Chd1l (chromodomain helicase DNA binding protein 1-like) - Rat Genome Database

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Gene: Chd1l (chromodomain helicase DNA binding protein 1-like) Mus musculus
Analyze
Symbol: Chd1l
Name: chromodomain helicase DNA binding protein 1-like
RGD ID: 1323648
MGI Page MGI
Description: Predicted to enable several functions, including ATP hydrolysis activity; histone reader activity; and poly-ADP-D-ribose modification-dependent protein binding activity. Predicted to be involved in DNA repair and chromatin remodeling. Predicted to be located in cytosol; nucleoplasm; and plasma membrane. Predicted to be active in nucleus and site of double-strand break. Is expressed in genitourinary system and liver. Orthologous to human CHD1L (chromodomain helicase DNA binding protein 1 like).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 4432404A22Rik; Alc1; amplified in liver cancer 1; chromodomain-helicase-DNA-binding protein 1-like; Sn; Snf2p
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39397,468,056 - 97,517,538 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl397,468,058 - 97,517,519 (-)EnsemblGRCm39 Ensembl
GRCm38397,560,740 - 97,610,222 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl397,560,742 - 97,610,203 (-)EnsemblGRCm38mm10GRCm38
MGSCv37397,364,671 - 97,414,113 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36397,646,153 - 97,695,595 (-)NCBIMGSCv36mm8
Celera398,960,418 - 99,009,880 (-)NCBICelera
Cytogenetic Map3F2.2NCBI
cM Map342.17NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Functional annotation of a full-length mouse cDNA collection. Kawai J, etal., Nature. 2001 Feb 8;409(6821):685-90.
2. MGDs mouse GO annotations MGD data from the GO Consortium
3. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8889548   PMID:10349636   PMID:10512203   PMID:10922068   PMID:11042159   PMID:11076861   PMID:12471446   PMID:12477932   PMID:12520002   PMID:14610273   PMID:15782199   PMID:15840001  
PMID:16141072   PMID:16141073   PMID:18287559   PMID:19701453   PMID:20335658   PMID:21267068   PMID:21873635   PMID:22922362   PMID:23429299   PMID:23926104   PMID:26201266   PMID:27100146  
PMID:28946814   PMID:33333017  


