RetrogeneDB ID:

retro_sscr_231

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:10:75934536..75935352(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSSCG00000026093
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MRPS27
Ensembl ID:ENSSSCG00000023818
Aliases:None
Description:mitochondrial ribosomal protein S27 [Source:HGNC Symbol;Acc:14512]


Retrocopy-Parental alignment summary:






>retro_sscr_231
CACAAATTTCGACACAGCCCCAACCGCTGGTACTTGAGAGATGGACTGTCCGCACGTGGGCTAGGTAGTGTCTAAAACAT
GGTGCACAGGACAAAGCCTTATACACCCTAAAAATAAGGTCCAATATGGCATTTTCCCGGATAACGATACATTTAATTTA
CTGATGGATCATTTCATAAAGAAAGAAAATTACAAAGATGCTTTATCCGTGGTTTTTGAGATCATGATGCAAGCAGCTTT
TGAAGTCCCTTCCACCCAGCTCCTCTCCCTCTGTGTTTTGTACTGCTGCCTTGCAGAGAAGACAGACTTGAGTTGGGAAG
AGAGAGGAACTTTGGTGCGTCCCTGTTACTCCCAGGCCTAAAGCAAAGGAACTCAGTGGGGCTGAGTTCCCAGCTGTGTG
GCTGTGCACTTCTTGGGAAGGTGGAACTGCAGCAAGGGCTGAGGGCTGTGTTCCGCAACGTGCCGCTGCTCTGGCAACCA
GGCTACCTCCACAGAGCCCTTCAAGTGATGGAGAAGGTGGCCTCCTCCCCAGAAGACGGACCGCTGTGTAGAGACGCGCT
CGGTGTGCCGGACAGAGTGCTGAAGGCTGTGACTGCTCCAGCCCAGGGGACTTCAGAGGAAGAGCCCCAGGAAGGTGAGG
AAAGCCAGAGGTCAGGAGAACGGGTAGAGCAGTGGGATGTGGAGGGAACTGCACAGTCCAAGCTTCCTCAGTACCTGGAA
CGATTTGAGGCTTTACATTCTAAGCTGCAGGCTCTGGGCAAAGTGGAGTCAGAAAGCCTGCGGACCCTGGGCACCCAGCT
CGCCAAGGCGCGGCTG

ORF - retro_sscr_231 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.96 %
Parental protein coverage: 76.04 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalYKFRHSPNCWYLRD-WTIHTWIRQCLKYGAQDKALYTLK-NKVQYGIFPDNYTFNLLMDYFIKKENYKDA
.KFRHSPN.WYLRD.WT..TW.R.CLK.GAQDKALYTLK.NKVQYGIFPDN.TFNLLMD.FIKKENYKDA
RetrocopyHKFRHSPNRWYLRD<WTVRTWAR*CLKHGAQDKALYTLK<NKVQYGIFPDNDTFNLLMDHFIKKENYKDA
ParentalLSVVFEIMMQEAFEVPSTQLLSLYVLYHCLAEKTDLSWEE-ERNFGASLLLPGLKQKNSVGLSSQLYGYA
LSVVFEIMMQ.AFEVPSTQLLSL.VLY.CLAEKTDLSWEE.ERNFGASLLLPGLKQ.NSVGLSSQL.G.A
RetrocopyLSVVFEIMMQAAFEVPSTQLLSLCVLYCCLAEKTDLSWEE<ERNFGASLLLPGLKQRNSVGLSSQLCGCA
ParentalLLGKVELQQGLRAVYCNMPLLWQPGYLHRALQVMEKVASSPEDGQLCGEALDVLDRVLKAVTAPAQGTSE
LLGKVELQQGLRAV..N.PLLWQPGYLHRALQVMEKVASSPEDG.LC..AL.V.DRVLKAVTAPAQGTSE
RetrocopyLLGKVELQQGLRAVFRNVPLLWQPGYLHRALQVMEKVASSPEDGPLCRDALGVPDRVLKAVTAPAQGTSE
ParentalEQPQEGEESQRSEELVEQLDVEETEQSKLPQYLERFEALRSKLQALGKVESESLLTLSTQLAKAQL
E.PQEGEESQRS.E.VEQ.DVE.T.QSKLPQYLERFEAL.SKLQALGKVESESL.TL.TQLAKA.L
RetrocopyEEPQEGEESQRSGERVEQWDVEGTAQSKLPQYLERFEALHSKLQALGKVESESLRTLGTQLAKARL

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
SRP014902_placenta 0 .00 RPM 11 .02 RPM
SRP014902_testis 0 .00 RPM 43 .57 RPM
SRP018288_heart 0 .05 RPM 56 .79 RPM
SRP018288_kidney 0 .00 RPM 38 .91 RPM
SRP018288_liver 0 .00 RPM 108 .26 RPM
SRP018288_lung 0 .00 RPM 19 .14 RPM
SRP018856_adipose 0 .00 RPM 27 .86 RPM
SRP035408_brain 0 .00 RPM 28 .77 RPM
SRP035408_liver 0 .03 RPM 100 .19 RPM
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_231 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_231 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_231 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000025651 retrocopy
Myotis lucifugus ENSMLUG000000073551 retrocopy
Sus scrofa ENSSSCG00000023818 2 retrocopies
retro_sscr_231 , retro_sscr_251,



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