RetrogeneDB ID:

retro_pabe_2930

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:6:3960863..3961231(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS25
Ensembl ID:ENSPPYG00000025915
Aliases:None
Description:ribosomal protein S25 [Source:HGNC Symbol;Acc:10413]


Retrocopy-Parental alignment summary:






>retro_pabe_2930
CCCAAGGACAACAAGAAGAAGAAAGACACCAAAAAGTTGGGCAAGAAAGACAAAGACCCAGTGAACAAATCCTGGGGCAA
AGCCAAAACGAAGAAGTGATCCAAAGGCAAAGTTTGGGACAAGCTCAATAACTTAGTCTTGTTTGACAAAGCTTCATATG
ACAAACTCTGTAAGGAAGTTCCCAACTATACACTTATAGCTCCAGCTGTGGTCTCTAAGAGACTAAAGATTCGAGGTTCC
CTGGCCAGAGCAGCCCTTCAGGAGTTCCTTAGCAAAGGACTTATCAAACTGTTTCAAAGCACAGAGTTCAAGTAATTCAC
ACCAGAAATACTAAGGGCAGGGATGCTCCAGCTGCTGGTGAAGATGCA

ORF - retro_pabe_2930 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.48 %
Parental protein coverage: 98.4 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalPKDDKKKKDAGKSAKKDKDPVNKSGGKAKKKKWSKGKVRDKLNNLVLFDKATYDKLCKEVPNYKLITPAV
PKD.KKKKD..K..KKDKDPVNKS.GKAK.KK.SKGKV.DKLNNLVLFDKA.YDKLCKEVPNY.LI.PAV
RetrocopyPKDNKKKKDTKKLGKKDKDPVNKSWGKAKTKK*SKGKVWDKLNNLVLFDKASYDKLCKEVPNYTLIAPAV
ParentalVSERLKIRGSLARAALQELLSKGLIKL-VSKHRAQVIYTRNTKGGDAPAAGEDA
VS.RLKIRGSLARAALQE.LSKGLIKL.VSKHR.QVI.TRNTKG.DAPAAGEDA
RetrocopyVSKRLKIRGSLARAALQEFLSKGLIKL<VSKHRVQVIHTRNTKGRDAPAAGEDA

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 63 .53 RPM
SRP007412_cerebellum 0 .00 RPM 76 .24 RPM
SRP007412_heart 0 .00 RPM 100 .58 RPM
SRP007412_kidney 0 .03 RPM 140 .58 RPM
SRP007412_liver 0 .00 RPM 145 .20 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2930 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2930 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2930 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3547
Pan troglodytes retro_ptro_2411
Gorilla gorilla retro_ggor_2395

Parental genes homology:
Parental genes homology involve 16 parental genes, and 110 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000277722 retrocopies
Callithrix jacchus ENSCJAG000000136911 retrocopy
Dasypus novemcinctus ENSDNOG000000078807 retrocopies
Homo sapiens ENSG000001181813 retrocopies
Gorilla gorilla ENSGGOG000000255407 retrocopies
Latimeria chalumnae ENSLACG000000175314 retrocopies
Macropus eugenii ENSMEUG000000141853 retrocopies
Mus musculus ENSMUSG0000000992715 retrocopies
Oryctolagus cuniculus ENSOCUG0000001725611 retrocopies
Otolemur garnettii ENSOGAG000000072653 retrocopies
Ochotona princeps ENSOPRG000000161949 retrocopies
Pongo abelii ENSPPYG00000025915 6 retrocopies
Sorex araneus ENSSARG000000022844 retrocopies
Tupaia belangeri ENSTBEG0000001024416 retrocopies
Tarsius syrichta ENSTSYG0000000542215 retrocopies
Vicugna pacos ENSVPAG000000002664 retrocopies



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