P41229 (KDM5C_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Lysine-specific demethylase 5C
EC=1.14.11.-

Alternative name(s):
Histone demethylase JARID1C
Jumonji/ARID domain-containing protein 1C
Protein SmcX
Protein Xe169

Gene names

Name:	KDM5C
Synonyms:	DXS1272E, JARID1C, SMCX, XE169

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	1560 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. Participates in transcriptional repression of neuronal genes by recruiting histone deacetylases and REST at neuron-restrictive silencer elements. Ref.8 Ref.9 Ref.10
Cofactor	Alpha-ketoglutarate. Ref.9 Binds 1 Fe2+ ion per subunit. Ref.9
Subunit structure	Part of two distinct complexes, one containing E2F6, and the other containing REST. Ref.10
Subcellular location	Nucleus Ref.10.
Tissue specificity	Expressed in all tissues examined. Highest levels found in brain and skeletal muscle. Ref.14
Domain	The first PHD-type zinc finger domain recognizes and binds H3-K9Me3. Both the JmjC domain and the JmjN domain are required for enzymatic activity.
Involvement in disease	Defects in KDM5C are the cause of mental retardation syndromic X-linked JARID1C-related (MRXSJ) [MIM:300534]. MRXSJ is characterized by significantly sub-average general intellectual functioning associated with impairments in adaptative behavior and manifested during the developmental period. MRXSJ patients manifest mental retardation associated with variable features such as slowly progressive spastic paraplegia, seizures, facial dysmorphism. Ref.9 Ref.10 Ref.14 Ref.15 Ref.16
Miscellaneous	Escapes X-inactivation.
Sequence similarities	Belongs to the JARID1 histone demethylase family. Contains 1 ARID domain. Contains 1 JmjC domain. Contains 1 JmjN domain. Contains 2 PHD-type zinc fingers.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Disease	Disease mutation Mental retardation
Domain	Repeat Zinc-finger
Ligand	Iron Metal-binding Zinc
Molecular function	Chromatin regulator Dioxygenase Oxidoreductase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	chromatin modification Inferred from electronic annotation. Source: UniProtKB-KW regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	DNA binding Inferred from electronic annotation. Source: InterPro oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors Inferred from electronic annotation. Source: InterPro oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen Inferred from electronic annotation. Source: UniProtKB-KW zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: P41229-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: P41229-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1370-1372: Missing.

Isoform 3 (identifier: P41229-3)

The sequence of this isoform differs from the canonical sequence as follows:
     77-117: Missing.
     1370-1372: Missing.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 1560

1560

Lysine-specific demethylase 5C

PRO_0000200586

Regions

Domain

14 – 55

42

JmjN

Domain

79 – 169

91

ARID

Domain

468 – 634

167

JmjC

Zinc finger

326 – 372

47

PHD-type 1

Zinc finger

1187 – 1248

62

PHD-type 2

Sites

Metal binding

514

1

Iron; catalytic By similarity

Metal binding

517

1

Iron; catalytic By similarity

Metal binding

602

1

Iron; catalytic By similarity

Amino acid modifications

Modified residue

317

1

Phosphoserine Ref.6 Ref.11

Modified residue

1359

1

Phosphoserine Ref.5 Ref.7 Ref.12

Natural variations

Alternative sequence

77 – 117

41

Missing in isoform 3.

VSP_026410

Alternative sequence

1370 – 1372

3

Missing in isoform 2 and isoform 3.

VSP_000315

Natural variant

87

1

D → G in MRXSJ; no effect on subcellular location and enzymatic activity. Ref.10 Ref.16

VAR_032986

Natural variant

388

1

A → P in MRXSJ; impairs enzymatic activity and binding to H3-K9Me3. Ref.9 Ref.14

VAR_022730

Natural variant

402

1

D → Y in MRXSJ; impairs enzymatic activity. Ref.10 Ref.14

VAR_022731

Natural variant

451

1

S → R in MRXSJ. Ref.15

VAR_032987

Natural variant

640

1

C → Y De novo mutation found in a patient with mental retardation. Ref.17

VAR_065091

Natural variant

642

1

F → L in MRXSJ; impairs enzymatic activity. Ref.9 Ref.16

VAR_032988

Natural variant

698

1

E → K in MRXSJ; abolishes function in vivo, but no effect on enzymatic activity or binding to H3-K9Me3. Ref.10 Ref.14

