Human Gene CHD2 (ENST00000394196.9_6) from GENCODE V47lift37
  Description: chromodomain helicase DNA binding protein 2, transcript variant 1 (from RefSeq NM_001271.4)
Gencode Transcript: ENST00000394196.9_6
Gencode Gene: ENSG00000173575.24_16
Transcript (Including UTRs)
   Position: hg19 chr15:93,443,554-93,571,226 Size: 127,673 Total Exon Count: 39 Strand: +
Coding Region
   Position: hg19 chr15:93,444,468-93,567,935 Size: 123,468 Coding Exon Count: 38 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:93,443,554-93,571,226)mRNA (may differ from genome)Protein (1828 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CHD2_HUMAN
DESCRIPTION: RecName: Full=Chromodomain-helicase-DNA-binding protein 2; Short=CHD-2; EC=3.6.4.12; AltName: Full=ATP-dependent helicase CHD2;
FUNCTION: Sequence-selective DNA-binding protein (By similarity).
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBCELLULAR LOCATION: Nucleus (By similarity).
SIMILARITY: Belongs to the SNF2/RAD54 helicase family.
SIMILARITY: Contains 2 chromo domains.
SIMILARITY: Contains 1 helicase ATP-binding domain.
SIMILARITY: Contains 1 helicase C-terminal domain.

-  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: CHD2
Diseases sorted by gene-association score: epileptic encephalopathy, childhood-onset* (1329), chd2 myoclonic encephalopathy* (418), lennox-gastaut syndrome* (260), myoclonic-astastic epilepsy* (247), photosensitive epilepsy (10), choanal atresia, posterior (5), intellectual disability (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -157.80572-0.276 Picture PostScript Text
3' UTR -1140.003291-0.346 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
IPR023780 - Chromo_domain
IPR000953 - Chromo_domain/shadow
IPR016197 - Chromodomain-like
IPR023779 - Chromodomain_CS
IPR025260 - DUF4208
IPR014001 - Helicase_ATP-bd
IPR001650 - Helicase_C
IPR000330 - SNF2_N

Pfam Domains:
PF00176 - SNF2-related domain
PF00271 - Helicase conserved C-terminal domain
PF00385 - Chromo (CHRromatin Organisation MOdifier) domain
PF04851 - Type III restriction enzyme, res subunit
PF13907 - Domain of unknown function (DUF4208)
PF18375 - CDH1/2 SANT-Helical linker 1

SCOP Domains:
46689 - Homeodomain-like
54160 - Chromo domain-like
52540 - P-loop containing nucleoside triphosphate hydrolases

ModBase Predicted Comparative 3D Structure on O14647
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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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0001046 core promoter sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0004003 ATP-dependent DNA helicase activity
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0042393 histone binding

Biological Process:
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006974 cellular response to DNA damage stimulus
GO:0007517 muscle organ development
GO:0032508 DNA duplex unwinding
GO:0060218 hematopoietic stem cell differentiation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  KJ890907 - Synthetic construct Homo sapiens clone ccsbBroadEn_00301 CHD2 gene, encodes complete protein.
LF207718 - JP 2014500723-A/15221: Polycomb-Associated Non-Coding RNAs.
CR627422 - Homo sapiens mRNA; cDNA DKFZp781D1727 (from clone DKFZp781D1727).
AF006514 - Homo sapiens CHD2 mRNA, complete cds.
BC107885 - Homo sapiens chromodomain helicase DNA binding protein 2, mRNA (cDNA clone IMAGE:6668384).
AK292850 - Homo sapiens cDNA FLJ76689 partial cds, highly similar to Homo sapiens chromodomain helicase DNA binding protein 2 (CHD2), mRNA.
BC007347 - Homo sapiens chromodomain helicase DNA binding protein 2, mRNA (cDNA clone IMAGE:3050321), complete cds.
BC020810 - Homo sapiens chromodomain helicase DNA binding protein 2, mRNA (cDNA clone IMAGE:4293394), complete cds.
