RetrogeneDB ID:

retro_pabe_2843

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:6:28097382..28097910(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL10
Ensembl ID:ENSPPYG00000020874
Aliases:None
Description:60S ribosomal protein L10 [Source:RefSeq peptide;Acc:NP_001126004]


Retrocopy-Parental alignment summary:






>retro_pabe_2843
AAGCAAGCAAAAATGGATGAGTTTCCGCTCCGTGATCACATGGCGTCAGATGAATATGAGTAGCTCTCCTCTGAAGCCCT
GGTGGCTGCCCAAATTTGTGCCAATAAGTACATAGTAAAAAGTTGTGGCAAAAATGGCTTTCATATCCGAGTGCGGCTGT
ACCCCTTCCACGTCATCTGCATCAACAGGATGTTGTCCTGTGCTGGGACTGACAGGCTCCAAACAGGTATGGGAGGTGCC
TTTGGAAAGCCCGCAGGGCGCTGTGGCCAGGATTCTCATTGGCCAATTTATCTTGTCCATTCGCACCAAGCTGCAGAACA
AGGAGCATGTGATTGAGGCCCTTCGCAGGGCCAAGTTCAAGTTCCCTGGCCGCCAGAAGGTCCACATTTCAAAGAAGGGG
GGCTTCACCAAGTTCAATGCAGATGAATTTGAAGACATGGTGGCTGAGAAGCGGCTCATCCCAGATGGCTGTGGGGTCAA
GCACATCCCCGATCGTGGCCCTCTGGACAAGGGCGGTCTTTGCACTCA

ORF - retro_pabe_2843 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.27 %
Parental protein coverage: 82.24 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalKKAKVDEFPLCGHMVSDEYEQLSSEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGA
K.AK.DEFPL..HM.SDEYE.LSSEAL.AA.ICANKY.VKSCGK.GFHIRVRL.PFHVI.IN.MLSCAG.
RetrocopyKQAKMDEFPLRDHMASDEYE*LSSEALVAAQICANKYIVKSCGKNGFHIRVRLYPFHVICINRMLSCAGT
ParentalDRLQTGMRGAFGKP-QGTVARVHIGQVIMSIRTKLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFN
DRLQTGM.GAFGKP.QG.VAR..IGQ.I.SIRTKLQNKEHVIEALRRAKFKFPGRQK.HISKK.GFTKFN
RetrocopyDRLQTGMGGAFGKP>QGAVARILIGQFILSIRTKLQNKEHVIEALRRAKFKFPGRQKVHISKKGGFTKFN
ParentalADEFEDMVAEKRLIPDGCGVKYIPNRGPLDK-WRALHS
ADEFEDMVAEKRLIPDGCGVK.IP.RGPLDK..R.LHS
RetrocopyADEFEDMVAEKRLIPDGCGVKHIPDRGPLDK<GRSLHS

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 173 .12 RPM
SRP007412_cerebellum 0 .00 RPM 94 .12 RPM
SRP007412_heart 0 .00 RPM 266 .99 RPM
SRP007412_kidney 0 .03 RPM 425 .70 RPM
SRP007412_liver 0 .00 RPM 442 .93 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2843 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2843 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2843 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 7 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000074542 retrocopies
Homo sapiens ENSG000001474033 retrocopies
Macropus eugenii ENSMEUG000000131633 retrocopies
Myotis lucifugus ENSMLUG000000143373 retrocopies
Monodelphis domestica ENSMODG000000087312 retrocopies
Mus musculus ENSMUSG000000086821 retrocopy
Pongo abelii ENSPPYG00000020874 5 retrocopies



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