VAR_022732

Natural variant

731

1

L → F in MRXSJ; impairs enzymatic activity. Ref.9 Ref.14

VAR_022733

Natural variant

750

1

R → W in MRXSJ. Ref.16

VAR_032989

Natural variant

751

1

Y → C in MRXSJ; impairs enzymatic activity. Ref.9 Ref.10 Ref.16

VAR_032990

Experimental info

Mutagenesis

514

1

H → A: Abolishes enzymatic activity. Ref.9 Ref.10

Sequence conflict

175

1

Missing in AAH54499. Ref.3

Sequence conflict

342

1

C → Y in CAA82758. Ref.4

Sequence conflict

1199

1

A → R in AAA61302. Ref.1

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

1560

Helix Strand Turn

Details...

Helix

73 – 76

4

Turn

79 – 81

3

Helix

82 – 94

13

Turn

95 – 97

3

Helix

112 – 122

11

Helix

125 – 130

6

Turn

131 – 133

3

Helix

134 – 140

7

Helix

149 – 159

11

Helix

162 – 172

11

Turn

178 – 180

3

Helix

181 – 185

5

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified November 14, 2006. Version 2. Checksum: 5DC673D0091E7C87	FASTA	1,560	175,720
	10 20 30 40 50 60 MEPGSDDFLP PPECPVFEPS WAEFRDPLGY IAKIRPIAEK SGICKIRPPA DWQPPFAVEV 70 80 90 100 110 120 DNFRFTPRIQ RLNELEAQTR VKLNYLDQIA KFWEIQGSSL KIPNVERRIL DLYSLSKIVV 130 140 150 160 170 180 EEGGYEAICK DRRWARVAQR LNYPPGKNIG SLLRSHYERI VYPYEMYQSG ANLVQCNTRP 190 200 210 220 230 240 FDNEEKDKEY KPHSIPLRQS VQPSKFNSYG RRAKRLQPDP EPTEEDIEKN PELKKLQIYG 250 260 270 280 290 300 AGPKMMGLGL MAKDKTLRKK DKEGPECPPT VVVKEELGGD VKVESTSPKT FLESKEELSH 310 320 330 340 350 360 SPEPCTKMTM RLRRNHSNAQ FIESYVCRMC SRGDEDDKLL LCDGCDDNYH IFCLLPPLPE 370 380 390 400 410 420 IPKGVWRCPK CVMAECKRPP EAFGFEQATR EYTLQSFGEM ADSFKADYFN MPVHMVPTEL 430 440 450 460 470 480 VEKEFWRLVN SIEEDVTVEY GADIHSKEFG SGFPVSDSKR HLTPEEEEYA TSGWNLNVMP 490 500 510 520 530 540 VLEQSVLCHI NADISGMKVP WLYVGMVFSA FCWHIEDHWS YSINYLHWGE PKTWYGVPSL 550 560 570 580 590 600 AAEHLEEVMK KLTPELFDSQ PDLLHQLVTL MNPNTLMSHG VPVVRTNQCA GEFVITFPRA 610 620 630 640 650 660 YHSGFNQGYN FAEAVNFCTA DWLPAGRQCI EHYRRLRRYC VFSHEELICK MAACPEKLDL 670 680 690 700 710 720 NLAAAVHKEM FIMVQEERRL RKALLEKGIT EAEREAFELL PDDERQCIKC KTTCFLSALA 730 740 750 760 770 780 CYDCPDGLVC LSHINDLCKC SSSRQYLRYR YTLDELPAML HKLKVRAESF DTWANKVRVA 790 800 810 820 830 840 LEVEDGRKRS LEELRALESE ARERRFPNSE LLQQLKNCLS EAEACVSRAL GLVSGQEAGP 850 860 870 880 890 900 HRVAGLQMTL TELRAFLDQM NNLPCAMHQI GDVKGVLEQV EAYQAEAREA LASLPSSPGL 910 920 930 940 950 960 LQSLLERGRQ LGVEVPEAQQ LQRQVEQARW LDEVKRTLAP SARRGTLAVM RGLLVAGASV 970 980 990 1000 1010 1020 APSPAVDKAQ AELQELLTIA ERWEEKAHLC LEARQKHPPA TLEAIIREAE NIPVHLPNIQ 1030 1040 1050 1060 1070 1080 ALKEALAKAR AWIADVDEIQ NGDHYPCLDD LEGLVAVGRD LPVGLEELRQ LELQVLTAHS 1090 1100 1110 1120 1130 1140 WREKASKTFL KKNSCYTLLE VLCPCADAGS DSTKRSRWME KELGLYKSDT ELLGLSAQDL 1150 1160 1170 1180 1190 1200 RDPGSVIVAF KEGEQKEKEG ILQLRRTNSA