RetrogeneDB ID: retro_sscr_126

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:140751040..140751853(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: MRPL3
• Ensembl ID: ENSSSCG00000011179
• Aliases: None
• Description: mitochondrial ribosomal protein L3 [Source:HGNC Symbol;Acc:10379]

Sequence

>retro_sscr_126
GCCCAGTTATTAAGTAAACCATGTCCTCTGAAAAATGAACCATGGCCTATACATTCTTGGGAACCAGATCGCTCTAGAGC
TGGCCTTATCACACTGAAGCTGGGCATGATGCCTTATGGACCAAGGATGGTCAAAAGTAATATCTCATTATTTAACATAT
AAGACTGTCACATCCTAAAATATACTCCAAAGGAAAACCATAATGGAAAATGGCAGCTCTAACTGTAGGAGGAAAAACCA
TATCACATTTCTGTAAATCTACATCTATATTGGAAATTTACTAAGAACTTGGATTGCTGCCAGTACCGAAAGTTAAAACC
TTTCACGTAACAGACAACGCAGTCATTAAACCAGGCACTCTTTGCTAGGCTGCTCATTTTCTCCCAAGACAGTATGTGAA
TGTCACAACAAAAACTGTATTCATAAAGGTTTTCAAGACGTCATGAAAATATGGGATTTAAAGGCCAGCCTATTATACAT
GGTCAAACAAAGATCCACGGGAGAGCTAGAACAATTTCAATCAATGATGTTGTCAGAGTCTGGCCTGGAACTAAAATGCC
TGGACAAATGGGAAGAACAGATAAGACAGCATATGGACGGAAAGTGTGGACACAAAGCAGTATTATAATCTACATAAAAT
GGCTCTGTAACTAGACATAAAAAATTGCTCAGAGATTCTAAACTGTCTGCATATCGGGATTTCTGTACAAATCTACCAAC
CCCTACATATTTTCCTAATGGAGATGAAGAACAACAACCAGAGGTTTATATGATAAAAACACGTGTCACCCCAGCACACC
TTCCATCACATTT

Alignment

ORF - retro_sscr_126 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.9 %
• Parental protein coverage: 69.42 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  AQLASKLCPLKDEPWPIHPWEPGSSRVGLIALKLGMMPLWTKDGQKHVVTLLQVQDCHVLKYTPKENHNG
          AQL.SK.CPLK.EPWPIH.WEP..SR.GLI.LKLGMMP............L....DCH.LKYTPKENHNG
Retrocopy AQLLSKPCPLKNEPWPIHSWEPDRSRAGLITLKLGMMPYGPRMVKSNI-SLFNI*DCHILKYTPKENHNG

Parental  R-MAALTVGGKTVSHFHKSASILEFYQELGLPPKQKVKIFNVTENAVIKPGTPLYAAH-FRPGQYVDVTA
          ..MAALTVGGKT.SHF.KS.SILE.Y.ELGL.P..KVK.F.VT.NAVIKPGT...AAH.F.P........
Retrocopy K<MAALTVGGKTISHFCKSTSILEIY*ELGLLPVPKVKTFHVTDNAVIKPGTLC*AAH<FSPKTVCECHN

Parental  KT-IGKGFQGVMRRW-GFKGQPATHGQTKTHRRPGAISTGDVARVWPGTKMPGQLGNIDRTAFGLKVWRI
          K..I.KGFQ.VM..W.GFKGQP..HGQTK.H.R...IS..DV.RVWPGTKMPGQ.G..D.TA.G.KVW..
Retrocopy KNCIHKGFQDVMKIW<GFKGQPIIHGQTKIHGRARTISINDVVRVWPGTKMPGQMGRTDKTAYGRKVW--

Parental  NTKHNIIYV-NGSVPGHKNCLVKIKDSKLPAYKDFCKNLPFPTYFPDGDEEALPE-DLYDENVCQPGAPS
          .....IIY..NGSV..HK..L....DSKL.AY.DFC.NLP.PTYFP.GDEE..PE..LYD.N.C.P..PS
Retrocopy TQSSIIIYI>NGSVTRHKKLL---RDSKLSAYRDFCTNLPTPTYFPNGDEEQQPE<GLYDKNTCHPSTPS

Parental  ITF
          ITF
Retrocopy ITF

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	10.75 RPM
SRP014902_testis	0.00 RPM	60.54 RPM
SRP018288_heart	0.03 RPM	44.50 RPM
SRP018288_kidney	0.00 RPM	56.54 RPM
SRP018288_liver	0.00 RPM	27.82 RPM
SRP018288_lung	0.00 RPM	24.44 RPM
SRP018856_adipose	0.00 RPM	38.57 RPM
SRP035408_brain	0.00 RPM	27.76 RPM
SRP035408_liver	0.00 RPM	22.78 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_126 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_126 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_126 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000021216	1 retrocopy	retro_cpor_324,
Dasypus novemcinctus	ENSDNOG00000014498	1 retrocopy	retro_dnov_178,
Homo sapiens	ENSG00000114686	1 retrocopy	retro_hsap_1236,
Gorilla gorilla	ENSGGOG00000011128	1 retrocopy	retro_ggor_969,
Microcebus murinus	ENSMICG00000009524	1 retrocopy	retro_mmur_1106,
Ochotona princeps	ENSOPRG00000000501	1 retrocopy	retro_opri_589,
Pan troglodytes	ENSPTRG00000015396	1 retrocopy	retro_ptro_850,
Sus scrofa	ENSSSCG00000011179	1 retrocopy	retro_sscr_126 ,