RetrogeneDB ID: retro_ecab_715

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 3:51232181..51232479(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENY2
• Ensembl ID: ENSECAG00000023565
• Aliases: None
• Description: enhancer of yellow 2 homolog (Drosophila) [Source:HGNC Symbol;Acc:24449]

Sequence

>retro_ecab_715
GTGCTTAGCAAGATGAACAAAGATGCGCAGATGAGAGCAGCAATGAACCAAAAGTTGATAGAAACTGGAGAAAGAGAAGA
CGTCAAAGAGTTGCTGAGAGCTAAATTAATTGAATGTGGCTGGGAGGATCAATTGGAGGCCCACTGTAAAGGGAATTAAA
GAAAAAGGACTAGAACACGTTACTGTTGATGACTTGGTGGCTGAAATCGCGCCAGAAGGCCGAGGCCTGGCAGCTGGCAG
GGTAGAGGAGGAGCTCCCACAAAGGGTAAGAGTGTGCCCTGCTCAGCGTGCCCGCCTT

Alignment

ORF - retro_ecab_715 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.55 %
• Parental protein coverage: 99.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VVSKMNKDAQMRAAINQKLIETGERERLKELLRAKLIECGWKDQLKAHCK-EVIKEK-GLEHVTVDDLVA
          V.SKMNKDAQMRAA.NQKLIETGERE..KELLRAKLIECGW.DQL.AHCK....K.K.GLEHVTVDDLVA
Retrocopy VLSKMNKDAQMRAAMNQKLIETGEREDVKELLRAKLIECGWEDQLEAHCK<RELKKK<GLEHVTVDDLVA

Parental  EITPKGRALVPDSVKKELLQRIRTFLAQHASL
          EI.P.GR.L....V..EL.QR.R...AQ.A.L
Retrocopy EIAPEGRGLAAGRVEEELPQRVRVCPAQRARL

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	7.20 RPM
SRP021940_cerebellum	0.00 RPM	8.36 RPM
SRP021940_embryo	0.05 RPM	17.98 RPM
SRP021940_placental_villous	0.10 RPM	10.83 RPM
SRP021940_synovial_membrane	0.00 RPM	8.43 RPM
SRP021940_testis	0.06 RPM	8.63 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_715 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_715 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_715 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003039	1 retrocopy	retro_acar_1,
Dasypus novemcinctus	ENSDNOG00000007377	1 retrocopy	retro_dnov_25,
Equus caballus	ENSECAG00000023565	1 retrocopy	retro_ecab_715 ,
Echinops telfairi	ENSETEG00000010882	2 retrocopies	retro_etel_1826, retro_etel_450,
Myotis lucifugus	ENSMLUG00000027585	1 retrocopy	retro_mluc_357,
Nomascus leucogenys	ENSNLEG00000004284	3 retrocopies	retro_nleu_2535, retro_nleu_2584, retro_nleu_2585,
Sarcophilus harrisii	ENSSHAG00000001787	4 retrocopies	retro_shar_454, retro_shar_675, retro_shar_815, retro_shar_816,
Tursiops truncatus	ENSTTRG00000001742	3 retrocopies	retro_ttru_46, retro_ttru_845, retro_ttru_997,