Genomics

Comparative Map Data
Chd1l
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39397,468,056 - 97,517,538 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl397,468,058 - 97,517,519 (-)EnsemblGRCm39 Ensembl
GRCm38397,560,740 - 97,610,222 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl397,560,742 - 97,610,203 (-)EnsemblGRCm38mm10GRCm38
MGSCv37397,364,671 - 97,414,113 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36397,646,153 - 97,695,595 (-)NCBIMGSCv36mm8
Celera398,960,418 - 99,009,880 (-)NCBICelera
Cytogenetic Map3F2.2NCBI
cM Map342.17NCBI
CHD1L
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381147,172,747 - 147,295,762 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1147,242,654 - 147,295,765 (+)EnsemblGRCh38hg38GRCh38
GRCh371146,644,326 - 146,767,443 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361145,180,915 - 145,234,067 (+)NCBINCBI36Build 36hg18NCBI36
Build 341143,939,149 - 143,992,257NCBI
Celera1122,216,559 - 122,269,716 (-)NCBICelera
Cytogenetic Map1q21.1NCBI
HuRef1120,126,695 - 120,180,299 (+)NCBIHuRef
CHM1_11148,610,767 - 148,663,892 (+)NCBICHM1_1
T2T-CHM13v2.01147,512,572 - 147,635,662 (-)NCBIT2T-CHM13v2.0
Chd1l
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82187,819,869 - 187,906,359 (-)NCBIGRCr8
mRatBN7.22185,138,526 - 185,217,498 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2185,139,308 - 185,217,595 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.02199,714,044 - 199,792,270 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2199,716,713 - 199,771,896 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02219,191,907 - 219,249,938 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42192,382,644 - 192,438,157 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12192,345,407 - 192,400,960 (-)NCBI
Celera2177,632,171 - 177,710,093 (-)NCBICelera
Cytogenetic Map2q34NCBI
Chd1l
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555681,132,857 - 1,189,024 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555681,132,594 - 1,189,176 (-)NCBIChiLan1.0ChiLan1.0
CHD1L
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21102,430,969 - 102,555,824 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11102,019,317 - 102,144,906 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01122,595,246 - 122,720,788 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11112,809,272 - 112,862,234 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1112,809,274 - 112,862,219 (-)Ensemblpanpan1.1panPan2
CHD1L
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11757,725,823 - 57,806,065 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1757,725,640 - 57,806,048 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1757,270,007 - 57,274,456 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01758,725,649 - 58,814,453 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1758,725,642 - 58,814,454 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11757,618,145 - 57,700,588 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01757,667,050 - 57,755,705 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01758,399,695 - 58,482,167 (+)NCBIUU_Cfam_GSD_1.0
Chd1l
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024412066277,313 - 309,747 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004937024164,327 - 216,851 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004937024164,309 - 216,967 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHD1L
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4100,264,968 - 100,425,692 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14100,264,963 - 100,425,728 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24110,096,642 - 110,255,293 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CHD1L
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Vero_WHO_p1.0NW_02366603814,959,047 - 15,013,195 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Chd1l
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462477216,178,139 - 16,241,624 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462477216,178,080 - 16,241,869 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Chd1l
1657 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:104
Count of miRNA genes:96
Interacting mature miRNAs:99
Transcripts:ENSMUST00000029730
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
26884378Skwq6_mskull length QTL 6, 10 week (mouse)351907421102307316Mouse
1302052Etohcta4_methanol conditioned taste aversion 4 (mouse)Not determined391000105125008748Mouse
27226732Tibmd3_mtibia midshaft diameter 3, 10 week (mouse)396607316147805636Mouse
11049572Lmr11c_mleishmaniasis resistance 11c (mouse)372139967106140094Mouse
1357583Sle18_msystematic lupus erythematosus susceptibility 18 (mouse)Not determined387208904125316236Mouse
1300595Tmevd2_mTheiler's murine encephalomyelitis virus induced demyelinating disease susceptibility 2 (mouse)Not determined375463302109463549Mouse
12738440Twq3_mtestis weight QTL 3 (mouse)387228015121228015Mouse
26884380Skwq1_mskull length QTL 1, 5 week (mouse)343954435101607316Mouse
1301904Iba2_minduction of brown adipocytes 2 (mouse)Not determined382147043116147184Mouse
11041900Lmr11a_mleishmaniasis resistance 11a (mouse)383463991117464137Mouse
11039511Ltpr3c_mLeishmania tropica response 3c (mouse)383463991117464137Mouse
1301398Rapop3_mradiation-induced apoptosis 3 (mouse)Not determined390511217100464137Mouse
11039509Ltpr3e_mLeishmania tropica response 3e (mouse)383463991117464137Mouse
4142178Ctrq2_mC. trachomatis resistance QTL 2 (mouse)Not determined389139967137453008Mouse
11039507Ltpr3g_mLeishmania tropica response 3g (mouse)383463991117464137Mouse
4142099Cq3_mcholesterol QTL 3 (mouse)Not determined384888918118889067Mouse
1301349Pgia26_mproteoglycan induced arthritis 26 (mouse)Not determined392251533126251650Mouse
4142399Aec1_mautoimmune exocrinopathy 1 (mouse)Not determined7586174102690034Mouse
26884427Cvht4_mcranial vault height 4, 10 week (mouse)316054164109707316Mouse
25314313Syncl1_msynaptonemal complex length 1 (mouse)367907333128393649Mouse
10766455Sle22_msystematic lupus erythematosus susceptibility 22 (mouse)390376936124377072Mouse
13207570Tcq12_mtotal cholesterol QTL 12 (mouse)316504164130163649Mouse
13208566Bmiq5_mbody mass index QTL 5 (mouse)340954435115793649Mouse
1301947Pcfm3_mperiosteal circumference and femur length 3 (mouse)Not determined381084652115084797Mouse
14746984Manh54_mmandible shape 54 (mouse)385289152119289152Mouse
11251721Ewc3_methanol withdrawal and consumption 3 (mouse)369568554103568554Mouse
26884382Bzwq1_mbi-zygomatic width QTL 1, 5 week (mouse)352207421137205761Mouse
11039519Ltpr3_mLeishmania tropica response 3 (mouse)356704102100464137Mouse
11039512Ltpr3b_mLeishmania tropica response 3b (mouse)383463991117464137Mouse
1301392Eae3_msusceptibility to experimental allergic encephalomyelitis 3 (mouse)Not determined379548730113548837Mouse
11039510Ltpr3d_mLeishmania tropica response 3d (mouse)383463991117464137Mouse
1301422Sle11_msystematic lupus erythematosus susceptibility 11 (mouse)Not determined370208904104209042Mouse
1300982Lmr11_mleishmaniasis resistance 11 (mouse)Not determined372139967106140094Mouse
1301272Cfsw1_mcystic fibrosis survival to weaning 1 (mouse)Not determined383882912117883044Mouse
14747001Mancz4_mmandible centroid size 4 (mouse)390378017124378017Mouse
26884436Zlq3_mzygomatic length QTL 3, 10 week (mouse)33265060142405761Mouse
26884422Cvht7_mcranial vault height 7, 16 week (mouse)328954149118893649Mouse
1302056Orgwq4_morgan weight QTL 4 (mouse)Not determined330067588147304689Mouse
1301705Sles3_msystemic lupus erythmatosus suppressor 3 (mouse)Not determined337174862143353183Mouse
1301971Cia5_mcollagen induced arthritis QTL 5 (mouse)Not determined366046658100046795Mouse
1301791Char4_mP. chabaudi malaria resistance QTL 4 (mouse)Not determined369625509100655290Mouse
11039508Ltpr3f_mLeishmania tropica response 3f (mouse)383463991117464137Mouse


