Human Gene CHD5 (ENST00000262450.8) from GENCODE V44
  Description: Homo sapiens chromodomain helicase DNA binding protein 5 (CHD5), mRNA. (from RefSeq NM_015557)
RefSeq Summary (NM_015557): This gene encodes a member of the chromodomain helicase DNA-binding protein family. Members of this family are characterized by a chromodomain, a helicase ATP-binding domain and an additional functional domain. This gene encodes a neuron-specific protein that may function in chromatin remodeling and gene transcription. This gene is a potential tumor suppressor gene that may play a role in the development of neuroblastoma. [provided by RefSeq, Feb 2012]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments.
Gencode Transcript: ENST00000262450.8
Gencode Gene: ENSG00000116254.18
Transcript (Including UTRs)
   Position: hg38 chr1:6,101,787-6,180,321 Size: 78,535 Total Exon Count: 42 Strand: -
Coding Region
   Position: hg38 chr1:6,106,280-6,180,023 Size: 73,744 Coding Exon Count: 41 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr1:6,101,787-6,180,321)mRNA (may differ from genome)Protein (1954 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Chromodomain-helicase-DNA-binding protein 5; Short=CHD-5; EC=; AltName: Full=ATP-dependent helicase CHD5;
FUNCTION: May play a role in the development of the nervous system and the pathogenesis of neural tumors.
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBCELLULAR LOCATION: Nucleus (By similarity).
TISSUE SPECIFICITY: Preferentially expressed in total brain, fetal brain, and cerebellum. It is also moderately expressed in the adrenal gland.
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.
SIMILARITY: Contains 2 PHD-type zinc fingers.

-  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: CHD5
Diseases sorted by gene-association score: neuroblastoma (3)

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 47.39 RPKM in Pituitary
Total median expression: 307.97 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  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 -182.80298-0.613 Picture PostScript Text
3' UTR -1650.003687-0.448 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
IPR012957 - CHD_C2
IPR012958 - CHD_N
IPR023780 - Chromo_domain
IPR000953 - Chromo_domain/shadow
IPR016197 - Chromodomain-like
IPR002464 - DNA/RNA_helicase_DEAH_CS
IPR009462 - DUF1086
IPR009463 - DUF1087
IPR014001 - Helicase_ATP-bd
IPR001650 - Helicase_C
IPR000330 - SNF2_N
IPR019786 - Zinc_finger_PHD-type_CS
IPR011011 - Znf_FYVE_PHD
IPR001965 - Znf_PHD
IPR019787 - Znf_PHD-finger
IPR001841 - Znf_RING

Pfam Domains:
PF08074 - CHDCT2 (NUC038) domain
PF08073 - CHDNT (NUC034) domain
PF00385 - Chromo (CHRromatin Organisation MOdifier) domain
PF06461 - Domain of Unknown Function (DUF1086)
PF06465 - Domain of Unknown Function (DUF1087)
PF00271 - Helicase conserved C-terminal domain
PF00628 - PHD-finger
PF00176 - SNF2 family N-terminal domain

ModBase Predicted Comparative 3D Structure on Q8TDI0
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
Genome BrowserGenome BrowserGenome BrowserGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein SequenceProtein SequenceProtein Sequence  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003677 DNA binding
GO:0004386 helicase activity
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
GO:0061628 H3K27me3 modified histone binding

Biological Process:
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007283 spermatogenesis
GO:0007399 nervous system development
GO:0008285 negative regulation of cell proliferation
GO:0021895 cerebral cortex neuron differentiation
GO:0030154 cell differentiation
GO:0035093 spermatogenesis, exchange of chromosomal proteins
GO:0043967 histone H4 acetylation
GO:0060850 regulation of transcription involved in cell fate commitment
GO:0098532 histone H3-K27 trimethylation
GO:1901798 positive regulation of signal transduction by p53 class mediator

Cellular Component:
GO:0000792 heterochromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005829 cytosol
GO:0016020 membrane
GO:0016581 NuRD complex
GO:0016607 nuclear speck

