Chpf2 (chondroitin polymerizing factor 2) - Rat Genome Database

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Gene: Chpf2 (chondroitin polymerizing factor 2) Mus musculus
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Symbol: Chpf2
Name: chondroitin polymerizing factor 2
RGD ID: 1314999
MGI Page MGI
Description: Predicted to have glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity. Predicted to be involved in chondroitin sulfate biosynthetic process. Orthologous to human CHPF2 (chondroitin polymerizing factor 2); PARTICIPATES IN chondroitin sulfate biosynthetic pathway; INTERACTS WITH 1,2-dimethylhydrazine; 2,3,7,8-tetrachlorodibenzodioxine; 4-hydroxyphenyl retinamide.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: 2010209O12Rik; AW060945; chondroitin sulfate glucuronyltransferase; Gm42230; mir-671; mKIAA1402; predicted gene, 42230
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39524,788,950 - 24,799,396 (+)NCBIGRCm39mm39
GRCm39 Ensembl524,791,739 - 24,799,554 (+)Ensembl
GRCm38524,586,744 - 24,594,398 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl524,586,741 - 24,594,556 (+)EnsemblGRCm38mm10GRCm38
MGSCv37524,092,568 - 24,098,305 (+)NCBIGRCm37mm9NCBIm37
Celera521,536,356 - 21,542,131 (+)NCBICelera
Cytogenetic Map5A3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:8889548   PMID:10349636   PMID:10922068   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:12693553   PMID:15782199   PMID:16141072   PMID:16141073  
PMID:20562862   PMID:21037258   PMID:21873635  


Genomics

Comparative Map Data
Chpf2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39524,788,950 - 24,799,396 (+)NCBIGRCm39mm39
GRCm39 Ensembl524,791,739 - 24,799,554 (+)Ensembl
GRCm38524,586,744 - 24,594,398 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl524,586,741 - 24,594,556 (+)EnsemblGRCm38mm10GRCm38
MGSCv37524,092,568 - 24,098,305 (+)NCBIGRCm37mm9NCBIm37
Celera521,536,356 - 21,542,131 (+)NCBICelera
Cytogenetic Map5A3NCBI
CHPF2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl7151,232,489 - 151,238,827 (+)EnsemblGRCh38hg38GRCh38
GRCh387151,232,483 - 151,238,822 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh377150,929,569 - 150,935,908 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 367150,560,518 - 150,566,838 (+)NCBINCBI36hg18NCBI36
Celera7145,486,944 - 145,493,264 (+)NCBI
Cytogenetic Map7q36.1NCBI
HuRef7144,741,123 - 144,747,445 (+)NCBIHuRef
CHM1_17150,937,986 - 150,944,308 (+)NCBICHM1_1
CRA_TCAGchr7v27150,259,122 - 150,265,442 (+)NCBI
Chpf2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2410,578,470 - 10,585,940 (-)NCBI
Rnor_6.0 Ensembl47,108,462 - 7,113,919 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.047,108,461 - 7,113,940 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.047,120,974 - 7,126,445 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.445,959,923 - 5,965,385 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.145,960,045 - 5,964,194 (-)NCBI
Celera46,196,444 - 6,201,906 (-)NCBICelera
Cytogenetic Map4q11NCBI
Chpf2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554915,648,044 - 5,653,158 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554915,649,079 - 5,653,158 (+)NCBIChiLan1.0ChiLan1.0
CHPF2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.17154,971,194 - 154,977,557 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7154,971,194 - 154,977,557 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v07142,818,243 - 142,825,718 (+)NCBIMhudiblu_PPA_v0panPan3
Chpf2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244051186,258,376 - 6,265,991 (-)NCBI
SpeTri2.0NW_0049365276,637,563 - 6,643,051 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHPF2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.121119,417,357 - 119,423,601 (+)NCBI
ChlSab1.1 Ensembl21119,418,793 - 119,423,455 (+)Ensembl
Vero_WHO_p1.0NW_02366607215,389,156 - 15,394,446 (+)NCBI
Chpf2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248005,406,606 - 5,412,396 (-)NCBI

