RetrogeneDB ID: retro_ecab_594

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 22:29424199..29424817(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATG3
• Ensembl ID: ENSECAG00000011954
• Aliases: None
• Description: autophagy related 3 [Source:HGNC Symbol;Acc:20962]

Sequence

>retro_ecab_594
AATGTGATTAACGTGGTGAAGGGAATGGCACTAGAAGTGACTGAGTACCTGAGCCTGGCCCTCAAGGAGTCAAAATTTAA
GGAAACAGACGTTGTCACCCCAGAACAGTTTGTGGCAGCTGGAGATGCCTCAGTCCACCACTGTCCAACATGCTGGTGGG
CTACAGGGAAAGAACTGAAAGTGAAGGCATACCCACCAATAGTAAACAATTTTTGGTAACCAAAAATGTGCCATGCTACA
AGTGGGCAAACAGATGCAATCTTCGCATGAATTATAAACTATCACTGAAGAAGATGATGGCGTTGGGGGATGGGTAGAGC
CACATCACAGCACAGGAAGTGCAGGGATAACCAAAACAGCTGAAGACATTACCCTGGAAAGCAAGGACAGTCTAAAACTC
CAAGTTTGCTCAAAATAATGTGAGGAGGAAGAAGAGGAAGATGAAAGAAAAGCTGCAAATATGGAAGAAAATGAAGAGAG
TGGATTGCTGGAAACGAGGCTATTCTAGATGCAAGGAAAACAGTAGAAGCTTGTAACCCTAAAACGGATGTTGGAGGTGA
GGCTGCTATTTTGCAAAGCAGAGCTTACGACCTCTACATCACTTATGAATATTACCAG

Alignment

ORF - retro_ecab_594 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.51 %
• Parental protein coverage: 66.56 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NVINTVKGKALEVAEYLTPVLKESKFKETGVITPEEFVAAGDHLVHHCPTWQWATGEELKVKAYLP-TGK
          NVIN.VKG.ALEV.EYL...LKESKFKET.V.TPE.FVAAGD..VHHCPT..WATG.ELKVKAY.P...K
Retrocopy NVINVVKGMALEVTEYLSLALKESKFKETDVVTPEQFVAAGDASVHHCPTCWWATGKELKVKAYPP<NSK

Parental  QFLVTKNVPCYKRC-KQMEYSDELEAIIEEDDGDGGWVDTYHNTGIAGITEAVKEITLESKDSIKLQDCS
          QFLVTKNVPCYK...KQM..S.EL..I.EEDDG.GGWV...H.TG.AGIT.....ITLESKDS.KLQ.CS
Retrocopy QFLVTKNVPCYKWA<KQMQSSHEL*TITEEDDGVGGWVEPHHSTGSAGITKTAEDITLESKDSLKLQVCS

Parental  ALCEEEEEEDEGEAADMEEYEESGLL-ETDEATLDTRKIVEACKAKTDAGGEDAILQTRTYDLYITYDKY
          ..CEEEE.E.....A...E..E...L....EA.LD.RK.VEAC..KTD.GGE.AILQ.R.YDLYITY..Y
Retrocopy K*CEEEE-EEDERKAANMEENEESGL<AGNEAILDARKTVEACNPKTDVGGEAAILQSRAYDLYITYE-Y

Parental  YQ
          YQ
Retrocopy YQ

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	12.81 RPM
SRP021940_cerebellum	0.00 RPM	24.72 RPM
SRP021940_embryo	0.00 RPM	17.42 RPM
SRP021940_placental_villous	0.00 RPM	22.61 RPM
SRP021940_synovial_membrane	0.00 RPM	19.33 RPM
SRP021940_testis	0.00 RPM	57.87 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_594 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_594 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_594 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2479
Pan troglodytes	retro_ptro_1434
Gorilla gorilla	retro_ggor_1544
Pongo abelii	retro_pabe_1827
Macaca mulatta	retro_mmul_594
Oryctolagus cuniculus	retro_ocun_1219

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018116	1 retrocopy	retro_amel_645,
Callithrix jacchus	ENSCJAG00000020358	1 retrocopy	retro_cjac_2756,
Equus caballus	ENSECAG00000011954	1 retrocopy	retro_ecab_594 ,
Homo sapiens	ENSG00000144848	1 retrocopy	retro_hsap_2479,
Gorilla gorilla	ENSGGOG00000006637	1 retrocopy	retro_ggor_1544,
Myotis lucifugus	ENSMLUG00000001573	1 retrocopy	retro_mluc_1025,
Macaca mulatta	ENSMMUG00000014232	1 retrocopy	retro_mmul_594,
Mustela putorius furo	ENSMPUG00000000321	2 retrocopies	retro_mputfur_1064, retro_mputfur_1614,
Nomascus leucogenys	ENSNLEG00000004302	2 retrocopies	retro_nleu_268, retro_nleu_331,
Oryctolagus cuniculus	ENSOCUG00000015651	1 retrocopy	retro_ocun_1219,
Pongo abelii	ENSPPYG00000013548	1 retrocopy	retro_pabe_1827,
Pan troglodytes	ENSPTRG00000015220	1 retrocopy	retro_ptro_1434,
Pteropus vampyrus	ENSPVAG00000009568	1 retrocopy	retro_pvam_1399,