041291, rs886041382, rs1057518991, rs1057518699, rs753254213, rs748294403, rs762552974, rs1135401795, rs1553121073, rs1553122926, rs1364690005, rs1554086554, rs1554210415, rs1554168326, rs1554776342, rs1553873247, rs1567860112, rs779009256, rs1557447255, rs1564568350, rs780011005, rs1597464953, rs1200336864, rs1569513017, rs1587459606, rs1570332505, rs748888652, rs1575155995, rs2087029320, rs1589669105, rs1601769604, rs1184981709, rs749201074
Infantile spasms	Infantile Spasm	rs387906686, rs1553579488, rs1553567561
Schizophrenia	Schizophrenia	rs74315508, rs74315509, rs13447324, rs1558507406, rs387906932, rs387906933, rs863223354, rs863223355, rs776061422, rs863223349, rs748809996, rs759748655, rs863223353, rs863223350, rs863223356, rs781821239, rs863223348, rs863223346, rs863223347, rs863223351, rs863223352, rs61734270, rs797045205, rs869312829, rs869312830, rs770913157, rs869312832, rs869312831, rs781720548, rs1262969313	21743468

Show/Hide Unknown Diseases (1)

Unknown
Disease name	Disease term	dbSNP ID	References
Cardiovascular diseases	Cardiovascular Diseases		30595370

| © 2021, Biomedical Informatics Centre, NIRRH |
ICMR-National Institute for Research in Reproductive Health, Jehangir Merwanji Street, Parel, Mumbai-400012
Tel: +91-22-24192104, Fax No: +91-22-24139412