JF432271 - Synthetic construct Homo sapiens clone IMAGE:100073443 chromodomain helicase DNA binding protein 2 (CHD2) gene, encodes complete protein.
CU675629 - Synthetic construct Homo sapiens gateway clone IMAGE:100020263 5' read CHD2 mRNA.
BT007050 - Homo sapiens chromodomain helicase DNA binding protein 2 mRNA, complete cds.
BC172425 - Synthetic construct Homo sapiens clone IMAGE:100069119, MGC:199130 chromodomain helicase DNA binding protein 2 (CHD2) mRNA, encodes complete protein.
AK295909 - Homo sapiens cDNA FLJ53879 complete cds, highly similar to Chromodomain-helicase-DNA-binding protein 2 (EC 3.6.1.-).
MA443295 - JP 2018138019-A/15221: Polycomb-Associated Non-Coding RNAs.
LF207720 - JP 2014500723-A/15223: Polycomb-Associated Non-Coding RNAs.
JD340258 - Sequence 321282 from Patent EP1572962.
JD537541 - Sequence 518565 from Patent EP1572962.
JD443938 - Sequence 424962 from Patent EP1572962.
JD406897 - Sequence 387921 from Patent EP1572962.
JD261224 - Sequence 242248 from Patent EP1572962.
JD130075 - Sequence 111099 from Patent EP1572962.
LF368390 - JP 2014500723-A/175893: Polycomb-Associated Non-Coding RNAs.
LF368388 - JP 2014500723-A/175891: Polycomb-Associated Non-Coding RNAs.
LF368387 - JP 2014500723-A/175890: Polycomb-Associated Non-Coding RNAs.
LF368386 - JP 2014500723-A/175889: Polycomb-Associated Non-Coding RNAs.
LF368384 - JP 2014500723-A/175887: Polycomb-Associated Non-Coding RNAs.
MA603967 - JP 2018138019-A/175893: Polycomb-Associated Non-Coding RNAs.
MA603965 - JP 2018138019-A/175891: Polycomb-Associated Non-Coding RNAs.
MA603964 - JP 2018138019-A/175890: Polycomb-Associated Non-Coding RNAs.
MA603963 - JP 2018138019-A/175889: Polycomb-Associated Non-Coding RNAs.
MA603961 - JP 2018138019-A/175887: Polycomb-Associated Non-Coding RNAs.
MA443297 - JP 2018138019-A/15223: Polycomb-Associated Non-Coding RNAs.
LF368366 - JP 2014500723-A/175869: Polycomb-Associated Non-Coding RNAs.
LF368365 - JP 2014500723-A/175868: Polycomb-Associated Non-Coding RNAs.
LF368362 - JP 2014500723-A/175865: Polycomb-Associated Non-Coding RNAs.
LF368358 - JP 2014500723-A/175861: Polycomb-Associated Non-Coding RNAs.
LF368357 - JP 2014500723-A/175860: Polycomb-Associated Non-Coding RNAs.
LF368356 - JP 2014500723-A/175859: Polycomb-Associated Non-Coding RNAs.
LF368355 - JP 2014500723-A/175858: Polycomb-Associated Non-Coding RNAs.
DQ088985 - Homo sapiens CDH2 isoform 1 mRNA, partial cds.
DQ088986 - Homo sapiens CDH2 isoform 2 mRNA, partial cds.
LF368354 - JP 2014500723-A/175857: Polycomb-Associated Non-Coding RNAs.
LF368349 - JP 2014500723-A/175852: Polycomb-Associated Non-Coding RNAs.
LF368348 - JP 2014500723-A/175851: Polycomb-Associated Non-Coding RNAs.
AY429527 - Homo sapiens CHD2v_1 mRNA sequence; alternatively spliced.
AY429528 - Homo sapiens CHD2v_2 mRNA sequence; alternatively spliced.
LF368341 - JP 2014500723-A/175844: Polycomb-Associated Non-Coding RNAs.
LF368340 - JP 2014500723-A/175843: Polycomb-Associated Non-Coding RNAs.
