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JMJD5 Gene

protein-coding   GIFtS: 47

GC16P027123
jumonji domain containing 5
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
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Aliases &
Descriptions
for JMJD5

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section
Aliases
FLJ13798 1, 2
Descriptions
Jumonji domain-containing protein 5 3
jumonji domain containing 5 2
External Ids
HGNC: 258401
Entrez Gene: 798312
UniProtKB: Q8N3713
Ensembl: ENSG000001556667
Search outside databases for aliases for JMJD5 gene

Summaries
for JMJD5

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

 EntrezGene summary for JMJD5:
This gene likely encodes a histone lysine demethylase. Studies of a similar protein in mouse
indicate a potential role for this protein as a tumor suppressor. Alternatively spliced transcript
variants have been described.

Genomic Location
for JMJD5

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

 Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the JMJD5 gene  

Entrez Gene cytogenetic band: 16p12.1   Ensembl cytogenetic band:  16p12.1   HGNC cytogenetic band: 16p12.1

JMJD5 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16P027123:     (about GC identifiers)

Start:
 27,122,317 bp from pter
End:
 27,140,544 bp from pter
Size:
 18,228 bases
Orientation:
 plus strand
RefSeq DNA sequence:
NC_000016.8  NT_010393.15  

Proteins
for JMJD5

(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
About This Section

 UniProtKB/Swiss-Prot: JMJD5_HUMAN, Q8N371 (See protein sequence)
Recommended Name: JmjC domain-containing protein 5  
Size: 416 amino acids; 47270 Da
Secondary accessions: Q6VAK5 Q9H8B1
Alternative splicing: 2 isoforms:  Q8N371-1   Q8N371-2   

REFSEQ proteins (2 alternative transcripts): 
NP_001138820.1  NP_079049.2  


ENSEMBL proteins: 
ENSP00000370335 ENSP00000286096 


Human Recombinant Proteins 
Browse Drug Discovery Central at Invitrogen for human recombinant proteins
Browse Purified and Recombinant Proteins at Millipore
Browse Human Recombinant Proteins at Sigma-Aldrich  
Browse R&D Systems for human recombinant proteins
Browse recombinant and purified proteins available from Enzo Life Sciences
Recombinant Proteins from Abcam (JMJD5)
Human Recombinant Proteins from Abnova (JMJD5)
                Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 


Antibodies for JMJD5: 
Browse Antibodies Central at Invitrogen
Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
Sigma-Aldrich Antibodies for JMJD5
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Antibodies from Abcam (JMJD5), each with their AbpromiseSM
Monoclonal and Polyclonal Antibodies from Abnova (JMJD5)
Novus Biologicals Antibody for JMJD5

Assays for JMJD5: 
Browse Invitrogen for biochemical assays
Browse Kits and Assays available from Millipore
Browse R&D Systems for biochemical assays
Browse biochemical assays available from Enzo Life Sciences

Protein Domains/
Families
for JMJD5

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
1 InterPro domain/family:
 IPR003347 TF_JmjC_AAH


   GeneDecks  JMJD5 for the domains selected above  
About GeneDecksing

Graphical View of Domain Structure for InterPro Entry Q8N371

ProtoNet protein and cluster: Q8N371

UniProtKB/Swiss-Prot: JMJD5_HUMAN, Q8N371
Similarity: Contains 1 JmjC domain

Gene Function
for JMJD5

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
About This Section
Inhib.
RNA:		Invitrogen RNAi Products for gene knock-down (JMJD5)
Browse for Gene Knock-down Tools from Millipore
Browse Abnova for Chimera RNAi Products
               OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_001145348

              Applied Biosystems Silencer® siRNAs for JMJD5

              Sigma-Aldrich siRNA for JMJD5  
                     Sigma-Aldrich shRNA for JMJD5  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Clones:Invitrogen Clones for JMJD5
Browse Clones for the Expression of Recombinant Proteins Available from Millipore
               OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): NM_001145348
                                 Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): NM_001145348
                                 untagged cDNA clones in CMV expression vector (see all 3): NM_001145348 

Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
              OriGene genome-wide validated SYBR primer pairs: NM_001145348

Pathways & Interactions
for JMJD5

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
About This Section



1 Interacting protein for JMJD5 (ENSP000002860963) via UniProtKB, MINT, and/or STRING
InteractantInteraction Details
GeneCardExternal ID(s)
DPAGT1ENSP000003461423STRING (score=.802)
About this table

