RetrogeneDB ID:

retro_cfam_1739

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:5:48647979..48648562(+)
Located in intron of:ENSCAFG00000023117
Retrocopy
information
Ensembl ID:ENSCAFG00000018860
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PRDX2
Ensembl ID:ENSCAFG00000017163
Aliases:None
Description:peroxiredoxin 2 [Source:HGNC Symbol;Acc:9353]


Retrocopy-Parental alignment summary:






>retro_cfam_1739
ATGACCTCTGGCAAGGCACACATCGGAAAGCCCATTGCGCCTTTCCAGGTCACTGCTGTGGTGGACAGCATCTTCAAGGA
GGCGAAGCTTTGCAACTACAAAGGGAAATACTTGGTCCCCTTTTTCTACCCGTTGGACATCACCTTCGTCTGCCCAATGG
AGATTACTGGCTTTAGCGAGCATGCCAAAGACTTCGGCAAGCTGCGCTGTGAGATGCTGGGGTCTCCGTGGACTCTCAGT
TCACCCACCTGCTTGGATCAACACTCCCAGGAAGGACGGAGGCCCCCTGAACATCCCCTGCTGGCTGCGTAACTAGAAGT
TTATCCGAAGATTATGGTGTGCTGAAGGAAGATGAGGGCATTGCCTACAGGGGCCTCTTTATCATCGATGGCAAGGTGTC
CCTCTCCAGATCACTGTCAATGATTTGTCTGTGGGGCACTCTGTGGATGAAGTTCTGCAACTGATTCAGGCCTTGCAGTA
CACGGATGAGCACAGGGAAGTCTACCCGCCTGGCTGGAAGCCAGGCAGTGACACAATCAAGCCTAACATGGACGACAGCA
AAGAATACTTCTCCAAACACAAC

ORF - retro_cfam_1739 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.77 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalMTSGKAHIGKPAPPFQATAVVDGAFKEVKLCDYKGKYLVLFFYPLDFTFVCPTEIIAFSEHAEDFRKLGC
MTSGKAHIGKP..PFQ.TAVVD..FKE.KLC.YKGKYLV.FFYPLD.TFVCP.EI..FSEHA.DF.KL.C
RetrocopyMTSGKAHIGKPIAPFQVTAVVDSIFKEAKLCNYKGKYLVPFFYPLDITFVCPMEITGFSEHAKDFGKLRC
ParentalEVLG-VSVDSQFTHL-AWINTPRKEGGLGPLNI-PLVAD-VTRSLSEDYGVLKEDEGIAYRGLFIIDGK-
E.LG.VSVDSQFTHL.AWINTPRK.GG..PLNI.PL.A..VTRSLSEDYGVLKEDEGIAYRGLFIIDGK.
RetrocopyEMLG<VSVDSQFTHL<AWINTPRKDGG--PLNI<PLLAA<VTRSLSEDYGVLKEDEGIAYRGLFIIDGK<
ParentalGVLRQITVNDLPVGRSVDEVLRLVQAFQYTDEHGEVCPAGWKPGSDTIKPNVDDSKEYFSKHN
GV..QITVNDL.VG.SVDEVL.L.QA.QYTDEH.EV.P.GWKPGSDTIKPN.DDSKEYFSKHN
RetrocopyGVPLQITVNDLSVGHSVDEVLQLIQALQYTDEHREVYPPGWKPGSDTIKPNMDDSKEYFSKHN

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






(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 312 .47 RPM
SRP017611_brain 0 .00 RPM 142 .75 RPM
SRP017611_kidney 0 .00 RPM 112 .26 RPM
SRP017611_liver 0 .07 RPM 5 .08 RPM
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1739 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1739 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1739 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 23 parental genes, and 51 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000123073 retrocopies
Canis familiaris ENSCAFG000000045675 retrocopies
Canis familiaris ENSCAFG000000121093 retrocopies
Canis familiaris ENSCAFG00000017163 3 retrocopies
retro_cfam_1603, retro_cfam_1624, retro_cfam_1739 ,
Ciona intestinalis ENSCING000000030021 retrocopy
Callithrix jacchus ENSCJAG000000048824 retrocopies
Dipodomys ordii ENSDORG000000090051 retrocopy
Felis catus ENSFCAG000000004731 retrocopy
Homo sapiens ENSG000001678153 retrocopies
Gorilla gorilla ENSGGOG000000250893 retrocopies
Macaca mulatta ENSMMUG000000056892 retrocopies
Monodelphis domestica ENSMODG000000069781 retrocopy
Mustela putorius furoENSMPUG000000045912 retrocopies
Mus musculus ENSMUSG000000051612 retrocopies
Nomascus leucogenys ENSNLEG000000128002 retrocopies
Otolemur garnettii ENSOGAG000000249982 retrocopies
Pongo abelii ENSPPYG000000096073 retrocopies
Pan troglodytes ENSPTRG000000105413 retrocopies
Rattus norvegicus ENSRNOG000000035202 retrocopies
Sorex araneus ENSSARG000000001461 retrocopy
Sarcophilus harrisii ENSSHAG000000155961 retrocopy
Sus scrofa ENSSSCG000000137362 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000258621 retrocopy



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