Position Markers
AW060945  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38524,592,254 - 24,592,391UniSTSGRCm38
MGSCv37524,098,072 - 24,098,209UniSTSGRCm37
Celera521,541,897 - 21,542,034UniSTS
Cytogenetic Map5A3UniSTS
Whitehead/MRC_RH5283.6UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
12904958Gmmq8_mgastrocnemius muscle mass QTL 8 (mouse)5129371157Mouse
10401122Pgia41_mproteoglycan induced arthritis 41 (mouse)Not determined561814634618282Mouse
15039371Nmrs21_mNAFLD-associated magnetic resonance shift 21 (mouse)5329982537299825Mouse
1301806Actd2_mactivity-distance traveled 2 (mouse)Not determined5517952239179654Mouse
4141207Imrfq1_mimmune response to Factor IX QTL 1 (mouse)Not determined5791911941919241Mouse
7394748Mom5_mmodifier of Min 5 (mouse)Not determined5879767233318293Mouse
1301693Sle6_msystemic lupus erythematosus susceptibility 6 (mouse)Not determined5884069387693978Mouse
1357478Kdnw1_mkidney weight 1 (mouse)Not determined5886594940372526Mouse
14696730Kidlq1_mkidney weight, left QTL 1 (mouse)51340580847405808Mouse
1301685Estq2_mestradiol regulated response QTL 2 (mouse)Not determined51547674049476846Mouse
1300719Iba5_minduction of brown adipocytes 5 (mouse)Not determined52052964954529790Mouse
1301776Skts3_mskin tumor susceptibility 3 (mouse)Not determined52150995255510060Mouse
11537368Hmtb10_mhemostasis and thrombosis 10 (mouse)52189582554342976Mouse
11537367Hmtb11_mhemostasis and thrombosis 11 (mouse)52189582564649236Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:737
Count of miRNA genes:451
Interacting mature miRNAs:529
Transcripts:ENSMUST00000088295, ENSMUST00000121863
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.


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_133913 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_155297 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_036164705 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC116136 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK008483 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK089404 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK122504 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK138814 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK179428 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK203222 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK207269 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK219661 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC019714 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC036970 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC047275 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BE854619 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH466586 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  LM609652 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSMUST00000088295   ⟹   ENSMUSP00000085633
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl524,586,741 - 24,594,395 (+)Ensembl
RefSeq Acc Id: ENSMUST00000121863   ⟹   ENSMUSP00000112804
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl524,586,750 - 24,592,484 (+)Ensembl
RefSeq Acc Id: ENSMUST00000197318   ⟹   ENSMUSP00000143185
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl524,586,825 - 24,591,220 (+)Ensembl
RefSeq Acc Id: ENSMUST00000197566
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl524,586,772 - 24,588,248 (+)Ensembl
RefSeq Acc Id: ENSMUST00000197933
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl524,593,487 - 24,594,556 (+)Ensembl
RefSeq Acc Id: ENSMUST00000198521
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl524,586,742 - 24,589,173 (+)Ensembl
RefSeq Acc Id: NM_133913   ⟹   NP_598674
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39524,791,748 - 24,797,485 (+)NCBI
GRCm38524,586,750 - 24,592,487 (+)NCBI
MGSCv37524,092,568 - 24,098,305 (+)RGD
Celera521,536,356 - 21,542,131 (+)RGD
cM Map5 ENTREZGENE
Sequence:
RefSeq Acc Id: NR_155297
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39524,791,742 - 24,799,396 (+)NCBI
GRCm38524,586,744 - 24,594,398 (+)NCBI
Sequence:
RefSeq Acc Id: XM_036164705   ⟹   XP_036020598
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39524,788,950 - 24,799,394 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_598674   ⟸   NM_133913
- Peptide Label: precursor
- UniProtKB: Q3UU43 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000143185   ⟸   ENSMUST00000197318
RefSeq Acc Id: ENSMUSP00000085633   ⟸   ENSMUST00000088295
RefSeq Acc Id: ENSMUSP00000112804   ⟸   ENSMUST00000121863
RefSeq Acc Id: XP_036020598   ⟸   XM_036164705
- Peptide Label: isoform X1

Promoters
RGD ID:6886158
Promoter ID:EPDNEW_M6530
Type:initiation region
Name:Chpf2_1
Description:Mus musculus chondroitin polymerizing factor 2 , transcript variant1, 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
GRCm38524,586,745 - 24,586,805EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1917522 AgrOrtholog
Ensembl Genes ENSMUSG00000038181 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000085633 ENTREZGENE, UniProtKB/TrEMBL
  ENSMUSP00000112804 ENTREZGENE, UniProtKB/TrEMBL
  ENSMUSP00000143185 UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000088295 ENTREZGENE, UniProtKB/TrEMBL
  ENSMUST00000121863 ENTREZGENE, UniProtKB/TrEMBL
  ENSMUST00000197318 UniProtKB/TrEMBL
InterPro Chond_GalNAc UniProtKB/TrEMBL
KEGG Report mmu:100910 UniProtKB/TrEMBL
MGD MGI:1917522 ENTREZGENE
NCBI Gene 100910 ENTREZGENE
Pfam CHGN UniProtKB/TrEMBL
PhenoGen Chpf2 PhenoGen
UniProt A0A0G2JFI5_MOUSE UniProtKB/TrEMBL
  Q3UU43 ENTREZGENE, UniProtKB/TrEMBL
  Q80VD4_MOUSE UniProtKB/TrEMBL
  Q8C228_MOUSE UniProtKB/TrEMBL
  Q8VCJ5_MOUSE UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-04-10 Chpf2  chondroitin polymerizing factor 2  Gm42230  predicted gene, 42230  Data Merged 737654 PROVISIONAL
2011-07-27 Chpf2  chondroitin polymerizing factor 2  2010209O12Rik  RIKEN cDNA 2010209O12 gene  Symbol and/or name change 5135510 APPROVED