RetrogeneDB ID:

retro_pabe_1339

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:16:5398681..5399291(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS3A
Ensembl ID:ENSPPYG00000025869
Aliases:None
Description:40S ribosomal protein S3a [Source:RefSeq peptide;Acc:NP_001126750]


Retrocopy-Parental alignment summary:






>retro_pabe_1339
ATGGCGGTTGTTAAGAACAAGTGCCTTGTGAAAGGTGGCAAAAAGGGAGTTAAGAAGAAAATAGTTGATCCATTTTCTAA
GAAAGATCAGTATGATGTGTAAGCACCTGCTATGTTCAATATAAGAAATATTGGAAAGACTTGGTCACCAGGACCCAAGG
AACCCAAATTGCATCTGACGGTCTCAAGGGTCTTGTGTTTGAAGTGAGTCTTGCTGATGTGCAGAATGATGAAGCTGCAT
TTAGAAAATTCAAGCTGATTACTGAAGATGTTCAGGGCAAAAACTGCCTGACTGACTTCTATGGCATGGGTCTTACCTGT
GACAAAATATGTTCCATGGTTGAAAAATGTTCAACAATGATTGAAGCTCATGTTGATGTCAAGACTACTGATGGTTACTT
CTTTCATCTGTTTTGTGTTGGTTTTACTAGAAAACACAACAATCAGATACTGAAGACCTCTTATCCTCAGCACCAACAGT
CCACCAAATCCAGAAGAAGATGATGGAAATCATGACCTGAGAGGTGCAGACAAACGACTTGAAAGAAGTGGTTAATAAAT
TGATTCCAGACAACATTGGAAAAGATGTAGAAAAGGCTTGACAATTTATC

ORF - retro_pabe_1339 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.01 %
Parental protein coverage: 77.27 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKT-LVTRTQGTKIASDGLKGRVFEV
MAV.KNK.L.KGGKKG.KKK.VDPFSKKD.YDV.APAMFNIRNIGKT.LVTRTQGT.IASDGLKG.VFEV
RetrocopyMAVVKNKCLVKGGKKGVKKKIVDPFSKKDQYDV*APAMFNIRNIGKT<LVTRTQGTQIASDGLKGLVFEV
ParentalSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFC
SLAD.QNDE.AFRKFKLITEDVQGKNCLT.F.GM.LT.DK.CSMV.K..TMIEAHVDVKTTDGY...LFC
RetrocopySLADVQNDEAAFRKFKLITEDVQGKNCLTDFYGMGLTCDKICSMVEKCSTMIEAHVDVKTTDGYFFHLFC
ParentalVGFTKKRNNQIRKTSYAQHQQ-VRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIEKACQSI
VGFT.K.NNQI.KTSY.QHQQ.V.QI.KKMMEIMT.EVQTNDLKEVVNKLIPD.IGKD.EKA.Q.I
RetrocopyVGFTRKHNNQILKTSYPQHQQ<VHQIQKKMMEIMT*EVQTNDLKEVVNKLIPDNIGKDVEKA*QFI

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 71 .93 RPM
SRP007412_cerebellum 0 .00 RPM 99 .96 RPM
SRP007412_heart 0 .00 RPM 95 .16 RPM
SRP007412_kidney 0 .00 RPM 145 .71 RPM
SRP007412_liver 0 .00 RPM 124 .70 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1339 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1339 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1339 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 14 parental genes, and 101 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG000000155699 retrocopies
Equus caballus ENSECAG000000095736 retrocopies
Felis catus ENSFCAG000000312885 retrocopies
Loxodonta africana ENSLAFG000000176603 retrocopies
Macaca mulatta ENSMMUG000000218211 retrocopy
Monodelphis domestica ENSMODG000000009696 retrocopies
Mustela putorius furoENSMPUG000000071398 retrocopies
Mus musculus ENSMUSG000000280812 retrocopies
Procavia capensis ENSPCAG000000150406 retrocopies
Pongo abelii ENSPPYG00000025869 27 retrocopies
Pteropus vampyrus ENSPVAG0000001540624 retrocopies
Rattus norvegicus ENSRNOG000000118931 retrocopy
Sarcophilus harrisii ENSSHAG000000150882 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000242031 retrocopy



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