RetrogeneDB ID:

retro_pabe_1208

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:14:105106895..105107350(-)
Located in intron of:ENSPPYG00000006170
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL10A
Ensembl ID:ENSPPYG00000016529
Aliases:None
Description:ribosomal protein L10a [Source:HGNC Symbol;Acc:10299]


Retrocopy-Parental alignment summary:






>retro_pabe_1208
GTGTGGGTCCTGGGGGAACAGCAGCACTGTGACGAGGCCAAGGCCATGGATATCCCCCCACATGGACACTGAGATGCCAA
AAAAACTCAAGAATAAGAAACTGGTCAAGAAACTGGCCAAGAAGTATGATGCATTTTTGGCTTCAGAGTCTCTGATCAAG
CATATCCCACGAATCCTCGGCATAGGCCTAACAAAGGCAGTAGAGTTCCCTTCCCTGCTCACACACGATGAAAACACGGC
AGCCAAAGTGGATGAGGCGAAGTCCACAATCAAGTTTCATATGAAGATGTTATGTTTGGCTGTGGCTGTTGGCCACGTGA
AGATGACAGACGACGAGCTTGTGTATAACATTCACCTGGCTGTTAACTTCTTAGTGTCACCGCTTGAGAAAAAACTGGCA
GAATGTCCGGGCCTTATATATCAAGAGCACCATGGGCAAGCCCCAGCGCCTATAT

ORF - retro_pabe_1208 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.71 %
Parental protein coverage: 80.1 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalVCVLGDQQHCDEAKAVDIP-HMDIEALKKLNKNKKLVKKLAKKYDAFLASESLIKQIPRILGPGLNKAGK
V.VLG.QQHCDEAKA.DIP.HMD.E..KKL.KN..........YDAFLASESLIK.IPRILG.GL.KA..
RetrocopyVWVLGEQQHCDEAKAMDIP>HMDTEMPKKL-KNXXXXXXXXXXYDAFLASESLIKHIPRILGIGLTKAVE
ParentalFPSLLTHNENMVAKVDEVKSTIKFQMKKVLCLAVAVGHVKMTDDELVYNIHLAVNFLVS-LLKKNWQNVR
FPSLLTH.EN..AKVDE.KSTIKF.M.K.LCLAVAVGHVKMTDDELVYNIHLAVNFLVS..L.KNWQNVR
RetrocopyFPSLLTHDENTAAKVDEAKSTIKFHM-KMLCLAVAVGHVKMTDDELVYNIHLAVNFLVS>RLRKNWQNVR
ParentalALYIKSTMGKPQRLY
ALYIKSTMGKPQRLY
RetrocopyALYIKSTMGKPQRLY

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 .06 RPM 74 .53 RPM
SRP007412_cerebellum 0 .12 RPM 76 .12 RPM
SRP007412_heart 0 .09 RPM 94 .83 RPM
SRP007412_kidney 0 .20 RPM 196 .86 RPM
SRP007412_liver 0 .06 RPM 146 .15 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1208 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1208 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1208 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1462
Pan troglodytes retro_ptro_994
Gorilla gorilla retro_ggor_1124

Parental genes homology:
Parental genes homology involve 8 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Equus caballus ENSECAG000000140902 retrocopies
Macropus eugenii ENSMEUG000000057606 retrocopies
Monodelphis domestica ENSMODG000000137662 retrocopies
Mus musculus ENSMUSG000000378058 retrocopies
Ornithorhynchus anatinus ENSOANG000000145741 retrocopy
Pongo abelii ENSPPYG00000016529 10 retrocopies
Sarcophilus harrisii ENSSHAG000000020471 retrocopy
Sus scrofa ENSSSCG000000015437 retrocopies



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