RetrogeneDB ID:

retro_ptro_2104

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:4:155650818..155651269(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS14
Ensembl ID:ENSPTRG00000017418
Aliases:None
Description:ribosomal protein S14 [Source:HGNC Symbol;Acc:10387]


Retrocopy-Parental alignment summary:






>retro_ptro_2104
CCTTCCAAGAGGAAGAAGAAAAAGGAAGAACAGGTCATCAGCCTCGGACCTCAGGTGGTTGAAGGAGAGAATGTATTTGG
TGCCTGCCACATCTTTGTCTCCTTCAATGACACCTTTGTCCATGTCACTGATGTTTCTGGCAAGGGAACTACCTGCCATG
TGGCTGCCAGGATGAAGATGAAAGCTGACAGGATGAATCCTCACCACACACTGCCATGTCGGCTGCCCAGGAGGTGGCCC
AGCAGTGCAAGGAGCTGGGGCATTACTGCCCTACACATTTGCAAACTCCAGGCCACAGCAGGAAATAGGACCAAGCACCC
TGGACCTAGGGCCCAGTCGGCCCTCAGAACCCTTGCCTGCTTGGGGATGAAGATCGGGGCAGATCGAGGATGTCACTCCC
ATTCCCCTCCGACAGCACTAGAGGAAGGAGGATTGCCATGGTCACCGCCTG

ORF - retro_ptro_2104 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.48 %
Parental protein coverage: 98.68 %
Number of stop codons detected: 0
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalPRKGKEKKEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGKETICRVTGGMKVKADR-DESSP
P.K.K.KKEEQVISLGPQV.EGENVFG.CHIF.SFNDTFVHVTD.SGK.T.C.V...MK.KADR.DESSP
RetrocopyPSKRKKKKEEQVISLGPQVVEGENVFGACHIFVSFNDTFVHVTDVSGKGTTCHVAARMKMKADR<DESSP
ParentalYAAMLAAQDVAQRCKEL-GITALHI-KLRATGGNRTKTPGPGAQSALRALARSGMKI-GRIEDVTPI-PS
..AM.AAQ.VAQ.CKEL.GITALHI.KL.AT.GNRTK.PGP.AQSALR.LA..GMKI.G.IEDVTPI.PS
RetrocopyHTAMSAAQEVAQQCKEL>GITALHICKLQATAGNRTKHPGPRAQSALRTLACLGMKI>GQIEDVTPI>PS
ParentalDSTR-RKGGRRGRRL
DSTR.RK....G.RL
RetrocopyDSTR<RKEDCHGHRL

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 194 .37 RPM
SRP007412_cerebellum 0 .00 RPM 223 .23 RPM
SRP007412_heart 0 .06 RPM 179 .92 RPM
SRP007412_kidney 0 .00 RPM 394 .87 RPM
SRP007412_liver 0 .03 RPM 302 .63 RPM
SRP007412_testis 0 .11 RPM 216 .77 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2104 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2104 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2104 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3113
Gorilla gorilla retro_ggor_2135
Pongo abelii retro_pabe_2571
Macaca mulatta retro_mmul_1983

Parental genes homology:
Parental genes homology involve 21 parental genes, and 60 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000046442 retrocopies
Bos taurus ENSBTAG000000085702 retrocopies
Canis familiaris ENSCAFG000000180942 retrocopies
Callithrix jacchus ENSCJAG000000209811 retrocopy
Cavia porcellus ENSCPOG000000244082 retrocopies
Dipodomys ordii ENSDORG000000071462 retrocopies
Gorilla gorilla ENSGGOG000000245938 retrocopies
Latimeria chalumnae ENSLACG000000161641 retrocopy
Loxodonta africana ENSLAFG000000311952 retrocopies
Macropus eugenii ENSMEUG000000149071 retrocopy
Microcebus murinus ENSMICG000000029002 retrocopies
Myotis lucifugus ENSMLUG000000132794 retrocopies
Macaca mulatta ENSMMUG000000028485 retrocopies
Mustela putorius furoENSMPUG000000137761 retrocopy
Nomascus leucogenys ENSNLEG000000103661 retrocopy
Oryctolagus cuniculus ENSOCUG000000115091 retrocopy
Otolemur garnettii ENSOGAG000000007211 retrocopy
Procavia capensis ENSPCAG000000159603 retrocopies
Pan troglodytes ENSPTRG00000017418 8 retrocopies
Rattus norvegicus ENSRNOG0000001877410 retrocopies
Sorex araneus ENSSARG000000142491 retrocopy



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