RetrogeneDB ID:

retro_ptro_2223

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:5:13392442..13392768(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS23
Ensembl ID:ENSPTRG00000017052
Aliases:None
Description:ribosomal protein S23 [Source:HGNC Symbol;Acc:10410]


Retrocopy-Parental alignment summary:






>retro_ptro_2223
AAGAATCTCCCTGTTCACTGACAGGAACATAAGTGGAATGACAAACAGTACAAGAAAGCCCATTTAGGCACAGCCTGAAG
GCCAACGCTTTTGGAAATGCTTCCCATACAAAGAGAACTGTGTTGGAAAAATAGGAGTTGAAGCCGAATGGCCAAATTCT
AATATCAGGAAGTGTACTATAGTTCAGCTGATTGAGAATGGCAAGAAAATCATAGTCTTTGTACCCAACGACGGTTGCTT
GAACTTTATTGAGGAAAAGATGAATTTCTGGTTGCTGAATTGGTCAAAAAGGTCATACTGTTGTTGACATTCCTGTAGTC
TGCTTT

ORF - retro_ptro_2223 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.42 %
Parental protein coverage: 82.71 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalRKLRSHRRDQKWHDKQYKKAHLGTA-LKANPFGGASHAKGIVLEK-VGVEAKQPNSAIRKCVRVQLIKNG
..L..H....KW.DKQYKKAHLGTA.LKAN.FG.ASH.K..VLEK..GVEA..PNS.IRKC..VQLI.NG
RetrocopyKNLPVH*QEHKWNDKQYKKAHLGTA<LKANAFGNASHTKRTVLEK<IGVEAEWPNSNIRKCTIVQLIENG
ParentalKKITAFVPNDGCLNFIEE-NDEVLVAG-FGRKGHAVGDIPGVRF
KKI..FVPNDGCLNFIEE..DE.LVA...G.KGH.V.DIP.V.F
RetrocopyKKIIVFVPNDGCLNFIEE<KDEFLVAE<IGQKGHTVVDIPVVCF

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
SRP007412_brain_prefrontal_cortex 0 .00 RPM 121 .96 RPM
SRP007412_cerebellum 0 .00 RPM 116 .40 RPM
SRP007412_heart 0 .00 RPM 97 .00 RPM
SRP007412_kidney 0 .00 RPM 199 .75 RPM
SRP007412_liver 0 .00 RPM 137 .68 RPM
SRP007412_testis 0 .32 RPM 64 .39 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2223 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2223 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2223 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3287
Gorilla gorilla retro_ggor_1316
Pongo abelii retro_pabe_2716

Parental genes homology:
Parental genes homology involve 21 parental genes, and 93 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000111361 retrocopy
Ailuropoda melanoleuca ENSAMEG000000159663 retrocopies
Bos taurus ENSBTAG000000133583 retrocopies
Callithrix jacchus ENSCJAG000000112472 retrocopies
Cavia porcellus ENSCPOG000000227052 retrocopies
Equus caballus ENSECAG000000205232 retrocopies
Erinaceus europaeus ENSEEUG000000018497 retrocopies
Felis catus ENSFCAG000000088397 retrocopies
Loxodonta africana ENSLAFG000000315063 retrocopies
Microcebus murinus ENSMICG000000139642 retrocopies
Myotis lucifugus ENSMLUG000000139392 retrocopies
Macaca mulatta ENSMMUG000000035784 retrocopies
Oryctolagus cuniculus ENSOCUG000000103632 retrocopies
Otolemur garnettii ENSOGAG0000000816311 retrocopies
Pan troglodytes ENSPTRG00000017052 6 retrocopies
Rattus norvegicus ENSRNOG0000001658012 retrocopies
Sorex araneus ENSSARG000000089048 retrocopies
Sarcophilus harrisii ENSSHAG000000083472 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000008243 retrocopies
Tarsius syrichta ENSTSYG000000113855 retrocopies
Tursiops truncatus ENSTTRG000000144916 retrocopies



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