RetrogeneDB ID: retro_sscr_251

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 10:75821194..75822011(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000011161
• 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_251
CACAAATTTCGACACAGCCCCAACCGCTGGTACTTGAGAGATGGACTGTCCGCACGTGGGCTAGGTAGTGTCTAAAACAT
GGTGCACAGGACAAAGCCTTATACACCCTTAAAAATAAGGTCCAATATGGCATTTTCCCGGATAACGATACATTTAATTT
ACTGATGGATCATTTCATAAAGAAAGAAAATTACAAAGATGCTTTATCCGTGGTTTTTGAGATCATGATGCAAGCAGCTT
TTGAAGTCCCTTCCACCCAGCTCCTCTCCCTCTGTGTTTTGTACTGCTGCCTTGCAGAGAAGACAGACTTGAGTTGGGAA
GAGAGAGGAACTTTGGTGCGTCCCTGTTACTCCCAGGCCTAAAGCAAAGGAACTCAGTGGGGCTGAGTTCCCAGCTGTGT
GGCTGTGCACTTCTTGGGAAGGTGGAACTGCAGCAAGGGCTGAGGGCTGTGTTCCGCAACGTGCCGCTGCTCTGGCAACC
AGGCTACCTCCACAGAGCCCTTCAAGTGATGGAGAAGGTGGCCTCCTCCCCAGAAGACGGACCGCTGTGTAGAGATGCGC
TCGGTGTGCCGGACAGAGTGCTGAAGGCTGTGACTGCTCCAGCCCAGGGGACTTCAGAGGAAGAGCCCCAGGAAGGTGAG
GAAAGCCAGAGGTCAGGAGAACGGGTAGAGCAGTGGGATGTGGAGGGAACTGCACAGTCCAAGCTTCCTCAGTACCTGGA
ACGATTTGAGGCTTTACATTCTAAGCTGCAGGCTCTGGGCAAAGTGGAGTCAGAAAGCCTGCGGACCCTGGGCACCCAGC
TCGCCAAGGCGCGGCTG

Alignment

ORF - retro_sscr_251 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.27 %
• Parental protein coverage: 76.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YKFRHSPNCWYLRD-WTIHTWIRQCLKYGAQDKALYTLKNKVQYGIFPDNYTFNLLMDYFIKKENYKDAL
          .KFRHSPN.WYLRD.WT..TW.R.CLK.GAQDKALYTLKNKVQYGIFPDN.TFNLLMD.FIKKENYKDAL
Retrocopy HKFRHSPNRWYLRD<WTVRTWAR*CLKHGAQDKALYTLKNKVQYGIFPDNDTFNLLMDHFIKKENYKDAL

Parental  SVVFEIMMQEAFEVPSTQLLSLYVLYHCLAEKTDLSWEE-ERNFGASLLLPGLKQKNSVGLSSQLYGYAL
          SVVFEIMMQ.AFEVPSTQLLSL.VLY.CLAEKTDLSWEE.ERNFGASLLLPGLKQ.NSVGLSSQL.G.AL
Retrocopy SVVFEIMMQAAFEVPSTQLLSLCVLYCCLAEKTDLSWEE<ERNFGASLLLPGLKQRNSVGLSSQLCGCAL

Parental  LGKVELQQGLRAVYCNMPLLWQPGYLHRALQVMEKVASSPEDGQLCGEALDVLDRVLKAVTAPAQGTSEE
          LGKVELQQGLRAV..N.PLLWQPGYLHRALQVMEKVASSPEDG.LC..AL.V.DRVLKAVTAPAQGTSEE
Retrocopy LGKVELQQGLRAVFRNVPLLWQPGYLHRALQVMEKVASSPEDGPLCRDALGVPDRVLKAVTAPAQGTSEE

Parental  QPQEGEESQRSEELVEQLDVEETEQSKLPQYLERFEALRSKLQALGKVESESLLTLSTQLAKAQL
          .PQEGEESQRS.E.VEQ.DVE.T.QSKLPQYLERFEAL.SKLQALGKVESESL.TL.TQLAKA.L
Retrocopy EPQEGEESQRSGERVEQWDVEGTAQSKLPQYLERFEALHSKLQALGKVESESLRTLGTQLAKARL

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	0.00 RPM	100.19 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_251 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_251 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_251 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 ,