RetrogeneDB ID:

retro_cfam_209

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:X:47070380..47071328(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCAFG00000028624
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:FOXR1
Ensembl ID:ENSCAFG00000012417
Aliases:None
Description:forkhead box R1 [Source:HGNC Symbol;Acc:29980]


Retrocopy-Parental alignment summary:






>retro_cfam_209
ATGGACATAAAACTAAAAAATCCCGATTTCTGGTACAGTCTCCATGGCCAGGTCCCAGGGCTGCTGGACTGGGACATGGG
GAATGAATTGTTCTTGCCCTCCACCACAGACCAATGCCACTTAACTGAGCAGAACCTTGCCCAATATAGACTCCGAGTAA
TGGAGCCCCCAAAGGTGCCTCAAGAGAGGAGAACCAGTCCAGACAAAGATGGTCCTGACTCTAAACCTAACCTGTGGATG
TGGGTAAATCCCAACATCATGTGCCCCCTTGGCAGCCAGGAGACCCTAAATCCCAGTAAAGAAAAGGATCTGACAAGCAT
GCTTCCTTACCCTCAGCCACTCCCAAAGAATGAGTCTAACTGCTCAAAGGCCACAGTGATGGAATCCCTGACAGCTTCCT
CCAGCAAGAAATCTTCCCCACAGAAGCGGTTCATCTATCCTCCCAGTGACTGGGAGCTCACAAAAGAAGAAACCGAGGAA
CAAGAGAACAACTGCTCTGTGTCCCTCCAATCCCCTAACAAAAGGGAGTGCTTCCAGAACCAGAAGCTATGGCAAGGCAA
CAGCCAGGAGAGGAAGTCCTGGCCCCGGCCTCCACTCAATTACAGTCACCTAATTGCCCTGGCATTAAGAAACAGCCCAC
CCTGTGGCCTCAATGTGCAAGAGATCTACAATTTCACCCGACAGCATTTCCCCTTTTTTTGGACAGCTCCAAATGGCTGG
AAAAACACCATCCGCCACAATCTCTGTTTCCTGGGCAGCTTTGAGAAGGCACCAGTCAATCTTCAGAATGGGACCCATGT
AAAGCCACGGTCTGGCCTCTGGAGGCTTACTGAAGAGGGACACCGGCGCTTTCAGGAGGAGACTCGTGCCTTAGCCTCTG
CTCGGAGGGAGAGCATCCAACAGTGTATGAGCCAACCAGATGTGATGACTTCCCTCTTTGGCCTTTGA

ORF - retro_cfam_209 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.37 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGNESFLAFTTAHLPLAEQNLARYRLRIVEPPKVPVEEAPSPDDDGPALEPNLWMWVNPNIVFPPGKLEV
MGNE.FL..TT....L.EQNLA.YRLR..EPPKVP.E...SPD.DGP...PNLWMWVNPNI..P.G..E.
RetrocopyMGNELFLPSTTDQCHLTEQNLAQYRLRVMEPPKVPQERRTSPDKDGPDSKPNLWMWVNPNIMCPLGSQET
ParentalPESPKWEDLPSTLPFAHAPLKEEDFTNSSETTAVESLP-SSSEQSPPRKRKRVASSPSTWELTEEEEAED
....K..DL.S.LP......K.E...N.S..T..ESL..SSS..S.P.KR......PS.WELT.EE..E.
RetrocopyLNPSKEKDLTSMLPYPQPLPKNE--SNCSKATVMESLTASSSKKSSPQKR--FIYPPSDWELTKEE-TEE
ParentalQDDSSSVALPSPYKRAPLQSRRLRQANSQEGRLWSRPPLNYFHLIALALRNSSPCGLNVQQIYSFTRQHF
Q....SV.L.SP.KR...Q...L.Q.NSQE...W.RPPLNY.HLIALALRNS.PCGLNVQ.IY.FTRQHF
RetrocopyQENNCSVSLQSPNKRECFQNQKLWQGNSQERKSWPRPPLNYSHLIALALRNSPPCGLNVQEIYNFTRQHF
ParentalPFFRTAPEGWKNTVRHNLCFRDSFEKVPVSMQSGVSPRPRSCLWKLTEEGHRRFTEEARALASTRLQSIQ
PFF.TAP.GWKNT.RHNLCF..SFEK.PV..Q.G....PRS.LW.LTEEGHRRF.EE.RALAS.R..SIQ
RetrocopyPFFWTAPNGWKNTIRHNLCFLGSFEKAPVNLQNGTHVKPRSGLWRLTEEGHRRFQEETRALASARRESIQ
ParentalQCMSQPDVMPFLFDL
QCMSQPDVM..LF.L
RetrocopyQCMSQPDVMTSLFGL

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP012049_cerebellum 0 .00 RPM 0 .00 RPM
SRP017611_brain 0 .00 RPM 0 .00 RPM
SRP017611_kidney 0 .00 RPM 0 .00 RPM
SRP017611_liver 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cfam_209 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_209 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_209 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 18 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000000531 retrocopy
retro_amel_39,
Bos taurus ENSBTAG000000146061 retrocopy
retro_btau_189,
Canis familiaris ENSCAFG00000012417 1 retrocopy
retro_cfam_209 ,
Callithrix jacchus ENSCJAG000000136561 retrocopy
retro_cjac_4066,
Dasypus novemcinctus ENSDNOG000000094141 retrocopy
retro_dnov_22,
Dipodomys ordii ENSDORG000000019601 retrocopy
retro_dord_651,
Homo sapiens ENSG000001763021 retrocopy
retro_hsap_72,
Microcebus murinus ENSMICG000000026801 retrocopy
retro_mmur_38,
Macaca mulatta ENSMMUG000000227221 retrocopy
retro_mmul_125,
Mustela putorius furoENSMPUG000000048901 retrocopy
retro_mputfur_161,
Nomascus leucogenys ENSNLEG000000073761 retrocopy
retro_nleu_50,
Otolemur garnettii ENSOGAG000000072581 retrocopy
retro_ogar_296,
Procavia capensis ENSPCAG000000101321 retrocopy
retro_pcap_12,
Pongo abelii ENSPPYG000000039471 retrocopy
retro_pabe_69,
Pan troglodytes ENSPTRG000000043581 retrocopy
retro_ptro_94,
Sorex araneus ENSSARG000000113191 retrocopy
retro_sara_38,
Sus scrofa ENSSSCG000000151011 retrocopy
retro_sscr_36,
Ictidomys tridecemlineatus ENSSTOG000000143211 retrocopy
retro_itri_158,


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