RetrogeneDB ID: retro_ecab_518

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 2:66105908..66106415(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000015686
• Aliases: None
• Description: None

Sequence

>retro_ecab_518
AAGAAACAAAATAATAGGTGCCAAATGAAAGAACAAGACAAAATCTCAGAAGAAACATCTTAATGAAACAGAGAGAAGTG
ATTTACCTGATTAAGAGTTCAAAATAACAATCAGAGAGATGCTCACTAAGCTCAGGAGAACAATGGATGAAAAAAGTGAG
ACCTTCAACAAAGAGACAGAAAATATAAGAAAGTACCAAATAGAACTCACAGAGCTGAAGAATATAATAATGAAGCCGAA
GAACACAATAGAGGGGTTCAACAGCAGACTAGGTGAAGCAGAAGAAAAGATCAGTGAACTCAAAGAGAGGGCAGTAGAAC
TCACTCAGAGCAACAAAAAGAAAAAAGAACAAAAAAAAGCAAAGATAGCTTAAATGACTTATGAGACAACAGCAAGCAGA
CCAACAACTGCATTATAGGGGTCCCAAAAATAGATGAGAGAAAGAGAGGAGCAAAAGACATCTTTAAAGAAATAATGCCT
GAAAACTTCCCTAATCTAGGGAAGGAA

Alignment

ORF - retro_ecab_518 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.97 %
• Parental protein coverage: 98.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KKQGNMFQM-KEQDKPEN-NLNEMEVSNLPNKEFQVKVIKMLTKLKRRMDEHSGNFNKETDSIRKCQIEV
          KKQ.N..QM.K...K.....LNE.E.S.LP..EF......MLTKL.R.MDE.S..FNKET..IRK.QIE.
Retrocopy KKQNNRCQM>KNKTKSQKKHLNETERSDLPD*EFKITIREMLTKLRRTMDEKSETFNKETENIRKYQIEL

Parental  TELKNTIPELTNTLEGFNSRLDEAEERISELNDRA-ELTQSEQQKEKRMKNTDNSLRELWDNIKHANIRI
          TELKN.I....NT.EGFNSRL.EAEE.ISEL..RA...T.SEQ...........SL..L.DN.K..N..I
Retrocopy TELKNIIMKPKNTIEGFNSRLGEAEEKISELKERA<SRTHSEQXXXXXXXXXKDSLNDL*DNSKQTNNCI

Parental  IGVPEGEERDKGAENLFVEIIQENFPNLRKE
          IGVP...ER..GA...F.EI..ENFPNL.KE
Retrocopy IGVPKIDERKRGAKDIFKEIMPENFPNLGKE

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	0.00 RPM
SRP021940_cerebellum	0.05 RPM	0.00 RPM
SRP021940_embryo	0.00 RPM	0.00 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.03 RPM	0.00 RPM
SRP021940_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_518 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_518 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_518 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015686	14 retrocopies	retro_ecab_1030, retro_ecab_1031, retro_ecab_1111, retro_ecab_1127, retro_ecab_207, retro_ecab_208, retro_ecab_326, retro_ecab_487, retro_ecab_491, retro_ecab_518 , retro_ecab_607, retro_ecab_625, retro_ecab_863, retro_ecab_881,