RetrogeneDB ID: retro_sscr_201

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:275565346..275565908(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RRAS
• Ensembl ID: ENSSSCG00000003183
• Aliases: None
• Description: related RAS viral (r-ras) oncogene homolog [Source:HGNC Symbol;Acc:10447]

Sequence

>retro_sscr_201
TACCGGCTCGTGGTGGTCTGTGGAGGCGGCGTGGGCAAGTCGGCGCTCACCATCCAGTTCATCCAGTCCTATGTTGTAAC
GGATTATGATCCAACCATCGAGGATTCCTACACAAAGCAATGTGTATTAGATGACCGGGCAGGCCGGCTAGATATTCTGG
ATACAGCAGGACAAGAGGAGTTTGGAGCTATGAGAGAACAGTATATGAGAACTGGCAAGGGTTTCCTGTTGGTCTTTTCA
GTCACAGATAGAGGCAGTTTTGAAGAAATCTCTAAGTTTCAAAGACAGATTCTCAGAGCAAAGGATCGTGAACGAGTTTC
TAATGATTTTAACTGGTAATAAAGTAGCTCTGGATCATCAAAGACAACGCAGGAAGGGACAGCAAGTGGCACGGCAGCTT
AAAGTAACATACATGGAGGCATCAGCAAAGATTAGGATGAATGTGGATCAAGCTATCCATGAACTTATCCTGGTTATAAG
GAAATTTCAAGAGCAGGAATGTCCTCCTTCACCAGAACCAATATGGAAAGAAAAAGACAAGAAAGGCTGCCATTGTGTCA
TT

Alignment

ORF - retro_sscr_201 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.05 %
• Parental protein coverage: 86.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HKLVVVGGGGVGKSALTIQFIQSYFVSDYDPTIEDSYTKICTVDGVPARLDILDTAGQEEFGAMREQYMR
          ..LVVV.GGGVGKSALTIQFIQSY.V.DYDPTIEDSYTK.C..D....RLDILDTAGQEEFGAMREQYMR
Retrocopy YRLVVVCGGGVGKSALTIQFIQSYVVTDYDPTIEDSYTKQCVLDDRAGRLDILDTAGQEEFGAMREQYMR

Parental  AGHGFLLVFAINDRQSFNEVGKLFTQILRVKDRD-DFPIVLVGNKADLETQRQVPRSEASAFSNSHHVAY
          .G.GFLLVF...DR.SF.E..K...QILR.KDR...F...L.GNK..L..QRQ..R...........V.Y
Retrocopy TGKGFLLVFSVTDRGSFEEISKFQRQILRAKDRE>EFLMILTGNKVALDHQRQ--RRKGQQVARQLKVTY

Parental  FEASAKLRLNVDEAFEQLVRAVRKFQEQELPPSPPSAPRKKD-RSCPCIL
          .EASAK.R.NVD.A...L....RKFQEQE.PPSP......KD...C.C..
Retrocopy MEASAKIRMNVDQAIHELILVIRKFQEQECPPSPEPIWKEKDKKGCHCVI

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	43.80 RPM	61.19 RPM
SRP014902_testis	16.55 RPM	20.51 RPM
SRP018288_heart	14.22 RPM	30.15 RPM
SRP018288_kidney	6.30 RPM	16.15 RPM
SRP018288_liver	4.48 RPM	14.39 RPM
SRP018288_lung	9.37 RPM	57.02 RPM
SRP018856_adipose	16.42 RPM	171.02 RPM
SRP035408_brain	4.10 RPM	10.42 RPM
SRP035408_liver	4.32 RPM	21.61 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_201 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_201 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_201 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
Otolemur garnettii	ENSOGAG00000010243	1 retrocopy	retro_ogar_1233,
Sus scrofa	ENSSSCG00000003183	2 retrocopies	retro_sscr_201 , retro_sscr_570,
Tursiops truncatus	ENSTTRG00000005524	1 retrocopy	retro_ttru_771,