RetrogeneDB ID: retro_sscr_98

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:13740522..13740810(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000007188
• Aliases: None
• Description: FKBP1A-like [Source:RefSeq peptide;Acc:NP_001033089]

Sequence

>retro_sscr_98
CCCAAGACCGGCGCACCTTTCCGAAGCGGCCAGCCCTGCGGGGTGCACTGCCCCGGGATGCTTGAGGGTGGAAAGAATTT
ATTCCTCCCAGGACAGAAACAAGCCCTTTAAGTTTGCGCTAAGCAAGCGGGAGGTGATCCGAGGCTGGGAGGCAGGGGTC
GCCCAGATGCGTGTGGGTCAGAGAGCCAAGCTATCTCCCCAGACTATGCCTATGGTGCCACTGGGCACCCAGGCATCATC
CCGCCAAATGCCACTCTCGTCTTTGATGTGGAGCTTCTAAAACTGGAC

Alignment

ORF - retro_sscr_98 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.31 %
• Parental protein coverage: 91.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PGDGRTFPKRGQTCVVHYTGMLEDGKK-FDSSRDRNKPFKFVLGKQEVIRGWEEGVAQMSV-GQRAKLTI
          P..G..F...GQ.C.VH..GML..G.K...SS.DRNKPFKF.L.K.EVIRGWE.GVAQM.V.G......I
Retrocopy PKTGAPF-RSGQPCGVHCPGML-EGGK>IYSSQDRNKPFKFALSKREVIRGWEAGVAQMRV<GSESQ-AI

Parental  SPDYAYGATGHPGIIPPNATLVFDVELLKLE
          SPDYAYGATGHPGIIPPNATLVFDVELLKL.
Retrocopy SPDYAYGATGHPGIIPPNATLVFDVELLKLD

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	0.40 RPM	324.79 RPM
SRP014902_testis	0.00 RPM	113.16 RPM
SRP018288_heart	0.00 RPM	241.06 RPM
SRP018288_kidney	0.00 RPM	170.91 RPM
SRP018288_liver	0.00 RPM	155.59 RPM
SRP018288_lung	0.00 RPM	304.87 RPM
SRP018856_adipose	0.00 RPM	407.33 RPM
SRP035408_brain	0.00 RPM	209.24 RPM
SRP035408_liver	0.00 RPM	82.70 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_98 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_98 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_98 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 22 parental genes, and 59 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008303	4 retrocopies	retro_btau_1220, retro_btau_1265, retro_btau_128, retro_btau_1760,
Callithrix jacchus	ENSCJAG00000020908	4 retrocopies	retro_cjac_1544, retro_cjac_3889, retro_cjac_4157, retro_cjac_537,
Ciona savignyi	ENSCSAVG00000006859	1 retrocopy	retro_csav_11,
Dasypus novemcinctus	ENSDNOG00000005868	16 retrocopies	retro_dnov_1289, retro_dnov_1577, retro_dnov_1666, retro_dnov_2236, retro_dnov_228, retro_dnov_2404, retro_dnov_2418, retro_dnov_2544, retro_dnov_2589, retro_dnov_263, retro_dnov_584, retro_dnov_621, retro_dnov_670, retro_dnov_684, retro_dnov_707, retro_dnov_937,
Echinops telfairi	ENSETEG00000007454	1 retrocopy	retro_etel_2059,
Felis catus	ENSFCAG00000026097	2 retrocopies	retro_fcat_168, retro_fcat_751,
Homo sapiens	ENSG00000088832	1 retrocopy	retro_hsap_1198,
Gorilla gorilla	ENSGGOG00000001729	3 retrocopies	retro_ggor_1494, retro_ggor_2344, retro_ggor_933,
Macaca mulatta	ENSMMUG00000015996	1 retrocopy	retro_mmul_10,
Monodelphis domestica	ENSMODG00000019554	2 retrocopies	retro_mdom_151, retro_mdom_733,
Mustela putorius furo	ENSMPUG00000017946	1 retrocopy	retro_mputfur_1649,
Mus musculus	ENSMUSG00000032966	1 retrocopy	retro_mmus_1293,
Nomascus leucogenys	ENSNLEG00000009356	5 retrocopies	retro_nleu_2009, retro_nleu_2628, retro_nleu_2728, retro_nleu_2730, retro_nleu_604,
Otolemur garnettii	ENSOGAG00000002629	1 retrocopy	retro_ogar_673,
Procavia capensis	ENSPCAG00000008816	2 retrocopies	retro_pcap_289, retro_pcap_37,
Pongo abelii	ENSPPYG00000010852	5 retrocopies	retro_pabe_1654, retro_pabe_1686, retro_pabe_2364, retro_pabe_2365, retro_pabe_998,
Pan troglodytes	ENSPTRG00000013163	2 retrocopies	retro_ptro_2983, retro_ptro_818,
Pteropus vampyrus	ENSPVAG00000013840	1 retrocopy	retro_pvam_1367,
Rattus norvegicus	ENSRNOG00000008822	1 retrocopy	retro_rnor_453,
Sus scrofa	ENSSSCG00000007188	1 retrocopy	retro_sscr_98 ,
Tursiops truncatus	ENSTTRG00000003547	3 retrocopies	retro_ttru_1227, retro_ttru_802, retro_ttru_904,
Vicugna pacos	ENSVPAG00000011511	1 retrocopy	retro_vpac_171,