-  Descriptions from all associated GenBank mRNAs
  LF213892 - JP 2014500723-A/21395: Polycomb-Associated Non-Coding RNAs.
MA449469 - JP 2018138019-A/21395: Polycomb-Associated Non-Coding RNAs.
AF425231 - Homo sapiens chromodomain helicase DNA binding protein 5 (CHD5) mRNA, complete cds.
AK127046 - Homo sapiens cDNA FLJ45103 fis, clone BRAWH3032571, moderately similar to Chromodomain helicase-DNA-binding protein 4.
BC146381 - Synthetic construct Homo sapiens clone IMAGE:100015145, MGC:180222 chromodomain helicase DNA binding protein 5 (CHD5) mRNA, encodes complete protein.
BC148803 - Synthetic construct Homo sapiens clone IMAGE:100015854, MGC:183196 chromodomain helicase DNA binding protein 5 (CHD5) mRNA, encodes complete protein.
AB527126 - Synthetic construct DNA, clone: pF1KB7323, Homo sapiens CHD5 gene for Chromodomain-helicase-DNA-binding protein 5, without stop codon, in Flexi system.
LF206748 - JP 2014500723-A/14251: Polycomb-Associated Non-Coding RNAs.
MA442325 - JP 2018138019-A/14251: Polycomb-Associated Non-Coding RNAs.
AB007913 - Homo sapiens mRNA for KIAA0444 protein, partial cds.
AK091386 - Homo sapiens cDNA FLJ34067 fis, clone FCBBF3001914, highly similar to Chromodomain helicase-DNA-binding protein 5 (EC 3.6.1.-).
AX746951 - Sequence 476 from Patent EP1308459.
JD387336 - Sequence 368360 from Patent EP1572962.
JD466667 - Sequence 447691 from Patent EP1572962.
JD045394 - Sequence 26418 from Patent EP1572962.
JD118638 - Sequence 99662 from Patent EP1572962.
JD388544 - Sequence 369568 from Patent EP1572962.
JD166837 - Sequence 147861 from Patent EP1572962.
JD488293 - Sequence 469317 from Patent EP1572962.
JD309514 - Sequence 290538 from Patent EP1572962.
JD268908 - Sequence 249932 from Patent EP1572962.
JD397590 - Sequence 378614 from Patent EP1572962.
JD256475 - Sequence 237499 from Patent EP1572962.
JD123109 - Sequence 104133 from Patent EP1572962.
JD488427 - Sequence 469451 from Patent EP1572962.
JD541380 - Sequence 522404 from Patent EP1572962.
JD456488 - Sequence 437512 from Patent EP1572962.
JD075585 - Sequence 56609 from Patent EP1572962.
JD533236 - Sequence 514260 from Patent EP1572962.
JD531312 - Sequence 512336 from Patent EP1572962.
JD327154 - Sequence 308178 from Patent EP1572962.
JD139594 - Sequence 120618 from Patent EP1572962.
JD375417 - Sequence 356441 from Patent EP1572962.
JD219643 - Sequence 200667 from Patent EP1572962.
JD561239 - Sequence 542263 from Patent EP1572962.
JD210346 - Sequence 191370 from Patent EP1572962.
JD216608 - Sequence 197632 from Patent EP1572962.
JD477487 - Sequence 458511 from Patent EP1572962.
JD394054 - Sequence 375078 from Patent EP1572962.
JD526401 - Sequence 507425 from Patent EP1572962.
JD254243 - Sequence 235267 from Patent EP1572962.
JD393727 - Sequence 374751 from Patent EP1572962.
JD089291 - Sequence 70315 from Patent EP1572962.
JD362175 - Sequence 343199 from Patent EP1572962.
JD108606 - Sequence 89630 from Patent EP1572962.
JD515357 - Sequence 496381 from Patent EP1572962.
JD452641 - Sequence 433665 from Patent EP1572962.
JD465013 - Sequence 446037 from Patent EP1572962.
JD144427 - Sequence 125451 from Patent EP1572962.
