RetrogeneDB ID: retro_ecab_462

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 19:28877769..28878164(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000011118
• Aliases: None
• Description: None

Sequence

>retro_ecab_462
CTCGTCCTTCGGGCCCTGGTAGGTGGGGCACAGGGGCTTCACCTCTAAGGCAGATCTTCAGAGAAGTGTCTAGATCACAG
ATGAGGTGATCCAGCACCTGGAGCATCTAGCTTTTGTGGACTTTGGCAGGAAAGAGGCTAAGGTGTATCTGGAGAAAGCC
ATCACCTTTGCCAACCTACTCCATGCTGTGGACATGAAGGGGTGGAGCCCATGGAGCCAGTATTGGGGGACAGATGTCTA
TTCTTGAGATCCAGCATGTGGTAGAAAGCAATTGTTCTCAGGACCTACTACAAACTTCCATTCAGCTATGGAGGAGTATT
TTGTGCTCCCCTCACCCGGCTCCCGGTAATATCTCTTTGCCAAAGCTGGATGAACAAGAGCCCTTCTCACATGGC

Alignment

ORF - retro_ecab_462 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.7 %
• Parental protein coverage: 94.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LGLRALVGG-RRGFTCKADTKGSGRITAEVIEHLERLALVDFGSQEAVARLEKAIAFADRLRAVDT-DGV
          L.LRALVGG..RGFT.KAD...S..IT.EVI.HLE.LA.VDFG..EA...LEKAI.FA..L.AVD...GV
Retrocopy LVLRALVGG>HRGFTSKADLQRSV*ITDEVIQHLEHLAFVDFGRKEAKVYLEKAITFANLLHAVDM<EGV

Parental  EPMESVLEDRCLYLRSD-HVIEGNCAEELLQNSHRVVEEYFVAP---PGNISLPKLDEQEPFSHG
          EPME.VL.DRCL.LRS..HV.E.NC...LLQ.S..........P...PGNISLPKLDEQEPFSHG
Retrocopy EPMEPVLGDRCLFLRSS<HVVESNCSQDLLQTSIQLWRSILCSPHPAPGNISLPKLDEQEPFSHG

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	5.90 RPM
SRP021940_cerebellum	0.00 RPM	9.40 RPM
SRP021940_embryo	0.00 RPM	11.46 RPM
SRP021940_placental_villous	0.00 RPM	9.67 RPM
SRP021940_synovial_membrane	0.00 RPM	9.25 RPM
SRP021940_testis	0.00 RPM	4.60 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_462 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_462 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_462 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013298	1 retrocopy	retro_amel_1364,
Equus caballus	ENSECAG00000011118	1 retrocopy	retro_ecab_462 ,
Felis catus	ENSFCAG00000024015	1 retrocopy	retro_fcat_1279,
Homo sapiens	ENSG00000257218	1 retrocopy	retro_hsap_3902,
Nomascus leucogenys	ENSNLEG00000015651	1 retrocopy	retro_nleu_1140,
Oryctolagus cuniculus	ENSOCUG00000009867	2 retrocopies	retro_ocun_585, retro_ocun_858,
Ochotona princeps	ENSOPRG00000004226	1 retrocopy	retro_opri_1008,
Pongo abelii	ENSPPYG00000005030	1 retrocopy	retro_pabe_3181,
Pan troglodytes	ENSPTRG00000005534	1 retrocopy	retro_ptro_2655,
Sus scrofa	ENSSSCG00000009907	1 retrocopy	retro_sscr_746,
Tarsius syrichta	ENSTSYG00000006845	1 retrocopy	retro_tsyr_1219,
Tursiops truncatus	ENSTTRG00000000144	1 retrocopy	retro_ttru_1695,