RetrogeneDB ID: retro_sscr_221

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 10:37112764..37113130(+)
• Located in intron of: ENSSSCG00000010987

Retrocopy information

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

Parental gene information

• Parental gene symbol: C15orf40
• Ensembl ID: ENSSSCG00000030131
• Aliases: None
• Description: chromosome 15 open reading frame 40 [Source:HGNC Symbol;Acc:28443]

Sequence

>retro_sscr_221
CCAGAGAAAGCTAGTGTGACAAACAAGGGTAAAAGTCAGAGCATGGAACCAGAGAAACCACCTCCTCCCTTAGGTCCCAT
GACAGTTGAATCTAAAGGTTGTGTCACCACAGCCATTCATGCAAAAGCCAGTTCCAAACAAAATGCTGTGACAGATCTGA
CAGCCAAGGCCGAAAGTGTAGCTACTCTAACGCCTCCGTCAGAAGGAGAGGCTAACACTGAGCTCTTCCAGTATCTTTCC
AAGATCTCAGAACTCGGGAAGAGTGATGTGGTTTTGGATAAGGGTGGTAAATCTCATGAAAAAGTAGCAAGGCTTTTGGC
CTCCACAACTCCAGAAAGGATCTTGGAGAAACTGAAAAAGCAGGTT

Alignment

ORF - retro_sscr_221 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.23 %
• Parental protein coverage: 96.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PKKAGATNKGKSQSKEQERPLPPLGPVTVDPKGCVTIAIHAKPGSKQNAVTDLTTEAVSVAIAAPPSEGE
          P.KA..TNKGKSQS.E.E.P.PPLGP.TV..KGCVT.AIHAK..SKQNAVTDLT..A.SVA...PPSEGE
Retrocopy PEKASVTNKGKSQSMEPEKPPPPLGPMTVESKGCVTTAIHAKASSKQNAVTDLTAKAESVATLTPPSEGE

Parental  ANAELCRYLSKVFELRKSDVVLDKGGKSREKVVKLLASTTPEEILEKLKKQV
          AN.EL..YLSK..EL.KSDVVLDKGGKS.EKV..LLASTTPE.ILEKLKKQV
Retrocopy ANTELFQYLSKISELGKSDVVLDKGGKSHEKVARLLASTTPERILEKLKKQV

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	8.23 RPM
SRP014902_testis	0.00 RPM	9.05 RPM
SRP018288_heart	0.03 RPM	19.44 RPM
SRP018288_kidney	0.20 RPM	44.92 RPM
SRP018288_liver	0.00 RPM	15.35 RPM
SRP018288_lung	0.10 RPM	7.64 RPM
SRP018856_adipose	0.00 RPM	14.95 RPM
SRP035408_brain	0.00 RPM	42.72 RPM
SRP035408_liver	0.00 RPM	21.87 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_221 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_221 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_221 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016522	2 retrocopies	retro_btau_1724, retro_btau_485,
Canis familiaris	ENSCAFG00000013185	2 retrocopies	retro_cfam_39, retro_cfam_420,
Callithrix jacchus	ENSCJAG00000015877	2 retrocopies	retro_cjac_1108, retro_cjac_4086,
Equus caballus	ENSECAG00000022459	1 retrocopy	retro_ecab_374,
Homo sapiens	ENSG00000169609	1 retrocopy	retro_hsap_1881,
Gorilla gorilla	ENSGGOG00000023062	1 retrocopy	retro_ggor_1378,
Microcebus murinus	ENSMICG00000009564	2 retrocopies	retro_mmur_1387, retro_mmur_1601,
Myotis lucifugus	ENSMLUG00000007515	1 retrocopy	retro_mluc_2487,
Macaca mulatta	ENSMMUG00000015890	1 retrocopy	retro_mmul_664,
Monodelphis domestica	ENSMODG00000019374	1 retrocopy	retro_mdom_145,
Nomascus leucogenys	ENSNLEG00000010930	1 retrocopy	retro_nleu_1803,
Oryctolagus cuniculus	ENSOCUG00000005072	1 retrocopy	retro_ocun_211,
Procavia capensis	ENSPCAG00000016446	1 retrocopy	retro_pcap_51,
Pongo abelii	ENSPPYG00000006737	1 retrocopy	retro_pabe_1561,
Rattus norvegicus	ENSRNOG00000019514	2 retrocopies	retro_rnor_1547, retro_rnor_2334,
Sorex araneus	ENSSARG00000006314	1 retrocopy	retro_sara_147,
Sarcophilus harrisii	ENSSHAG00000017947	2 retrocopies	retro_shar_233, retro_shar_442,
Sus scrofa	ENSSSCG00000030131	1 retrocopy	retro_sscr_221 ,
Tupaia belangeri	ENSTBEG00000014387	6 retrocopies	retro_tbel_1151, retro_tbel_2000, retro_tbel_3071, retro_tbel_3546, retro_tbel_4182, retro_tbel_4371,