LF368337 - JP 2014500723-A/175840: Polycomb-Associated Non-Coding RNAs.
LF368334 - JP 2014500723-A/175837: Polycomb-Associated Non-Coding RNAs.
LF368333 - JP 2014500723-A/175836: Polycomb-Associated Non-Coding RNAs.
LF368329 - JP 2014500723-A/175832: Polycomb-Associated Non-Coding RNAs.
LF368328 - JP 2014500723-A/175831: Polycomb-Associated Non-Coding RNAs.
LF368327 - JP 2014500723-A/175830: Polycomb-Associated Non-Coding RNAs.
LF368324 - JP 2014500723-A/175827: Polycomb-Associated Non-Coding RNAs.
LF368323 - JP 2014500723-A/175826: Polycomb-Associated Non-Coding RNAs.
LF368322 - JP 2014500723-A/175825: Polycomb-Associated Non-Coding RNAs.
LF368319 - JP 2014500723-A/175822: Polycomb-Associated Non-Coding RNAs.
LF368318 - JP 2014500723-A/175821: Polycomb-Associated Non-Coding RNAs.
LF368317 - JP 2014500723-A/175820: Polycomb-Associated Non-Coding RNAs.
LF368316 - JP 2014500723-A/175819: Polycomb-Associated Non-Coding RNAs.
LF368315 - JP 2014500723-A/175818: Polycomb-Associated Non-Coding RNAs.
LF368314 - JP 2014500723-A/175817: Polycomb-Associated Non-Coding RNAs.
AL831836 - Homo sapiens mRNA; cDNA DKFZp547I1315 (from clone DKFZp547I1315).
JD314647 - Sequence 295671 from Patent EP1572962.
LF368313 - JP 2014500723-A/175816: Polycomb-Associated Non-Coding RNAs.
JD064383 - Sequence 45407 from Patent EP1572962.
JD417259 - Sequence 398283 from Patent EP1572962.
JD066421 - Sequence 47445 from Patent EP1572962.
JD374900 - Sequence 355924 from Patent EP1572962.
JD511895 - Sequence 492919 from Patent EP1572962.
JD361706 - Sequence 342730 from Patent EP1572962.
JD477789 - Sequence 458813 from Patent EP1572962.
JD515981 - Sequence 497005 from Patent EP1572962.
JD552469 - Sequence 533493 from Patent EP1572962.
JD037102 - Sequence 18126 from Patent EP1572962.
JD307253 - Sequence 288277 from Patent EP1572962.
JD222540 - Sequence 203564 from Patent EP1572962.
JD095716 - Sequence 76740 from Patent EP1572962.
JD254925 - Sequence 235949 from Patent EP1572962.
JD455503 - Sequence 436527 from Patent EP1572962.
JD108304 - Sequence 89328 from Patent EP1572962.
JD223229 - Sequence 204253 from Patent EP1572962.
JD512360 - Sequence 493384 from Patent EP1572962.
BX537626 - Homo sapiens mRNA; cDNA DKFZp686E01200 (from clone DKFZp686E01200).
JD258586 - Sequence 239610 from Patent EP1572962.
JD233028 - Sequence 214052 from Patent EP1572962.
JD288204 - Sequence 269228 from Patent EP1572962.
JD223565 - Sequence 204589 from Patent EP1572962.
AK095933 - Homo sapiens cDNA FLJ38614 fis, clone HEART2006521.
JD083991 - Sequence 65015 from Patent EP1572962.
JD112952 - Sequence 93976 from Patent EP1572962.
JD334096 - Sequence 315120 from Patent EP1572962.
JD215760 - Sequence 196784 from Patent EP1572962.
JD162957 - Sequence 143981 from Patent EP1572962.
JD263591 - Sequence 244615 from Patent EP1572962.
JD499805 - Sequence 480829 from Patent EP1572962.
JD475352 - Sequence 456376 from Patent EP1572962.
JD142168 - Sequence 123192 from Patent EP1572962.
BC047036 - Homo sapiens, clone IMAGE:4940955, mRNA.
