RetrogeneDB ID: retro_sscr_303

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 12:37393287..37394035(-)
• Located in intron of: ENSSSCG00000017670

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000025312
• Aliases: None
• Description: Sus scrofa programmed cell death 2 (PDCD2), mRNA. [Source:RefSeq mRNA;Acc:NM_001244352]

Sequence

>retro_sscr_303
TTTAGAAATTAGCTATCCAGGAGAAATGACTTCTACTCCTATGAACCACCTTCTGAGGATCCTCTCCCAGAAACAGGAGA
ATCCCTGAGCCTCCTGCTCAGGTTTGGTGCTCATCTCTGCAGGGTTTGTTGGCTGTTTAGGCCCCAAAACATGCTCCAGA
TGTCACCAGGCACATTACTGCAGTAAGGAGCATCAGGCACTGGACTGGAGATGGGGACATAAGCAGGCTTCTGTACAAGC
AGATAATTTGGACAATACAGTCCCAGACCCCAACTTCCTTCTTCCAAAATGTGAAACTGTAATAGGAACAGAAGATGAGA
TTATGCCCGAAGTTGTAGAAAAAGAAGATGAATCAGAGATTACAGGGAGCATGGGCAAAGCACCCGATGAAGAACTGGAT
TCCATGGCAAAGCATGAATCTAGGGAAGATAGAATTTCCCATAAGTTTAAAACTAAAATATTCCTTGAACCAGAACAGAT
TTTCAGATATGGCAAAGGGGTTGCCCCCATCTGGATTGCTGGTGAAAATATTCCTCAAGAAAAGGATATTCCAGACTGCC
CCTGTGGTGCCAAGAGAATATTTGAATTCCAGATCATGCCTCAGCTGCCCCACCACCTCAAGGCTGACAGGCTGGGCAGG
AGTGTTGATTGGGGTGCCCTGGCCATCCTCACCTGTGCTGAAAGCTGTGGATTGGGCACTGGCTACACAAAGGAATTTGT
TTGGAAGCAAGATATACTAGACACAGCT

Alignment

ORF - retro_sscr_303 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84. %
• Parental protein coverage: 99.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FRNQLPRRNDFYSFEPPSEDPPPETGESLSLQLKSGAHLCRVC-GCLGPKTCSRCHQAHYCSKEHQALDW
          FRN.L.RRNDFYS.EPPSEDP.PETGESLSL.L..GAHLCRVC.GCLGPKTCSRCHQAHYCSKEHQALDW
Retrocopy FRN*LSRRNDFYSYEPPSEDPLPETGESLSLLLRFGAHLCRVC>GCLGPKTCSRCHQAHYCSKEHQALDW

Parental  RSGHKQACAQPDNLDNTIPDHNFLFPEFEIVIETEDEIMPEVVEKEDESEIIGSMGEASEEELDSMAKHE
          R.GHKQA..Q.DNLDNT.PD.NFL.P..E.VI.TEDEIMPEVVEKEDESEI.GSMG.A..EELDSMAKHE
Retrocopy RWGHKQASVQADNLDNTVPDPNFLLPKCETVIGTEDEIMPEVVEKEDESEITGSMGKAPDEELDSMAKHE

Parental  SREDRIFQKFKTKISLEPEQILRYGRGVAPIWISAENIPQEKDIPDCPCGAKRIFEFQVMPQLLNYLKAD
          SREDRI..KFKTKI.LEPEQI.RYG.GVAPIWI..ENIPQEKDIPDCPCGAKRIFEFQ.MPQL...LKAD
Retrocopy SREDRISHKFKTKIFLEPEQIFRYGKGVAPIWIAGENIPQEKDIPDCPCGAKRIFEFQIMPQLPHHLKAD

Parental  RLGRSVDWGVLAVFTCAESCGLGAGYTEEFVWKQDLLDTA
          RLGRSVDWG.LA..TCAESCGLG.GYT.EFVWKQD.LDTA
Retrocopy RLGRSVDWGALAILTCAESCGLGTGYTKEFVWKQDILDTA

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	7.03 RPM
SRP014902_testis	0.85 RPM	7.64 RPM
SRP018288_heart	0.08 RPM	10.01 RPM
SRP018288_kidney	0.30 RPM	21.28 RPM
SRP018288_liver	0.00 RPM	15.51 RPM
SRP018288_lung	0.00 RPM	14.97 RPM
SRP018856_adipose	0.11 RPM	5.62 RPM
SRP035408_brain	0.00 RPM	34.40 RPM
SRP035408_liver	0.00 RPM	23.48 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_303 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_303 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_303 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 17 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017075	2 retrocopies	retro_amel_1329, retro_amel_1404,
Callithrix jacchus	ENSCJAG00000020634	1 retrocopy	retro_cjac_3946,
Cavia porcellus	ENSCPOG00000002920	1 retrocopy	retro_cpor_168,
Equus caballus	ENSECAG00000016819	1 retrocopy	retro_ecab_533,
Felis catus	ENSFCAG00000007037	2 retrocopies	retro_fcat_305, retro_fcat_749,
Homo sapiens	ENSG00000071994	1 retrocopy	retro_hsap_4305,
Gorilla gorilla	ENSGGOG00000028229	2 retrocopies	retro_ggor_2876, retro_ggor_899,
Microcebus murinus	ENSMICG00000007474	1 retrocopy	retro_mmur_108,
Macaca mulatta	ENSMMUG00000019916	1 retrocopy	retro_mmul_1137,
Mustela putorius furo	ENSMPUG00000007227	2 retrocopies	retro_mputfur_621, retro_mputfur_707,
Nomascus leucogenys	ENSNLEG00000000295	2 retrocopies	retro_nleu_1458, retro_nleu_2633,
Otolemur garnettii	ENSOGAG00000014002	2 retrocopies	retro_ogar_2090, retro_ogar_2288,
Pongo abelii	ENSPPYG00000017193	2 retrocopies	retro_pabe_3505, retro_pabe_958,
Pan troglodytes	ENSPTRG00000018828	2 retrocopies	retro_ptro_2915, retro_ptro_788,
Pteropus vampyrus	ENSPVAG00000010822	1 retrocopy	retro_pvam_1150,
Sus scrofa	ENSSSCG00000025312	2 retrocopies	retro_sscr_303 , retro_sscr_450,
Ictidomys tridecemlineatus	ENSSTOG00000022768	2 retrocopies	retro_itri_1348, retro_itri_1635,