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000029730   ⟹   ENSMUSP00000029730
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl397,468,058 - 97,517,519 (-)Ensembl
GRCm38.p6 Ensembl397,560,742 - 97,610,203 (-)Ensembl
RefSeq Acc Id: ENSMUST00000195962
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl397,469,972 - 97,474,428 (-)Ensembl
GRCm38.p6 Ensembl397,562,656 - 97,567,112 (-)Ensembl
RefSeq Acc Id: ENSMUST00000197304
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl397,478,351 - 97,517,508 (-)Ensembl
GRCm38.p6 Ensembl397,571,035 - 97,610,192 (-)Ensembl
RefSeq Acc Id: NM_001418820   ⟹   NP_001405749
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39397,468,056 - 97,517,529 (-)NCBI
RefSeq Acc Id: NM_026539   ⟹   NP_080815
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39397,468,056 - 97,517,529 (-)NCBI
GRCm38397,560,748 - 97,610,190 (-)NCBI
MGSCv37397,364,671 - 97,414,113 (-)RGD
Celera398,960,418 - 99,009,880 (-)RGD
cM Map3 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_017319701   ⟹   XP_017175190
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39397,480,876 - 97,517,538 (-)NCBI
GRCm38397,573,801 - 97,610,222 (-)NCBI
Sequence:
RefSeq Acc Id: XM_036163259   ⟹   XP_036019152
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39397,480,872 - 97,517,538 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_080815   ⟸   NM_026539
- Peptide Label: isoform 1
- UniProtKB: Q3TMX1 (UniProtKB/Swiss-Prot),   Q6P5C0 (UniProtKB/Swiss-Prot),   Q9CXF7 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017175190   ⟸   XM_017319701
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSMUSP00000029730   ⟸   ENSMUST00000029730
RefSeq Acc Id: XP_036019152   ⟸   XM_036163259
- Peptide Label: isoform X3
RefSeq Acc Id: NP_001405749   ⟸   NM_001418820
- Peptide Label: isoform 2
Protein Domains
Helicase ATP-binding   Helicase C-terminal   Macro

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9CXF7-F1-model_v2 AlphaFold Q9CXF7 1-900 view protein structure

Promoters
RGD ID:6833573
Promoter ID:MM_KWN:35446
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day3,   3T3L1_Day4,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:ENSMUST00000029730,   UC008QOX.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36397,413,746 - 97,414,246 (-)MPROMDB
RGD ID:6881738
Promoter ID:EPDNEW_M4320
Type:initiation region
Name:Chd1l_1
Description:Mus musculus chromodomain helicase DNA binding protein 1-like, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38397,610,179 - 97,610,239EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1915308 AgrOrtholog
Ensembl Genes ENSMUSG00000028089 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000029730 ENTREZGENE
  ENSMUST00000029730.5 UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.220.10 UniProtKB/Swiss-Prot
  3.40.50.10810 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.50.300 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro ALC1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Helicase_ATP-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Helicase_C UniProtKB/Swiss-Prot
  Macro_dom UniProtKB/Swiss-Prot
  Macro_dom-like UniProtKB/Swiss-Prot
  P-loop_NTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SNF2-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SNF2/RAD54-like_C UniProtKB/Swiss-Prot
  SNF2_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:68058 UniProtKB/Swiss-Prot
MGD MGI:1915308 ENTREZGENE
NCBI Gene 68058 ENTREZGENE
PANTHER CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 1-LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR47157 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Helicase_C UniProtKB/Swiss-Prot
  SNF2_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Chd1l PhenoGen
PROSITE HELICASE_ATP_BIND_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HELICASE_CTER UniProtKB/Swiss-Prot
  MACRO UniProtKB/Swiss-Prot
SMART DEXDc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HELICc UniProtKB/Swiss-Prot
Superfamily-SCOP SSF52540 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52949 UniProtKB/Swiss-Prot
UniProt CHD1L_MOUSE UniProtKB/Swiss-Prot
  Q3TMX1 ENTREZGENE
  Q6P5C0 ENTREZGENE
  Q8BIZ9_MOUSE UniProtKB/TrEMBL
  Q9CRZ3_MOUSE UniProtKB/TrEMBL
  Q9CXF7 ENTREZGENE
UniProt Secondary Q3TMX1 UniProtKB/Swiss-Prot
  Q6P5C0 UniProtKB/Swiss-Prot