Cphx1 (cytoplasmic polyadenylated homeobox 1) - Rat Genome Database

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Gene: Cphx1 (cytoplasmic polyadenylated homeobox 1) Rattus norvegicus
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Symbol: Cphx1
Name: cytoplasmic polyadenylated homeobox 1
RGD ID: 1565219
Description: Orthologous to human CPHXL (cytoplasmic polyadenylated homeobox like); INTERACTS WITH 1-chloro-2,4-dinitrobenzene (ortholog); 4-hydroxyphenyl retinamide (ortholog); all-trans-retinoic acid (ortholog).
Type: protein-coding
RefSeq Status: MODEL
Previously known as: Cphx; cytoplasmic polyadenylated homeobox; LIM/homeobox protein Lhx3-like; LOC502042; paired box protein 6 homolog; RGD1565219; similar to RIKEN cDNA C330003B14
RGD Orthologs
Human
Mouse
Bonobo
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8161,540,653 - 1,544,288 (+)NCBIGRCr8
mRatBN7.2161,533,883 - 1,537,248 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl161,528,440 - 1,537,082 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0163,787,141 - 3,796,715 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl163,786,686 - 3,796,047 (-)EnsemblRnor6.0rn6Rnor6.0
RGSC_v3.4161,567,372 - 1,575,617 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera161,504,052 - 1,513,629 (+)NCBICelera
Cytogenetic Map16p16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Biological Process

Cellular Component
nucleus  (IBA)

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. GOA pipeline RGD automated data pipeline

Genomics

Comparative Map Data
Cphx1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8161,540,653 - 1,544,288 (+)NCBIGRCr8
mRatBN7.2161,533,883 - 1,537,248 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl161,528,440 - 1,537,082 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0163,787,141 - 3,796,715 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl163,786,686 - 3,796,047 (-)EnsemblRnor6.0rn6Rnor6.0
RGSC_v3.4161,567,372 - 1,575,617 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera161,504,052 - 1,513,629 (+)NCBICelera
Cytogenetic Map16p16NCBI
CPHXL2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381675,660,227 - 75,677,009 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1675,660,227 - 75,677,009 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p14 Ensembl1675,660,227 - 75,677,009 (-)NCBIGRCh38hg38GRCh38
GRCh371675,694,125 - 75,710,907 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map16q23.1NCBI
T2T-CHM13v2.01681,708,523 - 81,725,300 (-)NCBIT2T-CHM13v2.0
Cphx1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391425,941,983 - 25,956,798 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1425,938,728 - 25,956,780 (+)EnsemblGRCm39 Ensembl
GRCm381425,941,559 - 25,956,374 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1425,938,304 - 25,956,356 (+)EnsemblGRCm38mm10GRCm38
GRCm38.p6 Ensembl1426,081,516 - 26,096,127 (+)EnsemblGRCm38mm10GRCm38
GRCm38.p6 Ensembl1426,082,297 - 26,235,744 (+)EnsemblGRCm38mm10GRCm38
MGSCv371426,762,030 - 26,775,851 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361424,775,728 - 24,789,549 (+)NCBIMGSCv36mm8
MGSCv361421,033,090 - 21,046,916 (+)NCBIMGSCv36mm8
Cytogenetic Map14A3NCBI
cM Map1415.53NCBI
CPHXL2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21885,375,811 - 85,393,423 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11691,298,385 - 91,322,291 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01656,229,302 - 56,240,487 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11675,577,583 - 75,593,362 (-)NCBIpanpan1.1PanPan1.1panPan2

Variants

.
Variants in Cphx1
11 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:76
Count of miRNA genes:69
Interacting mature miRNAs:71
Transcripts:ENSRNOT00000035065
Prediction methods:Microtar, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2325838Bp347Blood pressure QTL 3470.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1613080679Rat
1357403Slep4Serum leptin concentration QTL 43.91blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1619639137Rat
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16122477621Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126727669Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126727669Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16126727669Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16130836262Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16132139025Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133418960Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139533930Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139533930Rat
631561Hcuc2Hepatic copper content QTL 22.8liver copper amount (VT:0003065)liver total copper weight (CMO:0001507)16139533949Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16143534949Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16144588133Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16144977551Rat
1549842Bp248Blood pressure QTL 2480.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)163802452995463Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683223646053497Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat
12903278Am16Aortic mass QTL 160.019aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)168323802995225Rat
12903279Cm115Cardiac mass QTL 1150.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)168323802995225Rat
12903281Cm116Cardiac mass QTL 1160.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)168323802995225Rat
12903952Cm117Cardiac mass QTL 1170.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)168323802995225Rat
12903954Bw186Body weight QTL 1860.011body mass (VT:0001259)body weight (CMO:0000012)168323802995225Rat
2301404Bp321Blood pressure QTL 3210.05arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)168323802995225Rat
12903955Kidm69Kidney mass QTL 690.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)168323804227609Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

hemolymphoid system nervous system reproductive system respiratory system
High
Medium 1
Low 5
Below cutoff 4 2 10 1

Sequence


RefSeq Acc Id: ENSRNOT00000035065   ⟹   ENSRNOP00000033244
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl161,528,440 - 1,537,082 (+)Ensembl
Rnor_6.0 Ensembl163,787,928 - 3,790,988 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000082024   ⟹   ENSRNOP00000071042
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl163,786,686 - 3,790,928 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000085044   ⟹   ENSRNOP00000070820
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl163,795,992 - 3,796,047 (-)Ensembl
RefSeq Acc Id: XM_039095224   ⟹   XP_038951152
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8161,540,653 - 1,544,288 (+)NCBI
mRatBN7.2161,533,883 - 1,537,248 (+)NCBI
Protein Sequences
Protein RefSeqs XP_038951152 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000033244.4
RefSeq Acc Id: ENSRNOP00000071042   ⟸   ENSRNOT00000082024
RefSeq Acc Id: ENSRNOP00000070820   ⟸   ENSRNOT00000085044
RefSeq Acc Id: ENSRNOP00000033244   ⟸   ENSRNOT00000035065
RefSeq Acc Id: XP_038951152   ⟸   XM_039095224
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M859-F1-model_v2 AlphaFold F1M859 1-206 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565219 AgrOrtholog
BioCyc Gene G2FUF-12262 BioCyc
Ensembl Genes ENSRNOG00000025433 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000035065.4 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro Homeobox-like_sf UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/TrEMBL
NCBI Gene 502042 ENTREZGENE
PANTHER CYTOPLASMIC POLYADENYLATED HOMEOBOX-LIKE UniProtKB/TrEMBL
  HOMEOBOX PROTEIN ENGRAILED UniProtKB/TrEMBL
Pfam Homeodomain UniProtKB/TrEMBL
PhenoGen Cphx1 PhenoGen
PROSITE HOMEOBOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000025433 RatGTEx
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/TrEMBL
UniProt F1M859_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-05-25 Cphx1  cytoplasmic polyadenylated homeobox 1  Cphx  cytoplasmic polyadenylated homeobox  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Cphx  cytoplasmic polyadenylated homeobox  RGD1565219_predicted  similar to RIKEN cDNA C330003B14 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1565219_predicted  similar to RIKEN cDNA C330003B14 (predicted)  LOC502042  similar to RIKEN cDNA C330003B14  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC502042  similar to RIKEN cDNA C330003B14      Symbol and Name status set to provisional 70820 PROVISIONAL