RetrogeneDB ID: retro_sscr_477

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 15:134839818..134840226(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFA8
• Ensembl ID: ENSSSCG00000005528
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 8, 19kDa [Source:HGNC Symbol;Acc:7692]

Sequence

>retro_sscr_477
ATGTCGGGGATAGTGGAGCTGCCCACTCTGGAAGATCTGAAAGTGCGGGAAGGGAAAGTCAGTTCTTCAATGCTGAAAGC
TGCACCCCATCACTTTGGAGCTCAGTGCGTTAAGCCCAACAAGGAGTTCACGCTCTGCCAGTGTGAAGAGAAGCACCCAA
GGCGATGTTTAGAGGGAGACAAGCTTCTCAGCCACTGTGCCCTAAACTTCTCTAGGCAGATGAAGCAGCACTGTGTGGAG
ACTTTTACGGAAAACTGGACCGGCAGAGATTACTCTGGCCTGCAGGGTTTTCGTCACTGTCGCTGTTGCAAGCAAGAGGC
ACAGTTTGACAAGCACATGCTGGACAAACTGGGCTGAGTGCGACCTGACCTGGGAGAGGTGTCAAAGGTCACCAAAGTGA
AAACAGAT

Alignment

ORF - retro_sscr_477 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.26 %
• Parental protein coverage: 77.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPGIVELPTLEDLKVQEVKVSSSVLKAAAHHYGAQCDKPNKEFMLCRWEEKDPRRCLEEGKLVNQCALDF
          M.GIVELPTLEDLKV.E.KVSSS.LKAA.HH.GAQC.KPNKEF.LC..EEK.PRRCLE..KL...CAL.F
Retrocopy MSGIVELPTLEDLKVREGKVSSSMLKAAPHHFGAQCVKPNKEFTLCQCEEKHPRRCLEGDKLLSHCALNF

Parental  FRQIKRHCAEPFTEYWTCIDYSGLQLFRHCR--KQQAKFDECVLDKLGWVRPDLGELSKVTKVKTD
          .RQ.K.HC.E.FTE.WT..DYSGLQ.FRHCR..KQ.A.FD...LDKLG.VRPDLGE.SKVTKVKTD
Retrocopy SRQMKQHCVETFTENWTGRDYSGLQGFRHCRCCKQEAQFDKHMLDKLG*VRPDLGEVSKVTKVKTD

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	25.88 RPM
SRP014902_testis	0.00 RPM	71.57 RPM
SRP018288_heart	0.00 RPM	135.19 RPM
SRP018288_kidney	0.00 RPM	85.90 RPM
SRP018288_liver	0.00 RPM	34.54 RPM
SRP018288_lung	0.00 RPM	20.77 RPM
SRP018856_adipose	0.02 RPM	45.29 RPM
SRP035408_brain	0.00 RPM	51.55 RPM
SRP035408_liver	0.00 RPM	29.71 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_477 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_477 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_477 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000015093	1 retrocopy	retro_ogar_1487,
Rattus norvegicus	ENSRNOG00000005668	1 retrocopy	retro_rnor_2583,
Sarcophilus harrisii	ENSSHAG00000011368	1 retrocopy	retro_shar_198,
Sus scrofa	ENSSSCG00000005528	1 retrocopy	retro_sscr_477 ,