KPSPLASSST ASSTTSICVC GQVLAGAGAL 1210 1220 1230 1240 1250 1260 QCDLCQDWFH GRCVSVPRLL SSPRPNPTSS PLLAWWEWDT KFLCPLCMRS RRPRLETILA 1270 1280 1290 1300 1310 1320 LLVALQRLPV RLPEGEALQC LTERAISWQG RARQALASED VTALLGRLAE LRQRLQAEPR 1330 1340 1350 1360 1370 1380 PEEPPNYPAA PASDPLREGS GKDMPKVQGL LENGDSVTSP EKVAPEEGSG KRDLELLSSL 1390 1400 1410 1420 1430 1440 LPQLTGPVLE LPEATRAPLE ELMMEGDLLE VTLDENHSIW QLLQAGQPPD LERIRTLLEL 1450 1460 1470 1480 1490 1500 EKAERHGSRA RGRALERRRR RKVDRGGEGD DPAREELEPK RVRSSGPEAE EVQEEEELEE 1510 1520 1530 1540 1550 1560 ETGGEGPPAP IPTTGSPSTQ ENQNGLEPAE GTTSGPSAPF STLTPRLHLP CPQQPPQQQL
	Isoform 2 [UniParc]. Checksum: B1823D7AD5F78374	FASTA	1,557	175,379
	10 20 30 40 50 60 MEPGSDDFLP PPECPVFEPS WAEFRDPLGY IAKIRPIAEK SGICKIRPPA DWQPPFAVEV 70 80 90 100 110 120 DNFRFTPRIQ RLNELEAQTR VKLNYLDQIA KFWEIQGSSL KIPNVERRIL DLYSLSKIVV 130 140 150 160 170 180 EEGGYEAICK DRRWARVAQR LNYPPGKNIG SLLRSHYERI VYPYEMYQSG ANLVQCNTRP 190 200 210 220 230 240 FDNEEKDKEY KPHSIPLRQS VQPSKFNSYG RRAKRLQPDP EPTEEDIEKN PELKKLQIYG 250 260 270 280 290 300 AGPKMMGLGL MAKDKTLRKK DKEGPECPPT VVVKEELGGD VKVESTSPKT FLESKEELSH 310 320 330 340 350 360 SPEPCTKMTM RLRRNHSNAQ FIESYVCRMC SRGDEDDKLL LCDGCDDNYH IFCLLPPLPE 370 380 390 400 410 420 IPKGVWRCPK CVMAECKRPP EAFGFEQATR EYTLQSFGEM ADSFKADYFN MPVHMVPTEL 430 440 450 460 470 480 VEKEFWRLVN SIEEDVTVEY GADIHSKEFG SGFPVSDSKR HLTPEEEEYA TSGWNLNVMP 490 500 510 520 530 540 VLEQSVLCHI NADISGMKVP WLYVGMVFSA FCWHIEDHWS YSINYLHWGE PKTWYGVPSL 550 560 570 580 590 600 AAEHLEEVMK KLTPELFDSQ PDLLHQLVTL MNPNTLMSHG VPVVRTNQCA GEFVITFPRA 610 620 630 640 650 660 YHSGFNQGYN FAEAVNFCTA DWLPAGRQCI EHYRRLRRYC VFSHEELICK MAACPEKLDL 670 680 690 700 710 720 NLAAAVHKEM FIMVQEERRL RKALLEKGIT EAEREAFELL PDDERQCIKC KTTCFLSALA 730 740 750 760 770 780 CYDCPDGLVC LSHINDLCKC SSSRQYLRYR YTLDELPAML HKLKVRAESF DTWANKVRVA 790 800 810 820 830 840 LEVEDGRKRS LEELRALESE ARERRFPNSE LLQQLKNCLS EAEACVSRAL GLVSGQEAGP 850 860 870 880 890 900 HRVAGLQMTL TELRAFLDQM NNLPCAMHQI GDVKGVLEQV EAYQAEAREA LASLPSSPGL 910 920 930 940 950 960 LQSLLERGRQ LGVEVPEAQQ LQRQVEQARW LDEVKRTLAP SARRGTLAVM RGLLVAGASV 970 980 990 1000 1010 1020 APSPAVDKAQ AELQELLTIA ERWEEKAHLC LEARQKHPPA TLEAIIREAE NIPVHLPNIQ 1030 1040 1050 1060 1070 1080 ALKEALAKAR AWIADVDEIQ NGDHYPCLDD LEGLVAVGRD LPVGLEELRQ LELQVLTAHS 1090 1100 1110 1120 1130 1140 WREKASKTFL KKNSCYTLLE VLCPCADAGS DSTKRSRWME KELGLYKSDT ELLGLSAQDL 1150 1160 1170 1180 1190 1200 RDPGSVIVAF KEGEQKEKEG ILQLRRTNSA KPSPLASSST ASSTTSICVC GQVLAGAGAL 1210 1220 1230 1240 1250 1260 QCDLCQDWFH GRCVSVPRLL SSPRPNPTSS PLLAWWEWDT KFLCPLCMRS RRPRLETILA 1270 1280 1290 1300 1310 1320 LLVALQRLPV RLPEGEALQC LTERAISWQG RARQALASED VTALLGRLAE LRQRLQAEPR 1330 1340 1350 1360 1370 1380 PEEPPNYPAA PASDPLREGS GKDMPKVQGL LENGDSVTSP EKVAPEEGSD LELLSSLLPQ 1390 1400 1410 1420 1430 1440 LTGPVLELPE ATRAPLEELM MEGDLLEVTL DENHSIWQLL QAGQPPDLER IRTLLELEKA 1450 1460 1470 1480 1490 1500 ERHGSRARGR ALERRRRRKV DRGGEGDDPA REELEPKRVR SSGPEAEEVQ EEEELEEETG 1510 1520 1530 1540 1550 GEGPPAPIPT TGSPSTQENQ NGLEPAEGTT SGPSAPFSTL TPRLHLPCPQ QPPQQQL
