RetrogeneDB ID: retro_sscr_218

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 10:14945588..14945989(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MSRB2
• Ensembl ID: ENSSSCG00000011077
• Aliases: None
• Description: methionine sulfoxide reductase B2 [Source:HGNC Symbol;Acc:17061]

Sequence

>retro_sscr_218
CTCCAAGAGTGAGAGTGGCAAGAGAAGCTGACTCGACAGCAATTCCCCGTCAGGAGAGAAAAAGGGATGGAACAGCTTTT
CAGTGGGACCTACCTGCCTAACAAGGAAGCAGGGATGTGTCGCTGTGTACACTGTGACAGTCACTCTTCACCGCTGAGGA
AAAGTACTTCTCGGGCACTGGATGGCCTTCATTTTCTGAGGCTCACGGCACATCTGGCTCTGATGAGGGTGACCCAGGAA
TCCTGAGACGTGTGGACACCTCACTGGGACCAGCTGGCCCGGAGGTTGTCTGCAAGCAGTGCGAAGCTCACCTTGGCCAC
GTGTTTCCTGATGGACCTGGGCATAGTGGTCACAGGGTTCGCATCAACAGTGTGGCGCTCACGGTCAGTTCAGGGAAATA
C

Alignment

ORF - retro_sscr_218 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.59 %
• Parental protein coverage: 73.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSKSEWQKKLTPEQFHVTREKGTEPPFSGTYLNNKEAGMYHCVCCDS-PLFSSEKKYCSGTGWPSFSEAH
          L...EWQ.KLT..QF.V.REKG.E..FSGTYL.NKEAGM..CV.CDS..LF..E.KY.SGTGWPSFSEAH
Retrocopy LQE*EWQEKLTRQQFPVRREKGMEQLFSGTYLPNKEAGMCRCVHCDS<SLFTAEEKYFSGTGWPSFSEAH

Parental  GTSGSDESDTGILRRVDTSLGTARTEVVCKQCEAHLGHVFPDGPGPTGQRFCINSVALKFKPRKH
          GTSGSDE.D.GILRRVDTSLG.A..EVVCKQCEAHLGHVFPDGPG..G.R..INSVAL.....K.
Retrocopy GTSGSDEGDPGILRRVDTSLGPAGPEVVCKQCEAHLGHVFPDGPGHSGHRVRINSVALTVSSGKY

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	3.72 RPM
SRP014902_testis	0.00 RPM	22.77 RPM
SRP018288_heart	0.00 RPM	27.50 RPM
SRP018288_kidney	0.30 RPM	24.53 RPM
SRP018288_liver	0.00 RPM	15.83 RPM
SRP018288_lung	0.61 RPM	20.06 RPM
SRP018856_adipose	0.00 RPM	23.28 RPM
SRP035408_brain	0.00 RPM	27.92 RPM
SRP035408_liver	0.00 RPM	14.82 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_218 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_218 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_218 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006388	1 retrocopy	retro_amel_505,
Canis familiaris	ENSCAFG00000004215	1 retrocopy	retro_cfam_1147,
Equus caballus	ENSECAG00000013072	1 retrocopy	retro_ecab_593,
Nomascus leucogenys	ENSNLEG00000012892	1 retrocopy	retro_nleu_2871,
Pongo abelii	ENSPPYG00000002148	1 retrocopy	retro_pabe_3127,
Sus scrofa	ENSSSCG00000011077	1 retrocopy	retro_sscr_218 ,