RetrogeneDB ID:

retro_pabe_1435

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:17:16423227..16423548(+)
Located in intron of:ENSPPYG00000008013
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL22
Ensembl ID:ENSPPYG00000001951
Aliases:None
Description:ribosomal protein L22 [Source:HGNC Symbol;Acc:10315]


Retrocopy-Parental alignment summary:






>retro_pabe_1435
CAGGTTCTGAAGTATACCCTTGACTGGACCTACCCCGTAGATGATGCTGCCAATTGTGAGCAGTTTCTCCAAGACAGAAT
TAAAGTGAATGGAAAAGCTGGGAATCTTGGTGGAGGGGTAGTAACTATTGAAAGGAGCAAGAACACAAGCACCGTAACTT
CTGAGGTGCCTTTTTCCAAAGGGTATTTGAAATAGCTCATCAAAAAATATCTGAAGAATAAGCTATGTGATTGGTCGTGC
ATAGCTGCTAATAGCAAAGAGAATTTCGGATTATGTTACTTCCAAATTAACCAGGACAAAGAAGAGAAGGAAGATGAGGA
T

ORF - retro_pabe_1435 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.11 %
Parental protein coverage: 87.5 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalQVLKFTLDCTHPVEDGIMDAANFEQFLQERIKVNGKAGNLGGGVVTIERSKSKITVTSEVPFSKRYLKYL
QVLK.TLD.T.PV.....DAAN.EQFLQ.RIKVNGKAGNLGGGVVTIERSK...TVTSEVPFSK.YLK.L
RetrocopyQVLKYTLDWTYPVD----DAANCEQFLQDRIKVNGKAGNLGGGVVTIERSKNTSTVTSEVPFSKGYLK*L
ParentalTKKYLKKNNLRDWLRVVANSKESYELRYFQINQDEEEEEDED
.KKYL.KN.L.DW....ANSKE...L.YFQINQD.EE.EDED
RetrocopyIKKYL-KNKLCDWSCIAANSKENFGLCYFQINQDKEEKEDED

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 181 .85 RPM
SRP007412_cerebellum 0 .00 RPM 143 .98 RPM
SRP007412_heart 0 .00 RPM 119 .00 RPM
SRP007412_kidney 0 .00 RPM 274 .42 RPM
SRP007412_liver 0 .00 RPM 148 .82 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1435 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1435 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1435 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1720
Pan troglodytes retro_ptro_3056
Gorilla gorilla retro_ggor_2268

Parental genes homology:
Parental genes homology involve 28 parental genes, and 225 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000098647 retrocopies
Bos taurus ENSBTAG000000144234 retrocopies
Choloepus hoffmanni ENSCHOG000000074772 retrocopies
Callithrix jacchus ENSCJAG0000000013212 retrocopies
Cavia porcellus ENSCPOG000000201392 retrocopies
Dasypus novemcinctus ENSDNOG000000131668 retrocopies
Felis catus ENSFCAG000000063203 retrocopies
Homo sapiens ENSG0000011625116 retrocopies
Gorilla gorilla ENSGGOG0000002773910 retrocopies
Loxodonta africana ENSLAFG000000063525 retrocopies
Macropus eugenii ENSMEUG000000088011 retrocopy
Macaca mulatta ENSMMUG0000001834712 retrocopies
Monodelphis domestica ENSMODG000000062251 retrocopy
Mustela putorius furoENSMPUG000000070876 retrocopies
Mus musculus ENSMUSG000000289365 retrocopies
Nomascus leucogenys ENSNLEG0000001033710 retrocopies
Otolemur garnettii ENSOGAG000000147767 retrocopies
Pongo abelii ENSPPYG00000001951 11 retrocopies
Pongo abelii ENSPPYG000000259001 retrocopy
Pan troglodytes ENSPTRG0000000007614 retrocopies
Rattus norvegicus ENSRNOG000000111045 retrocopies
Sarcophilus harrisii ENSSHAG000000187311 retrocopy
Sus scrofa ENSSSCG000000033674 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000028324 retrocopies
Tupaia belangeri ENSTBEG0000000917233 retrocopies
Tarsius syrichta ENSTSYG0000000364932 retrocopies
Tursiops truncatus ENSTTRG000000104888 retrocopies
Vicugna pacos ENSVPAG000000094661 retrocopy



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