JD044006 - Sequence 25030 from Patent EP1572962.
JD047276 - Sequence 28300 from Patent EP1572962.
JD373857 - Sequence 354881 from Patent EP1572962.
JD277089 - Sequence 258113 from Patent EP1572962.
JD162215 - Sequence 143239 from Patent EP1572962.
JD082536 - Sequence 63560 from Patent EP1572962.
JD143678 - Sequence 124702 from Patent EP1572962.
JD489762 - Sequence 470786 from Patent EP1572962.
JD263701 - Sequence 244725 from Patent EP1572962.
JD409886 - Sequence 390910 from Patent EP1572962.
JD188870 - Sequence 169894 from Patent EP1572962.
MA603943 - JP 2018138019-A/175869: Polycomb-Associated Non-Coding RNAs.
MA603942 - JP 2018138019-A/175868: Polycomb-Associated Non-Coding RNAs.
MA603939 - JP 2018138019-A/175865: Polycomb-Associated Non-Coding RNAs.
MA603935 - JP 2018138019-A/175861: Polycomb-Associated Non-Coding RNAs.
MA603934 - JP 2018138019-A/175860: Polycomb-Associated Non-Coding RNAs.
MA603933 - JP 2018138019-A/175859: Polycomb-Associated Non-Coding RNAs.
MA603932 - JP 2018138019-A/175858: Polycomb-Associated Non-Coding RNAs.
MA603931 - JP 2018138019-A/175857: Polycomb-Associated Non-Coding RNAs.
MA603926 - JP 2018138019-A/175852: Polycomb-Associated Non-Coding RNAs.
MA603925 - JP 2018138019-A/175851: Polycomb-Associated Non-Coding RNAs.
MA603918 - JP 2018138019-A/175844: Polycomb-Associated Non-Coding RNAs.
MA603917 - JP 2018138019-A/175843: Polycomb-Associated Non-Coding RNAs.
MA603914 - JP 2018138019-A/175840: Polycomb-Associated Non-Coding RNAs.
MA603911 - JP 2018138019-A/175837: Polycomb-Associated Non-Coding RNAs.
MA603910 - JP 2018138019-A/175836: Polycomb-Associated Non-Coding RNAs.
MA603906 - JP 2018138019-A/175832: Polycomb-Associated Non-Coding RNAs.
MA603905 - JP 2018138019-A/175831: Polycomb-Associated Non-Coding RNAs.
MA603904 - JP 2018138019-A/175830: Polycomb-Associated Non-Coding RNAs.
MA603901 - JP 2018138019-A/175827: Polycomb-Associated Non-Coding RNAs.
MA603900 - JP 2018138019-A/175826: Polycomb-Associated Non-Coding RNAs.
MA603899 - JP 2018138019-A/175825: Polycomb-Associated Non-Coding RNAs.
MA603896 - JP 2018138019-A/175822: Polycomb-Associated Non-Coding RNAs.
MA603895 - JP 2018138019-A/175821: Polycomb-Associated Non-Coding RNAs.
MA603894 - JP 2018138019-A/175820: Polycomb-Associated Non-Coding RNAs.
MA603893 - JP 2018138019-A/175819: Polycomb-Associated Non-Coding RNAs.
MA603892 - JP 2018138019-A/175818: Polycomb-Associated Non-Coding RNAs.
MA603891 - JP 2018138019-A/175817: Polycomb-Associated Non-Coding RNAs.
MA603890 - JP 2018138019-A/175816: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: C6G482, CHD2_HUMAN, ENST00000394196.1, ENST00000394196.2, ENST00000394196.3, ENST00000394196.4, ENST00000394196.5, ENST00000394196.6, ENST00000394196.7, ENST00000394196.8, NM_001271, O14647, Q96IP5, uc318wls.1, uc318wls.2
UCSC ID: ENST00000394196.9_6
RefSeq Accession: NM_001271.4
Protein: O14647 (aka CHD2_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene CHD2:
chd2-dis (CHD2-Related Neurodevelopmental Disorders)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.