RetrogeneDB ID:

retro_cjac_248

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:GL290436.1:61..616(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000023175
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL17
Ensembl ID:ENSCJAG00000004779
Aliases:None
Description:ribosomal protein L17 [Source:HGNC Symbol;Acc:10307]


Retrocopy-Parental alignment summary:






>retro_cjac_248
ATGGTTCACTATTCACTTGATCCAGAGAACCCCACAAAGTCATGCAAATCAAGCGGTTCCAATCTTTGTGTTCACTTTAA
CAACACACGTGAAACTGCCCAGGCCATCAAGCGTATGCATATACGAAAAGCCACGAAGTATCTGAAAGATGTCACTTTAC
AGAAACAGTGCATACCATTCCAACGTTACAATGGTGGAGTTGGCAGGTGTGCCCAGGCCAAGCAGCGGGTCTGGACACAA
GGTTGGTGGCCCAAAAATAGTGCTGAATTTTTTCTGCACATGCTTAAAAATGCAGAGAGTAATGCTGAACTTAAGGGTTT
AGATGTAGATTCTCTGGTCATTGAGCATATCCAGGTGAACAAAGCACCCAAGATGCACCACAGGACCTACAGAGCTCATG
GTCGAATTAACCCATACATGAGTTCTCCCTGCCACATTGAGATGATCCTTACTGAAAAGGAACAGATTGTTCCTAAACCA
GAAGAGGAGGTTGCTCACAAGAAGAAGATATCCCAGAAGAAACTGAAGAAACAAAAGCTTATGGCATGGGAGTAA

ORF - retro_cjac_248 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.3 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMVRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDVTLQKQCVPFRRYNGGVGRC
MV.YSLDPENPTKSCKS.GSNL.VHF.NTRETAQAIK.MHIRKATKYLKDVTLQKQC.PF.RYNGGVGRC
RetrocopyMVHYSLDPENPTKSCKSSGSNLCVHFNNTRETAQAIKRMHIRKATKYLKDVTLQKQCIPFQRYNGGVGRC
ParentalAQAKQWGWTQGRWPKKSAEFLLHMLKNAESNAELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINPYM
AQAKQ..WTQG.WPK.SAEF.LHMLKNAESNAELKGLDVDSLVIEHIQVNKAPKM..RTYRAHGRINPYM
RetrocopyAQAKQRVWTQGWWPKNSAEFFLHMLKNAESNAELKGLDVDSLVIEHIQVNKAPKMHHRTYRAHGRINPYM
ParentalSSPCHIEMILTEKEQIVPKPEEEVAQKKKISQKKLKKQKLMARE
SSPCHIEMILTEKEQIVPKPEEEVA.KKKISQKKLKKQKLMA.E
RetrocopySSPCHIEMILTEKEQIVPKPEEEVAHKKKISQKKLKKQKLMAWE

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
SRP051959_colon 0 .22 RPM 103 .59 RPM
SRP051959_heart 0 .35 RPM 99 .56 RPM
SRP051959_kidney 0 .16 RPM 123 .31 RPM
SRP051959_liver 0 .09 RPM 134 .32 RPM
SRP051959_lung 0 .16 RPM 131 .03 RPM
SRP051959_lymph_node 0 .21 RPM 209 .88 RPM
SRP051959_skeletal_muscle 0 .04 RPM 103 .14 RPM
SRP051959_spleen 0 .19 RPM 168 .89 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_248 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_248 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_248 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 23 parental genes, and 502 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000000949840 retrocopies
Canis familiaris ENSCAFG000000190447 retrocopies
Choloepus hoffmanni ENSCHOG0000000787250 retrocopies
Callithrix jacchus ENSCJAG00000004779 4 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
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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