Drugs & Compounds
for JMJD5

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Browse drugs & compounds from Enzo Life Sciences
Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for JMJD5

Transcripts
for JMJD5

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section
Inhib.
RNA:		Invitrogen RNAi Products for gene knock-down (JMJD5)
Browse for Gene Knock-down Tools from Millipore
Browse Abnova for Chimera RNAi Products
               OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_001145348

              Sigma-Aldrich siRNA for JMJD5  
                     Sigma-Aldrich shRNA for JMJD5  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Applied Biosystems Silencer® siRNAs: 

NM_024773  

REFSEQ mRNAs for JMJD5 gene (2 alternative transcripts): 

NM_001145348.1   NM_024773.2   

Applied Biosystems TaqMan ® Gene Expression Assays: 

NM_024773  

               OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): NM_001145348
                                 Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): NM_001145348
                                 untagged cDNA clones in CMV expression vector (see all 3): NM_001145348 

Additional cDNA sequence: 

AK023860.1 AK055679.1 AK225066.1 AK297166.1 AK298410.1 AK308499.1 AK310885.1 AY345239.1 
BC027911.1 CR608978.1 

10 DOTS entries:

DT.40305942  DT.102823164  DT.70104071  DT.100736450  DT.101978080  DT.100664964  DT.120661097  DT.95153259 
DT.100725007  DT.100736452 

24/52 AceView cDNA sequences (see all 52 ):

BQ057705 CB160363 AY345239 CR608978 BQ689669 BQ066794 BP338003 BM478152 
BQ022832 AW665036 AK055679 AU141170 AA491024 BU430384 AI401500 AK023860 
BU741638 BQ894437 BX283857 BM724364 BP345887 CB158529 BI768810 BX497544 

highest scoring ESTs for JMJD5:

AI122764 AA383674 AI288219 AI401500 AK023860 AW276493 BC027911 BI090168 BM724364 BQ022832 

Unigene Cluster for JMJD5:

Jumonji domain containing 5
Hs.145717  [show with all ESTs]
Unigene Representative Sequence: NM_001145348


GeneLoc Exon Structure

5/10 Alternative Splicing Database (ASD) splice patterns (SP) for JMJD5 (see all 10 )

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11a · 11b · 11c ^ 12a · 12b ^ 13a · 13b · 13c ·
SP1:                                                                                                                                -                           
SP2:                    -     -                       -                                                                                                         
SP3:                                                                                                                          -     -     -                     
SP4:                    -     -     -                                                                                                                           
SP5:                    -     -     -                                   -     -                                                                                 

ExUns: 13d
SP1:      
SP2:      
SP3:      
SP4:      
SP5:      

About this scheme

ECgene alternative splicing isoforms for JMJD5

2 Ensembl transcripts including schematic representations:
ENST00000380948  ENST00000286096  

Expression
for JMJD5

(Experimental results according to 1GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
About This Section

JMJD5 expression in normal and diseased human tissues

 Applied Biosystems TaqMan ® Gene Expression Assays for JMJD5

1 / 2 / 3

3 probe-sets matching JMJD5 gene


Affymetrix
probe-set		 Array  GeneAnnot data GeneNote data GeneTide data
# genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
79326_at2, 3 U95-D 1 1.00 1.00 1.00 1.00 AI122764 1.00 1.00 1.00 1

220070_at2, 3 U133-A 1 1.00 1.00 -- -- NM_024773 0.60 1.00 0.82 1

220070_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
GeneDecks  JMJD5 for binary patterns associated with the probe-sets selected above  
About GeneDecksing
About this table    
Data from (Publications) and GNF BioGPS
    About these images
About these images

CGAP SAGE TAG: GCTCAAGGAT

SOURCE GeneReport for Unigene cluster: Hs.145717

Orthologs
for JMJD5

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section
Orthologs for JMJD5 gene from 5/13 species (see all 13 )
Organism Gene Locus Description Human
Similarity		 NCBI accessions
dog
(Canis familiaris)		 JMJD51   -- jumonji domain containing 5 83.37(n)
80.87(a)		 608058  XM_844945.1  XP_850038.1 
chimpanzee
(Pan troglodytes)		 JMJD51   -- jumonji domain containing 5 99.28(n)
99.04(a)		 454003  XM_510890.2  XP_510890.2 
cow
(Bos taurus)		 JMJD51   -- jumonji domain containing 5 83.29(n)
82.47(a)		 507905  NM_001075339.1  NP_001068807.1 
rat
(Rattus norvegicus)		 Jmjd51   -- jumonji domain containing 5 79.34(n)
78.93(a)		 308976  NM_001037196.1  NP_001032273.1 
mouse
(Mus musculus)		 Jmjd51, 5 75
 jumonji domain containing 51, 5 79.1(n)1
78.21(a)1		 770351  NM_029842.21  NP_084118.11 
 AI4814115  AK0140065  (see all 6)
About this table        Species with no ortholog for JMJD5

