RetrogeneDB ID:

retro_fcat_305

Retrocopy
location
Organism:Cat (Felis catus)
Coordinates:A2:2097032..2097493(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PDCD2
Ensembl ID:ENSFCAG00000007037
Aliases:None
Description:programmed cell death 2 [Source:HGNC Symbol;Acc:8762]


Retrocopy-Parental alignment summary:






>retro_fcat_305
GAATTTGAAATTGTAATAAGAACAGAAGATGAGGTTATACTTGAAGATGTTGAAAAGGGAAGGGAAGCAGAAATTACAGG
AAGCATGGGTGAAGCACCTGATGAAGAATTGGATTCCATGGCAAAACATGAACCCAAGGAAGATAAAAATTCCAGAAGTT
TAAAACTAAAATAGCCCTAGAGCCAGAACAGATTCTTAGATATGCCAGAGGGATTGCACCCATCTGGATCTCTGGTGAAA
ATGTCCCTCAAGAAAAGGATATTCCAGTTTGCCCCTGTGGGGCCAAGAGAATATTTGAATTCCAGGTCATGCCTCAGTGG
CTCAACCACCTAAAGGCCAACAGACTCGGCAGGAGTGTTGATTGGGGTGTTCTGGCTGTCTCCACCTGTGTTGAAAGCTG
TAGACAGGTGATTGGCTACACAGAGGAACTGGTTTGGAAGCAAGATATAACAGATACACCT

ORF - retro_fcat_305 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.29 %
Parental protein coverage: 61.11 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalEFEIVIETEDEITPEVVEKENESEIIGSMGEVPEEELDSMAKHESREDKI-FQKFKTKIALEPEQVLRYG
EFEIVI.TEDE...E.VEK..E.EI.GSMGE.P.EELDSMAKHE..EDK..FQKFKTKIALEPEQ.LRY.
RetrocopyEFEIVIRTEDEVILEDVEKGREAEITGSMGEAPDEELDSMAKHEPKEDKN<FQKFKTKIALEPEQILRYA
ParentalRGIAPIWISGENIPQEKDIPDCPCGAKRIFEFQVMPQLLNYLKADTLGRSVDWGVVAVFTCAESCRLGIG
RGIAPIWISGEN.PQEKDIP.CPCGAKRIFEFQVMPQ.LN.LKA..LGRSVDWGV.AV.TC.ESCR..IG
RetrocopyRGIAPIWISGENVPQEKDIPVCPCGAKRIFEFQVMPQWLNHLKANRLGRSVDWGVLAVSTCVESCRQVIG
ParentalYTEEFVWKQDITDTP
YTEE.VWKQDITDTP
RetrocopyYTEELVWKQDITDTP

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
SRP017611_brain 0 .00 RPM 10 .79 RPM
SRP017611_kidney 0 .00 RPM 9 .38 RPM
SRP017611_liver 0 .00 RPM 9 .10 RPM
Felis catus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_fcat_305 retrocopy.
Felis catus was not studied using FANTOM5 data.
retro_fcat_305 was not experimentally validated.

Retrocopy orthology:
Felis catus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:
Parental genes homology involve 15 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000170752 retrocopies
Callithrix jacchus ENSCJAG000000206341 retrocopy
Equus caballus ENSECAG000000168191 retrocopy
Felis catus ENSFCAG00000007037 2 retrocopies
retro_fcat_305 , retro_fcat_749,
Homo sapiens ENSG000000719941 retrocopy
Gorilla gorilla ENSGGOG000000282292 retrocopies
Microcebus murinus ENSMICG000000074741 retrocopy
Macaca mulatta ENSMMUG000000199161 retrocopy
Mustela putorius furoENSMPUG000000072272 retrocopies
Nomascus leucogenys ENSNLEG000000002952 retrocopies
Otolemur garnettii ENSOGAG000000140022 retrocopies
Pongo abelii ENSPPYG000000171932 retrocopies
Pan troglodytes ENSPTRG000000188282 retrocopies
Pteropus vampyrus ENSPVAG000000108221 retrocopy
Sus scrofa ENSSSCG000000253122 retrocopies



Copyright © RetrogeneDB 2014-2017