RetrogeneDB ID:

retro_pabe_2800

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:5:173945933..173946520(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL19
Ensembl ID:ENSPPYG00000008492
Aliases:None
Description:60S ribosomal protein L19 [Source:UniProtKB/Swiss-Prot;Acc:Q5RB99]


Retrocopy-Parental alignment summary:






>retro_pabe_2800
ATGAGTATGTTCGGGCTTCAGAAGAGGCCCGCTGCTAGTGTCCTCTGCTGTGGCAAGAAGAAGGTCTGGTTGGACCCCAA
TGAGGCCAGTGAAATTGCCAATGCCAACTCCCGTCAGCAGATCTGGGAGCTGATCAAAGATGGGCTGATTATCTGTAAGC
CTGTGACTGTCCATTCCCAGGCTCAATGCCGGAAAAACACCTTGGCCCACCGGAAGGGCAGGCACATGGGTACGGGTAAG
CGAAAGGGTACAGCCAATGCCCCAATGCCAGAGAAGGTCACGTGGTGAGGAGAATGAGGATTCTGCACCCACTGCTCAGA
AGATACCGTGAATCTAAGAAGATCAATTGCCACATGTATCACAGCCTGTACCTGAAGGTGAAGGGGAATATGTTCAAAGA
CAAGCGGATTCTCATGGAACACATCCACAAGCTGAAGGCAGACAAAGCCTGCAAGAAGCTCCTGGCTGACCAGGCTGAGG
CCCGCAGGCCTAAGACCAAGGAAGCACGAAAGCAACGTGAAGAGTGCCTCCAGGCCAAGAAGGAGGGGATCATCAAGACT
TTGTCCAAGGACGAAGAGATGAAGAAA

ORF - retro_pabe_2800 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.77 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSMLRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLIIRKPVTVHSRARCRKNTLAR
MSM..LQKR.A.SVL.CGKKKVWLDPNE..EIANANSRQQI..LIKDGLII.KPVTVHS.A.CRKNTLA.
RetrocopyMSMFGLQKRPAASVLCCGKKKVWLDPNEASEIANANSRQQIWELIKDGLIICKPVTVHSQAQCRKNTLAH
ParentalRKGRHMGIGKRKGTANARMPEKVTW-MRRMRILRRLLRRYRESKKIDRHMYHSLYLKVKGNVFKNKRILM
RKGRHMG.GKRKGTANA.MPEKVTW..RRMRIL..LLRRYRESKKI..HMYHSLYLKVKGN.FK.KRILM
RetrocopyRKGRHMGTGKRKGTANAPMPEKVTW<VRRMRILHPLLRRYRESKKINCHMYHSLYLKVKGNMFKDKRILM
ParentalEHIHKLKADKARKKLLADQAEARRSKTKEARKRREERLQAKKEEIIKTLSKEEETKK
EHIHKLKADKA.KKLLADQAEARR.KTKEARK.REE.LQAKKE.IIKTLSK.EE.KK
RetrocopyEHIHKLKADKACKKLLADQAEARRPKTKEARKQREECLQAKKEGIIKTLSKDEEMKK

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 99 .36 RPM
SRP007412_cerebellum 0 .00 RPM 98 .38 RPM
SRP007412_heart 0 .00 RPM 118 .85 RPM
SRP007412_kidney 0 .00 RPM 308 .13 RPM
SRP007412_liver 0 .03 RPM 250 .14 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2800 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2800 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2800 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3401
Pan troglodytes retro_ptro_2311

Parental genes homology:
Parental genes homology involve 30 parental genes, and 300 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000041215 retrocopies
Bos taurus ENSBTAG000000020605 retrocopies
Canis familiaris ENSCAFG0000001649314 retrocopies
Choloepus hoffmanni ENSCHOG000000060237 retrocopies
Callithrix jacchus ENSCJAG000000085204 retrocopies
Dasypus novemcinctus ENSDNOG000000197427 retrocopies
Dipodomys ordii ENSDORG000000043301 retrocopy
Equus caballus ENSECAG000000250806 retrocopies
Homo sapiens ENSG0000010829821 retrocopies
Loxodonta africana ENSLAFG000000182573 retrocopies
Macropus eugenii ENSMEUG0000001390010 retrocopies
Microcebus murinus ENSMICG000000026635 retrocopies
Myotis lucifugus ENSMLUG0000001255511 retrocopies
Macaca mulatta ENSMMUG000000042352 retrocopies
Monodelphis domestica ENSMODG000000126932 retrocopies
Mustela putorius furoENSMPUG000000150415 retrocopies
Mus musculus ENSMUSG0000001740425 retrocopies
Nomascus leucogenys ENSNLEG0000000074819 retrocopies
Ochotona princeps ENSOPRG000000070922 retrocopies
Procavia capensis ENSPCAG000000152281 retrocopy
Pongo abelii ENSPPYG00000008492 20 retrocopies
Pan troglodytes ENSPTRG0000000908622 retrocopies
Pteropus vampyrus ENSPVAG000000084989 retrocopies
Rattus norvegicus ENSRNOG0000000474137 retrocopies
Sarcophilus harrisii ENSSHAG000000164824 retrocopies
Sus scrofa ENSSSCG000000175093 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000111205 retrocopies
Tupaia belangeri ENSTBEG0000000807731 retrocopies
Tarsius syrichta ENSTSYG0000000869810 retrocopies
Tursiops truncatus ENSTTRG000000066874 retrocopies



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