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 symbol: MRPS27
• Ensembl ID: ENSSSCG00000023818
• Aliases: None
• Description: mitochondrial ribosomal protein S27 [Source:HGNC Symbol;Acc:14512]

Sequence

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

Alignment

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:

Parental  YKFRHSPNCWYLRD-WTIHTWIRQCLKYGAQDKALYTLK-NKVQYGIFPDNYTFNLLMDYFIKKENYKDA
          .KFRHSPN.WYLRD.WT..TW.R.CLK.GAQDKALYTLK.NKVQYGIFPDN.TFNLLMD.FIKKENYKDA
Retrocopy HKFRHSPNRWYLRD<WTVRTWAR*CLKHGAQDKALYTLK<NKVQYGIFPDNDTFNLLMDHFIKKENYKDA

Parental  LSVVFEIMMQEAFEVPSTQLLSLYVLYHCLAEKTDLSWEE-ERNFGASLLLPGLKQKNSVGLSSQLYGYA
          LSVVFEIMMQ.AFEVPSTQLLSL.VLY.CLAEKTDLSWEE.ERNFGASLLLPGLKQ.NSVGLSSQL.G.A
Retrocopy LSVVFEIMMQAAFEVPSTQLLSLCVLYCCLAEKTDLSWEE<ERNFGASLLLPGLKQRNSVGLSSQLCGCA

Parental  LLGKVELQQGLRAVYCNMPLLWQPGYLHRALQVMEKVASSPEDGQLCGEALDVLDRVLKAVTAPAQGTSE
          LLGKVELQQGLRAV..N.PLLWQPGYLHRALQVMEKVASSPEDG.LC..AL.V.DRVLKAVTAPAQGTSE
Retrocopy LLGKVELQQGLRAVFRNVPLLWQPGYLHRALQVMEKVASSPEDGPLCRDALGVPDRVLKAVTAPAQGTSE

Parental  EQPQEGEESQRSEELVEQLDVEETEQSKLPQYLERFEALRSKLQALGKVESESLLTLSTQLAKAQL
          E.PQEGEESQRS.E.VEQ.DVE.T.QSKLPQYLERFEAL.SKLQALGKVESESL.TL.TQLAKA.L
Retrocopy EEPQEGEESQRSGERVEQWDVEGTAQSKLPQYLERFEALHSKLQALGKVESESLRTLGTQLAKARL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

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

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_231 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_231 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_231 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002565	1 retrocopy	retro_chof_2697,
Myotis lucifugus	ENSMLUG00000007355	1 retrocopy	retro_mluc_771,
Sus scrofa	ENSSSCG00000023818	2 retrocopies	retro_sscr_231 , retro_sscr_251,