ENSEMBL Gene Tree for JMJD5

Paralogs
for JMJD5

(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section

Paralogs for JMJD5 gene
HSPBAP12  C2orf602  HIF1AN2  

SNPs/Variants
for JMJD5

(According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
About This Section


10/75 NCBI SNPs in JMJD5 are shown (see all 75 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 53)
ABGenomic DataTranscription DataAllele Frequencies
SNP IDValidChr 16 posSequenceRecsAA
Chg		TypeMoreRecsAllele
freq		PopTotal
sample		More
------------
rs11343671,2
A,C,F,H27140384(+) cctccC/Taccac 1 -- ut31 trp34Minor allele frequency- T:0.35EU EA WA 412
rs47879391,2
A,C,F,H27121465(+) gaataA/Tgactc 1 -- ng51 tfbs34Minor allele frequency- T:0.09EU EA WA 412
rs71971861,2
A,C,F,H27121866(+) AAGGCC/GTGCAT 1 -- ng514Minor allele frequency- G:0.10EU EA WA 420
rs99231781,2
A,C,F,H27139934(+) CGCTGC/TGCACC 1 -- ut31 ese34Minor allele frequency- T:0.35EU EA WA 400
rs71966341,2
A,C,F,H27121725(+) CGATCT/CTCATA 1 -- ng514Minor allele frequency- C:0.10EU EA WA 420
rs120512431,2
C,F,H27121959(+) GGAGTT/GTGTCC 1 -- ng5110Minor allele frequency- G:0.44EU EA WA MN 2080
rs97889091,2
C,F,H27140519(+) GTTTTG/AGCCAT 1 -- ut31 ese34Minor allele frequency- A:0.27EU EA WA 388
rs71983711,2
C,F,H27121890(+) AGGAGA/TGTGTG 1 -- ng514Minor allele frequency- T:0.04EU EA WA 420
rs344455731,2
C,F27137845(-) TCCTCC/GTCCTC 1 E/D mis15Minor allele frequency- G:0.00NA EU EA WA 484
rs99316151,2
F,H27121824(+) CAGTAC/GGAACA 1 -- ng514Minor allele frequency- G:0.01EU EA WA 420
About this table

HapMap Linkage Disequilibrium images for JMJD5 (up to first 250kb)

Disorders & Mutations
for JMJD5

(in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
About This Section

 OMIM: 611917

Medical News
for JMJD5

(Possibly Related Articles in Doctor's Guide)
About This Section

   --

Publications
for JMJD5

(in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
About This Section

9 PubMed articles for JMJD5 gene:

Search for JMJD5

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

 ANDOR
Aliases
Free Text  
  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

Genome Databases showing JMJD5

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
About This Section
Entrez Gene: 79831 HGNC: 25840 AceView: FLJ13798 Ensembl:ENSG00000155666 euGenes: HUgn79831
ECgene: JMJD5 H-InvDB: JMJD5

Other Databases showing JMJD5

(According to HUGE)
About This Section

   --

Specialized Databases showing JMJD5

(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

   --

Licensable Technologies
for JMJD5

(Available from WIS Yeda, Salk, Tufts)
About This Section

  --

Services
for JMJD5

(Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
Enzo Life Sciences, and/or Tocris Bioscience)
About This Section



Products for JMJD5:
 TaqMan ® Gene Expression Assays
 TaqMan ® Genotyping Assays
  Free SNP selection tool



  Invitrogen iPath Pathways  Invitrogen BLOCK-iT™ RNAi
  Invitrogen Antibodies  Invitrogen Assays
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 Lentivirus-delivered shRNAs for JMJD5 Browse small molecules at Sigma-Aldrich
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 Search Tocris compounds for JMJD5




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 Antibodies for JMJD5

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