RetrogeneDB ID: retro_ecab_548

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 20:21419381..21419705(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5J
• Ensembl ID: ENSECAG00000017858
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial Fo complex, subunit F6 [Source:HGNC Symbol;Acc:847]

Sequence

>retro_ecab_548
ATGATCGTTCAGACGCTGTTCAAGTTCTTCTCTGTCGTTCAGTCTGCAACCTCAGTGCATTTGCAGAGGAACGTTGGTGT
CACAGCAGTGGCATTTAATAAGGAACTTGATCTTTTACAGGAGTTCTTTGTGGACAAGATTAGAGAATACAAATCTAAGG
GATGGGTTTCTGGAGGACCTGTTGAGATTGGCCCGGAGTATCAGCAAGCGCTCGAGAGGGAGCTTTTTAAGTTTAAGCAA
ATATACGGTAAAGCAAAGATGACTGTGTTCCCTAACTTTATATTTGAAGATCCTGATTTTGAAATGATGGGAAAACCCCA
GTCT

Alignment

ORF - retro_ecab_548 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.3 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MILRRLFRLSSVVQSAISVHLRRNIGVTAVAF-KELDPIQKLFVDKIREYRTKRQTSGGPVDIGPEYQQD
          MI...LF...SVVQSA.SVHL.RN.GVTAVAF.KELD..Q..FVDKIREY..K...SGGPV.IGPEYQQ.
Retrocopy MIVQTLFKFFSVVQSATSVHLQRNVGVTAVAFNKELDLLQEFFVDKIREYKSKGWVSGGPVEIGPEYQQA

Parental  LERELFKLKQMYGKADMNTFPNFKFEDPKFEVFDKPQS
          LERELFK.KQ.YGKA.M..FPNF.FEDP.FE...KPQS
Retrocopy LERELFKFKQIYGKAKMTVFPNFIFEDPDFEMMGKPQS

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	17.83 RPM
SRP021940_cerebellum	0.00 RPM	33.91 RPM
SRP021940_embryo	0.00 RPM	37.77 RPM
SRP021940_placental_villous	0.00 RPM	32.19 RPM
SRP021940_synovial_membrane	0.00 RPM	19.49 RPM
SRP021940_testis	0.00 RPM	31.27 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_548 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_548 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_548 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Sus scrofa	retro_sscr_896

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017167	1 retrocopy	retro_amel_1858,
Bos taurus	ENSBTAG00000000605	1 retrocopy	retro_btau_1653,
Canis familiaris	ENSCAFG00000024922	2 retrocopies	retro_cfam_1664, retro_cfam_1993,
Callithrix jacchus	ENSCJAG00000013803	3 retrocopies	retro_cjac_1531, retro_cjac_2559, retro_cjac_665,
Equus caballus	ENSECAG00000017858	2 retrocopies	retro_ecab_548 , retro_ecab_644,
Erinaceus europaeus	ENSEEUG00000011228	2 retrocopies	retro_eeur_693, retro_eeur_695,
Echinops telfairi	ENSETEG00000006438	4 retrocopies	retro_etel_1847, retro_etel_2218, retro_etel_468, retro_etel_832,
Felis catus	ENSFCAG00000029970	1 retrocopy	retro_fcat_1451,
Homo sapiens	ENSG00000154723	3 retrocopies	retro_hsap_2548, retro_hsap_3990, retro_hsap_4920,
Gorilla gorilla	ENSGGOG00000008265	2 retrocopies	retro_ggor_1593, retro_ggor_2678,
Myotis lucifugus	ENSMLUG00000015988	1 retrocopy	retro_mluc_1266,
Macaca mulatta	ENSMMUG00000008725	1 retrocopy	retro_mmul_2306,
Monodelphis domestica	ENSMODG00000021011	1 retrocopy	retro_mdom_1010,
Mustela putorius furo	ENSMPUG00000001001	2 retrocopies	retro_mputfur_1573, retro_mputfur_1582,
Nomascus leucogenys	ENSNLEG00000002412	1 retrocopy	retro_nleu_539,
Oryctolagus cuniculus	ENSOCUG00000006681	5 retrocopies	retro_ocun_1517, retro_ocun_1888, retro_ocun_326, retro_ocun_419, retro_ocun_789,
Pongo abelii	ENSPPYG00000011305	2 retrocopies	retro_pabe_1874, retro_pabe_1875,
Pan troglodytes	ENSPTRG00000013809	3 retrocopies	retro_ptro_1485, retro_ptro_2708, retro_ptro_3312,
Sorex araneus	ENSSARG00000000742	3 retrocopies	retro_sara_165, retro_sara_225, retro_sara_501,
Sus scrofa	ENSSSCG00000022586	1 retrocopy	retro_sscr_896,