	Isoform 3 [UniParc]. Checksum: F82BDA8A82C57C01	FASTA	1,516	170,561
	10 20 30 40 50 60 MEPGSDDFLP PPECPVFEPS WAEFRDPLGY IAKIRPIAEK SGICKIRPPA DWQPPFAVEV 70 80 90 100 110 120 DNFRFTPRIQ RLNELEIVVE EGGYEAICKD RRWARVAQRL NYPPGKNIGS LLRSHYERIV 130 140 150 160 170 180 YPYEMYQSGA NLVQCNTRPF DNEEKDKEYK PHSIPLRQSV QPSKFNSYGR RAKRLQPDPE 190 200 210 220 230 240 PTEEDIEKNP ELKKLQIYGA GPKMMGLGLM AKDKTLRKKD KEGPECPPTV VVKEELGGDV 250 260 270 280 290 300 KVESTSPKTF LESKEELSHS PEPCTKMTMR LRRNHSNAQF IESYVCRMCS RGDEDDKLLL 310 320 330 340 350 360 CDGCDDNYHI FCLLPPLPEI PKGVWRCPKC VMAECKRPPE AFGFEQATRE YTLQSFGEMA 370 380 390 400 410 420 DSFKADYFNM PVHMVPTELV EKEFWRLVNS IEEDVTVEYG ADIHSKEFGS GFPVSDSKRH 430 440 450 460 470 480 LTPEEEEYAT SGWNLNVMPV LEQSVLCHIN ADISGMKVPW LYVGMVFSAF CWHIEDHWSY 490 500 510 520 530 540 SINYLHWGEP KTWYGVPSLA AEHLEEVMKK LTPELFDSQP DLLHQLVTLM NPNTLMSHGV 550 560 570 580 590 600 PVVRTNQCAG EFVITFPRAY HSGFNQGYNF AEAVNFCTAD WLPAGRQCIE HYRRLRRYCV 610 620 630 640 650 660 FSHEELICKM AACPEKLDLN LAAAVHKEMF IMVQEERRLR KALLEKGITE AEREAFELLP 670 680 690 700 710 720 DDERQCIKCK TTCFLSALAC YDCPDGLVCL SHINDLCKCS SSRQYLRYRY TLDELPAMLH 730 740 750 760 770 780 KLKVRAESFD TWANKVRVAL EVEDGRKRSL EELRALESEA RERRFPNSEL LQQLKNCLSE 790 800 810 820 830 840 AEACVSRALG LVSGQEAGPH RVAGLQMTLT ELRAFLDQMN NLPCAMHQIG DVKGVLEQVE 850 860 870 880 890 900 AYQAEAREAL ASLPSSPGLL QSLLERGRQL GVEVPEAQQL QRQVEQARWL DEVKRTLAPS 910 920 930 940 950 960 ARRGTLAVMR GLLVAGASVA PSPAVDKAQA ELQELLTIAE RWEEKAHLCL EARQKHPPAT 970 980 990 1000 1010 1020 LEAIIREAEN IPVHLPNIQA LKEALAKARA WIADVDEIQN GDHYPCLDDL EGLVAVGRDL 1030 1040 1050 1060 1070 1080 PVGLEELRQL ELQVLTAHSW REKASKTFLK KNSCYTLLEV LCPCADAGSD STKRSRWMEK 1090 1100 1110 1120 1130 1140 ELGLYKSDTE LLGLSAQDLR DPGSVIVAFK EGEQKEKEGI LQLRRTNSAK PSPLASSSTA 1150 1160 1170 1180 1190 1200 SSTTSICVCG QVLAGAGALQ CDLCQDWFHG RCVSVPRLLS SPRPNPTSSP LLAWWEWDTK 1210 1220 1230 1240 1250 1260 FLCPLCMRSR RPRLETILAL LVALQRLPVR LPEGEALQCL TERAISWQGR ARQALASEDV 1270 1280 1290 1300 1310 1320 TALLGRLAEL RQRLQAEPRP EEPPNYPAAP ASDPLREGSG KDMPKVQGLL ENGDSVTSPE 1330 1340 1350 1360 1370 1380 KVAPEEGSDL ELLSSLLPQL TGPVLELPEA TRAPLEELMM EGDLLEVTLD ENHSIWQLLQ 1390 1400 1410 1420 1430 1440 AGQPPDLERI RTLLELEKAE RHGSRARGRA LERRRRRKVD RGGEGDDPAR EELEPKRVRS 1450 1460 1470 1480 1490 1500 SGPEAEEVQE EEELEEETGG EGPPAPIPTT GSPSTQENQN GLEPAEGTTS GPSAPFSTLT 1510 PRLHLPCPQQ PPQQQL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Isolation and characterization of XE169, a novel human gene that escapes X-inactivation." Wu J., Ellison J., Salido E., Yen P., Mohandas T., Shapiro L.J. Hum. Mol. Genet. 3:153-160(1994) [PubMed: 8162017] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1). Tissue: Fibroblast.