JD133809 - Sequence 114833 from Patent EP1572962.
JD392417 - Sequence 373441 from Patent EP1572962.
JD206829 - Sequence 187853 from Patent EP1572962.
JD149741 - Sequence 130765 from Patent EP1572962.
JD405004 - Sequence 386028 from Patent EP1572962.
JD461214 - Sequence 442238 from Patent EP1572962.
JD478098 - Sequence 459122 from Patent EP1572962.
JD560838 - Sequence 541862 from Patent EP1572962.
JD432366 - Sequence 413390 from Patent EP1572962.
BC048142 - Homo sapiens cDNA clone IMAGE:5286952.
JD362609 - Sequence 343633 from Patent EP1572962.
JD082986 - Sequence 64010 from Patent EP1572962.
JD176712 - Sequence 157736 from Patent EP1572962.
JD401483 - Sequence 382507 from Patent EP1572962.
JD560134 - Sequence 541158 from Patent EP1572962.
JD100815 - Sequence 81839 from Patent EP1572962.
JD450913 - Sequence 431937 from Patent EP1572962.
JD479890 - Sequence 460914 from Patent EP1572962.
JD160103 - Sequence 141127 from Patent EP1572962.
JD390449 - Sequence 371473 from Patent EP1572962.
JD392421 - Sequence 373445 from Patent EP1572962.
JD420044 - Sequence 401068 from Patent EP1572962.
JD067619 - Sequence 48643 from Patent EP1572962.
JD128421 - Sequence 109445 from Patent EP1572962.
JD192516 - Sequence 173540 from Patent EP1572962.
JD157845 - Sequence 138869 from Patent EP1572962.
JD496375 - Sequence 477399 from Patent EP1572962.
JD271123 - Sequence 252147 from Patent EP1572962.
JD159323 - Sequence 140347 from Patent EP1572962.
JD118196 - Sequence 99220 from Patent EP1572962.
JD457100 - Sequence 438124 from Patent EP1572962.
JD219520 - Sequence 200544 from Patent EP1572962.
JD349180 - Sequence 330204 from Patent EP1572962.
JD521821 - Sequence 502845 from Patent EP1572962.
JD465297 - Sequence 446321 from Patent EP1572962.
JD402499 - Sequence 383523 from Patent EP1572962.
JD253574 - Sequence 234598 from Patent EP1572962.
JD161491 - Sequence 142515 from Patent EP1572962.
JD133917 - Sequence 114941 from Patent EP1572962.
JD240123 - Sequence 221147 from Patent EP1572962.
AL137693 - Homo sapiens mRNA; cDNA DKFZp434P202 (from clone DKFZp434P202).
AL110281 - Homo sapiens mRNA; cDNA DKFZp434K213 (from clone DKFZp434K213).
AK126012 - Homo sapiens cDNA FLJ44024 fis, clone TESTI4026524, moderately similar to Chromodomain helicase-DNA-binding protein 4.
AL117491 - Homo sapiens mRNA; cDNA DKFZp434N231 (from clone DKFZp434N231).
JD075628 - Sequence 56652 from Patent EP1572962.
JD403348 - Sequence 384372 from Patent EP1572962.
JD297446 - Sequence 278470 from Patent EP1572962.
JD106380 - Sequence 87404 from Patent EP1572962.
LF357513 - JP 2014500723-A/165016: Polycomb-Associated Non-Coding RNAs.
MA593090 - JP 2018138019-A/165016: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: CHD5_HUMAN, ENST00000262450.1, ENST00000262450.2, ENST00000262450.3, ENST00000262450.4, ENST00000262450.5, ENST00000262450.6, ENST00000262450.7, KIAA0444, NM_015557, O75032, Q5TG89, Q7LGH2, Q8TDI0, Q9UFR9, uc001amb.1, uc001amb.2, uc001amb.3, uc001amb.4
UCSC ID: ENST00000262450.8
RefSeq Accession: NM_015557
Protein: Q8TDI0 (aka CHD5_HUMAN)

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