RetrogeneDB ID: retro_sscr_311

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:19161481..19161733(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C2orf76
• Ensembl ID: ENSSSCG00000015718
• Aliases: None
• Description: chromosome 2 open reading frame 76 [Source:HGNC Symbol;Acc:27017]

Sequence

>retro_sscr_311
GTATTTCTAAAGCTAGATGCCCCTTTAAGGACAAGTCTGCCACCACCACTCAGAAATTATAAATATGAGAAACTAAAGAT
ATTCCTCAAGCACATACACCAAAGACAAATGAACTCGTGTTGAGATTTAAAGACAGCAACAGACTCTCATTAAAAGAAGA
CAGCTCTCAGAGCAGCTGGAATCATGATGAGACAGAAACGGCATCTTCTGTGAAGATTACAAAACTACAAAGCTAATCCC
ATTTCATCCTGG

Alignment

ORF - retro_sscr_311 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.44 %
• Parental protein coverage: 63.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VFLKQDIPLKTSLPPPFRNYEYDKLKI-VHQAHKSKTNELVLSLEDDDKLLLKEDSTLKAAGIANETEIA
          VFLK.D.PL.TSLPPP.RNY.Y.KLKI...QAH..KTNELVL...D...L.LKEDS.........ETE.A
Retrocopy VFLKLDAPLRTSLPPPLRNYKYEKLKI<IPQAHTPKTNELVLRFKDSNRLSLKEDSS-QSSWNHDETETA

Parental  -FFCEEDYK-NYKANPISSW
          ..FC.EDYK.NYKANPISSW
Retrocopy <IFC-EDYK<NYKANPISSW

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	0.93 RPM
SRP014902_testis	0.00 RPM	3.68 RPM
SRP018288_heart	0.00 RPM	1.96 RPM
SRP018288_kidney	0.00 RPM	4.14 RPM
SRP018288_liver	0.00 RPM	3.68 RPM
SRP018288_lung	0.00 RPM	2.95 RPM
SRP018856_adipose	0.00 RPM	4.08 RPM
SRP035408_brain	0.00 RPM	2.73 RPM
SRP035408_liver	0.00 RPM	3.05 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_311 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_311 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_311 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008507	2 retrocopies	retro_amel_1062, retro_amel_1693,
Bos taurus	ENSBTAG00000010599	1 retrocopy	retro_btau_965,
Canis familiaris	ENSCAFG00000004896	2 retrocopies	retro_cfam_1119, retro_cfam_1727,
Equus caballus	ENSECAG00000002063	1 retrocopy	retro_ecab_384,
Myotis lucifugus	ENSMLUG00000004031	1 retrocopy	retro_mluc_1204,
Mustela putorius furo	ENSMPUG00000000943	1 retrocopy	retro_mputfur_726,
Mus musculus	ENSMUSG00000026388	1 retrocopy	retro_mmus_947,
Pteropus vampyrus	ENSPVAG00000011615	1 retrocopy	retro_pvam_337,
Sus scrofa	ENSSSCG00000015718	1 retrocopy	retro_sscr_311 ,