[2]	"The DNA sequence of the human X chromosome." Ross M.T., Grafham D.V., Coffey A.J., Scherer S., McLay K., Muzny D., Platzer M., Howell G.R., Burrows C., Bird C.P., Frankish A., Lovell F.L., Howe K.L., Ashurst J.L., Fulton R.S., Sudbrak R., Wen G., Jones M.C. , Hurles M.E., Andrews T.D., Scott C.E., Searle S., Ramser J., Whittaker A., Deadman R., Carter N.P., Hunt S.E., Chen R., Cree A., Gunaratne P., Havlak P., Hodgson A., Metzker M.L., Richards S., Scott G., Steffen D., Sodergren E., Wheeler D.A., Worley K.C., Ainscough R., Ambrose K.D., Ansari-Lari M.A., Aradhya S., Ashwell R.I., Babbage A.K., Bagguley C.L., Ballabio A., Banerjee R., Barker G.E., Barlow K.F., Barrett I.P., Bates K.N., Beare D.M., Beasley H., Beasley O., Beck A., Bethel G., Blechschmidt K., Brady N., Bray-Allen S., Bridgeman A.M., Brown A.J., Brown M.J., Bonnin D., Bruford E.A., Buhay C., Burch P., Burford D., Burgess J., Burrill W., Burton J., Bye J.M., Carder C., Carrel L., Chako J., Chapman J.C., Chavez D., Chen E., Chen G., Chen Y., Chen Z., Chinault C., Ciccodicola A., Clark S.Y., Clarke G., Clee C.M., Clegg S., Clerc-Blankenburg K., Clifford K., Cobley V., Cole C.G., Conquer J.S., Corby N., Connor R.E., David R., Davies J., Davis C., Davis J., Delgado O., Deshazo D., Dhami P., Ding Y., Dinh H., Dodsworth S., Draper H., Dugan-Rocha S., Dunham A., Dunn M., Durbin K.J., Dutta I., Eades T., Ellwood M., Emery-Cohen A., Errington H., Evans K.L., Faulkner L., Francis F., Frankland J., Fraser A.E., Galgoczy P., Gilbert J., Gill R., Gloeckner G., Gregory S.G., Gribble S., Griffiths C., Grocock R., Gu Y., Gwilliam R., Hamilton C., Hart E.A., Hawes A., Heath P.D., Heitmann K., Hennig S., Hernandez J., Hinzmann B., Ho S., Hoffs M., Howden P.J., Huckle E.J., Hume J., Hunt P.J., Hunt A.R., Isherwood J., Jacob L., Johnson D., Jones S., de Jong P.J., Joseph S.S., Keenan S., Kelly S., Kershaw J.K., Khan Z., Kioschis P., Klages S., Knights A.J., Kosiura A., Kovar-Smith C., Laird G.K., Langford C., Lawlor S., Leversha M., Lewis L., Liu W., Lloyd C., Lloyd D.M., Loulseged H., Loveland J.E., Lovell J.D., Lozado R., Lu J., Lyne R., Ma J., Maheshwari M., Matthews L.H., McDowall J., McLaren S., McMurray A., Meidl P., Meitinger T., Milne S., Miner G., Mistry S.L., Morgan M., Morris S., Mueller I., Mullikin J.C., Nguyen N., Nordsiek G., Nyakatura G., O'dell C.N., Okwuonu G., Palmer S., Pandian R., Parker D., Parrish J., Pasternak S., Patel D., Pearce A.V., Pearson D.M., Pelan S.E., Perez L., Porter K.M., Ramsey Y., Reichwald K., Rhodes