RetrogeneDB ID: retro_ecab_533

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 20:3676304..3676831(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000021718
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PDCD2
• Ensembl ID: ENSECAG00000016819
• Aliases: None
• Description: programmed cell death 2 [Source:HGNC Symbol;Acc:8762]

Sequence

>retro_ecab_533
GAGCAGGGCTGGACACAATCAGGTAGTGTGGACCGTGCAGCTCCGGACCGCAACTTCCTCTCCCCAGAATTTGAAATCCT
AATAGAAACAGAAGGTGAGATTATGCCTGAAGTTTTGGAAAAGGAAGATGACTCAGAGACTCCCGGGCGCACAGGAGAAG
CGCCTGAAGAAGAATTGGGTTCCAGAGCAAAACATGAGTCCAGGGAAGAGAAAACTTTCCGGAAGTTTAAAACTAAAATA
GTCCTTGAACCAGAACAGAGTCTCAGACATGGCAGAGGGATTGCTGCCATCTGGATTTCTGGAGAAAATATTCCTGAAGA
ACAGGAGATTCCAGACTGCCCCTGTGGTGCCCAGAGGACATTTGAATTCCAGATCATGTCTCAGCTGCTCAGCTGCACAC
AGGCTGGCAGACTGGGCGGGAGCATCGTCCTGGGCAGCCAGGCTGGCTTCGCCTGTGCAGAAAACTACAGACTGGGCACC
GGCTACACAGAGGACTCTGTGTGGAAGCAAGAGGTAACGATACACCT

Alignment

ORF - retro_ecab_533 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.41 %
• Parental protein coverage: 61.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KQACTQADNLDNTVPDHNFLFPEFEIVIETEDEITPEVVEKEEESEIIGSMGEAPEEELDSMAKHESRED
          .Q..TQ....D...PD.NFL.PEFEI.IETE.EI.PEV.EKE..SE..G..GEAPEEEL.S.AKHESRE.
Retrocopy EQGWTQSGSVDRAAPDRNFLSPEFEILIETEGEIMPEVLEKEDDSETPGRTGEAPEEELGSRAKHESREE

Parental  KVFQKFKTKVALEPEQILRYGRGTAPIWISAENIPQEEDVPDCPCGAKRIFEFQVMPQLLNYLKADRLGR
          K.F.KFKTK..LEPEQ.LR.GRG.A.IWIS.ENIP.E...PDCPCGA.R.FEFQ.M.QLL....A.RLG.
Retrocopy KTFRKFKTKIVLEPEQSLRHGRGIAAIWISGENIPEEQEIPDCPCGAQRTFEFQIMSQLLSCTQAGRLGG

Parental  SVDWGVLAVFTCAESCRLGTGYAEEFVWKQDIT-DTP
          S...G..A.F.CAE..RLGTGY.E..VWKQ..T.DTP
Retrocopy SIVLGSQAGFACAENYRLGTGYTEDSVWKQEVT<DTP

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
SRP021940_articular_cartilage	0.00 RPM	12.16 RPM
SRP021940_cerebellum	0.00 RPM	9.35 RPM
SRP021940_embryo	0.00 RPM	17.82 RPM
SRP021940_placental_villous	0.00 RPM	9.81 RPM
SRP021940_synovial_membrane	0.00 RPM	10.46 RPM
SRP021940_testis	0.00 RPM	29.16 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_533 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_533 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_533 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 24 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,
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,