RetrogeneDB ID:

retro_cfam_34

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:13:12340871..12341426(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCAFG00000028960
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCAFG00000019044
Aliases:RPL17, RPL17L
Description:None


Retrocopy-Parental alignment summary:






>retro_cfam_34
ATGGTTCGCTACTCGCTGGACCCAGAAAACCCTACAAAATCATGCAACTCAAGAGGTTCAAATCTTCGTGTTCACTTTAA
GAACACACGTGAAACTGCCCAGGCCATCAAGGGTATGCATATTCGAAAAGCCACCAAGTATCTGAAAGATGTCACTTTGC
AGAAGCAGTGTGTGCCATTCCATCGCTACAATGGTGGAGTTGGTAGGTGTGCGCAGGCCAAACAGTGGGGCTGGACACAG
GGTCGGTGGCCCAAGAATAGTGCTGAATTTTTACTGCACATGCTTAAAAATGCGGAGAGTAATGCTGAACTTAAGGGTTT
AGATGTAGATTCTCTGGTCATTGAGCACATCCAGGTGAATAAAGCCCCCAAGATGCGACGTAGAACCTACAGGGCTCATG
GCCGGATTAATCCATACATGAGCTCTCCCTGCCACATTGAGATGATTCTTACTGAAAAAGAGCAGATTGTTCCTAAACCA
GAAGAGGAGGTTGCACAGAAGAAAAAGATATCCCAGAAGAAACTGAAGAAACAAAAACTTATGGCCCGGGAGTAA

ORF - retro_cfam_34 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.37 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMVRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDVTLQKQCVPFRRYNGGVGRC
MVRYSLDPENPTKSC.SRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDVTLQKQCVPF.RYNGGVGRC
RetrocopyMVRYSLDPENPTKSCNSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDVTLQKQCVPFHRYNGGVGRC
ParentalAQAKQWGWTQGRWPKKSAEFLLHMLKNAESNAELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINPYM
AQAKQWGWTQGRWPK.SAEFLLHMLKNAESNAELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINPYM
RetrocopyAQAKQWGWTQGRWPKNSAEFLLHMLKNAESNAELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINPYM
ParentalSSPCHIEMILTEKEQIVPKPEEEVAQKKKISQKKLKKQKLMARE
SSPCHIEMILTEKEQIVPKPEEEVAQKKKISQKKLKKQKLMARE
RetrocopySSPCHIEMILTEKEQIVPKPEEEVAQKKKISQKKLKKQKLMARE

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 .04 RPM 261 .06 RPM
SRP017611_brain 0 .00 RPM 80 .42 RPM
SRP017611_kidney 0 .07 RPM 763 .59 RPM
SRP017611_liver 0 .00 RPM 84 .55 RPM
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_34 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_34 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_34 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 24 parental genes, and 553 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000000949840 retrocopies
Canis familiaris ENSCAFG00000019044 7 retrocopies
Choloepus hoffmanni ENSCHOG0000000787250 retrocopies
Callithrix jacchus ENSCJAG000000047794 retrocopies
Echinops telfairi ENSETEG0000001132210 retrocopies
Felis catus ENSFCAG0000001134243 retrocopies
Homo sapiens ENSG000002154721 retrocopy
Homo sapiens ENSG0000026568133 retrocopies
Gorilla gorilla ENSGGOG000000266971 retrocopy
Latimeria chalumnae ENSLACG000000088351 retrocopy
Loxodonta africana ENSLAFG0000000556916 retrocopies
Macropus eugenii ENSMEUG0000001670926 retrocopies
Microcebus murinus ENSMICG0000001710214 retrocopies
Macaca mulatta ENSMMUG0000001883726 retrocopies
Mustela putorius furoENSMPUG000000008017 retrocopies
Procavia capensis ENSPCAG000000031038 retrocopies
Pongo abelii ENSPPYG0000000915143 retrocopies
Pan troglodytes ENSPTRG0000001001251 retrocopies
Pteropus vampyrus ENSPVAG0000000196976 retrocopies
Sarcophilus harrisii ENSSHAG0000000306014 retrocopies
Sus scrofa ENSSSCG0000002964230 retrocopies
Tarsius syrichta ENSTSYG0000000740220 retrocopies
Tursiops truncatus ENSTTRG0000000579731 retrocopies
Vicugna pacos ENSVPAG000000095681 retrocopy



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