S., Ridler K.A., Schlessinger D., Schueler M.G., Sehra H.K., Shaw-Smith C., Shen H., Sheridan E.M., Shownkeen R., Skuce C.D., Smith M.L., Sotheran E.C., Steingruber H.E., Steward C.A., Storey R., Swann R.M., Swarbreck D., Tabor P.E., Taudien S., Taylor T., Teague B., Thomas K., Thorpe A., Timms K., Tracey A., Trevanion S., Tromans A.C., d'Urso M., Verduzco D., Villasana D., Waldron L., Wall M., Wang Q., Warren J., Warry G.L., Wei X., West A., Whitehead S.L., Whiteley M.N., Wilkinson J.E., Willey D.L., Williams G., Williams L., Williamson A., Williamson H., Wilming L., Woodmansey R.L., Wray P.W., Yen J., Zhang J., Zhou J., Zoghbi H., Zorilla S., Buck D., Reinhardt R., Poustka A., Rosenthal A., Lehrach H., Meindl A., Minx P.J., Hillier L.W., Willard H.F., Wilson R.K., Waterston R.H., Rice C.M., Vaudin M., Coulson A., Nelson D.L., Weinstock G., Sulston J.E., Durbin R.M., Hubbard T., Gibbs R.A., Beck S., Rogers J., Bentley D.R. Nature 434:325-337(2005) [PubMed: 15772651] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Tissue: Eye.
[4]	"A novel X gene with a widely transcribed Y-linked homologue escapes X-inactivation in mouse and human." Agulnik A.I., Mitchell M.J., Mattei M.-G., Borsani G., Avner P.A., Lerner J.L., Bishop C.E. Hum. Mol. Genet. 3:879-884(1994) [PubMed: 7951230] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 280-344. Tissue: Blood.
[5]	"Large-scale characterization of HeLa cell nuclear phosphoproteins." Beausoleil S.A., Jedrychowski M., Schwartz D., Elias J.E., Villen J., Li J., Cohn M.A., Cantley L.C., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 101:12130-12135(2004) [PubMed: 15302935] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1359, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[6]	"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks." Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M. Cell 127:635-648(2006) [PubMed: 17081983] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-317, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[7]	"A probability-based approach for high-throughput protein phosphorylation analysis and site localization." Beausoleil S.A., Villen J., Gerber S.A., Rush J., Gygi S.P. Nat. Biotechnol. 24:1285-1292(2006) [PubMed: 16964243] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1359, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[8]	"RBP2 belongs to a family of demethylases, specific for tri-and dimethylated lysine 4 on histone 3." Christensen J., Agger K., Cloos P.A.C., Pasini D., Rose S., Sennels L., Rappsilber J., Hansen K.H., Salcini A.E., Helin K. Cell 128:1063-1076(2007) [PubMed: 17320161] [Abstract] Cited for: FUNCTION.
[9]	"The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases." Iwase S., Lan F., Bayliss P., de la Torre-Ubieta L., Huarte M., Qi H.H., Whetstine J.R., Bonni A., Roberts T.M., Shi Y. Cell 128:1077-1088(2007) [PubMed: 17320160] [Abstract] Cited for: FUNCTION, COFACTOR, MUTAGENESIS OF HIS-514, CHARACTERIZATION OF VARIANTS MRXSJ PRO-388; LEU-642; PHE-731 AND CYS-751.
[10]	"The histone H3K4 demethylase SMCX links REST target genes to X-linked mental retardation." Tahiliani M., Mei P., Fang R., Leonor T., Rutenberg M., Shimizu F., Li J., Rao A., Shi Y. Nature 447:601-605(2007) [PubMed: 17468742] [Abstract] Cited for: FUNCTION, SUBUNIT, MUTAGENESIS OF HIS-514, SUBCELLULAR LOCATION, CHARACTERIZATION OF VARIANTS MRXSJ GLY-87; TYR-402; LYS-698 AND CYS-751.
[11]	"A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed: 18669648] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-317, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[12]	"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions." Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K. Sci. Signal. 2:RA46-RA46(2009) [PubMed: 19690332] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1359, MASS SPECTROMETRY. Tissue: Leukemic T-cell.
[13]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed: 21269460] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[14]	"Mutations in the JARID1C gene, which is involved in transcriptional regulation and chromatin remodeling, cause X-linked mental retardation." Jensen L.R., Amende M., Gurok U., Moser B., Gimmel V., Tzschach A., Janecke A.R., Tariverdian G., Chelly J., Fryns J.-P., Van Esch H., Kleefstra T., Hamel B.C.J., Moraine C., Gecz J., Turner G., Reinhardt R., Kalscheuer V.M., Ropers H.-H., Lenzner S. Am. J. Hum. Genet. 76:227-236(2005) [PubMed: 15586325] [Abstract] Cited for: VARIANTS MRXSJ PRO-388; TYR-402; LYS-698 AND PHE-731, TISSUE SPECIFICITY.
[15]	"A novel mutation in JARID1C gene associated with mental retardation." Santos C., Rodriguez-Revenga L., Madrigal I., Badenas C., Pineda M., Mila M. Eur. J. Hum. Genet. 14:583-586(2006) [PubMed: 16538222] [Abstract] Cited for: VARIANT MRXSJ ARG-451.
[16]	"Novel JARID1C/SMCX mutations in patients with X-linked mental retardation." Tzschach A., Lenzner S., Moser B., Reinhardt R., Chelly J., Fryns J.-P., Kleefstra T., Raynaud M., Turner G., Ropers H.-H., Kuss A., Jensen L.R. Hum. Mutat. 27:389-389(2006) [PubMed: 16541399] [Abstract] Cited for: VARIANTS MRXSJ GLY-87; LEU-642; TRP-750 AND CYS-751.
[17]	"A de novo paradigm for mental retardation." Vissers L.E., de Ligt J., Gilissen C., Janssen I., Steehouwer M., de Vries P., van Lier B., Arts P., Wieskamp N., del Rosario M., van Bon B.W., Hoischen A., de Vries B.B., Brunner H.G., Veltman J.A. Nat. Genet. 42:1109-1112(2010) [PubMed: 21076407] [Abstract] Cited for: VARIANT TYR-640.
+	Additional computationally mapped references.

Web resources

GeneReviews

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

L25270 mRNA. Translation: AAA61302.1.
AL139396 Genomic DNA. Translation: CAI39836.1.
AL139396 Genomic DNA. Translation: CAI39837.1.
AL139396 Genomic DNA. Translation: CAI39838.1.
BC054499 mRNA. Translation: AAH54499.1.
Z29650 mRNA. Translation: CAA82758.1.

IPI

IPI00013185.
IPI00219412.
IPI00640875.

PIR

I54361.

RefSeq

NP_001140174.1. NM_001146702.1.
NP_004178.2. NM_004187.3.

UniGene

Hs.631768.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2JRZ	NMR	-	A	73-188	[»]

ProteinModelPortal

P41229.

SMR

P41229. Positions 72-188, 319-653, 1182-1253.

ModBase

Search...

Protein-protein interaction databases

IntAct

P41229. 3 interactions.

STRING

P41229.

PTM databases

PhosphoSite

P41229.

Polymorphism databases

DMDM

117949812.

Proteomic databases

PRIDE

P41229.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000375401; ENSP00000364550; ENSG00000126012.

GeneID

8242.

KEGG

hsa:8242.

NMPDR

fig|9606.3.peg.32833.

UCSC

uc004drz.1. human.

Organism-specific databases

CTD

8242.

GeneCards

GC0XM053237.

HGNC

HGNC:11114. KDM5C.

MIM

300534. phenotype.
314690. gene.

neXtProt

NX_P41229.

Orphanet

85279. Syndromic X-linked intellectual deficit due to JARID1C mutation.

PharmGKB

PA162392368.
PA35964.

GenAtlas

Search...

Phylogenomic databases

eggNOG

prNOG08641.

GeneTree

ENSGT00530000063118.

InParanoid

P41229.

OMA

ERAISWQ.

OrthoDB

EOG4894KP.

PhylomeDB

P41229.

Gene expression databases

ArrayExpress

P41229.

Bgee

P41229.

CleanEx

HS_JARID1C.

Genevestigator

P41229.

GermOnline

ENSG00000126012. Homo sapiens.

Family and domain databases

InterPro

IPR001606. ARID/BRIGHT_DNA-bd.
IPR013637. Lys_sp_deMease_like_dom.
IPR013129. TF_JmjC.
IPR003347. TF_JmjC_AAH.
IPR003349. TF_JmjN.
IPR019786. Zinc_finger_PHD-type_CS.
IPR004198. Znf_C5HC2.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]

Gene3D

G3DSA:1.10.150.60. ARID. 1 hit.
G3DSA:3.30.40.10. Znf_RING/FYVE/PHD. 2 hits.

KO

K11446.

Pfam

PF01388. ARID. 1 hit.
PF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
PF00628. PHD. 2 hits.
PF08429. PLU-1. 1 hit.
PF02928. zf-C5HC2. 1 hit.
[Graphical view]

SMART

SM00501. BRIGHT. 1 hit.
SM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 2 hits.
[Graphical view]

SUPFAM

SSF46774. ARID. 1 hit.
SSF57903. FYVE_PHD_ZnF. 2 hits.

PROSITE

PS51011. ARID. 1 hit.
PS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
PS01359. ZF_PHD_1. 2 hits.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

31002.

SOURCE

Search...

Entry information

Entry name

KDM5C_HUMAN

Accession

Primary (citable) accession number: P41229
Secondary accession number(s): Q5JUX3 , Q5JUX4, Q5JUX5, Q7Z5S5

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	November 14, 2006
Last modified:	January 25, 2012
This is version 121 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.