RetrogeneDB ID: retro_ecab_925

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 7:28900680..28901348(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000009821
• Aliases: None
• Description: None

Sequence

>retro_ecab_925
GATATGAAGAACACAATTAATGAGATAAAAAATAATCTAGAATCCATAAAAAATAGATTTGACATTATGAAGGACAGAAT
TAGTGATTGAGAGGATAGAAATATAGAAATGCTTCAGGTGGAGGAGAAGAGAGAACTAAGATTTTAACAAAATGAAGAAA
TTCTTTGAGAAATATCTGATTCAATCAGGAAAAGCAACATGAGAATTATAGGTATTCAAGAGGGAGAAAGGAGCAGGGAG
CTTGTTCAAAGAAATAATAGCTGAGAACTTTGCCAAACCTGGGGAAGTAACTGGACTTACAAGTACATAAAACAATAGAA
CTCCTAAGTATATCAATGTAAAAACACCTTCTCTAAGGCATATACTATTAAAACTGGCAAAAGCCAATGACAAAGAAAAA
ATATTAAGGGCAGCAAGGCAGAAGAAAATAACCTACAATGGGACTCCTATCAGGCTTTCAGTGGATTCCTTGGCAGAAAC
CTTACAGGCTAGGAGAGAATGGAATGGTATATTCAAAATACTGAAAGCCAAAAACTTTCAGCCCAGAATGCTTTATCCAG
TGAAACTAACCCTCAGATACAGTGGAGAAATAAAAACTTCCCAGATAAACAAAAGCTGAGGGAGTTCATTGCCACTAGAC
CTCCTTACAAGAAAAAATGAAAGAAGCC

Alignment

ORF - retro_ecab_925 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.19 %
• Parental protein coverage: 92.53 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  EMKNTTLEMKSSLERLNSRVSDTHEQMSEIDERLEEISQAEQKKEKRIRQNENSLRELWDNIKCTNIRFI
          .MKNT..E.K..LE....R........S....R..E..Q.E.K.E.R..QNE..L.E..D.I...N.R.I
Retrocopy DMKNTINEIKNNLESIKNRFDIMKDRISD*EDRNIEMLQVEEKRELRF*QNEEIL*EISDSIRKSNMRII

Parental  GVPEGEERDKEAENR-VAENF-PNLKKETDIHIQEA-QRTPKKISPKRATPRHIIIKISKMNDKERIPRA
          G..EGE...........AENF.PNL.K..D........RTPK.I..K....RHI..K..K.NDKE.I.RA
Retrocopy GIQEGERSRELVQRN>IAENF>PNLGK*LDLQVHKT<NRTPKYINVKTPSLRHILLKLAKANDKEKILRA

Parental  ARQKKISYKGTPIRLSVHFSTETLQARRDWNDIFKTLKDKNLQPRILYPAKIFFRYEGEI-KSFPDNQKL
          ARQKKI.Y.GTPIRLSV....ETLQARR.WN.IFK.LK.KN.QPR.LYP.K...RY.GEI.K.FPD.QKL
Retrocopy ARQKKITYNGTPIRLSVDSLAETLQARREWNGIFKILKAKNFQPRMLYPVKLTLRYSGEI<KNFPDKQKL

Parental  RDFVATSPP-LQEILKKA
          R.F.AT.PP.LQE..K.A
Retrocopy REFIATRPP<LQEKMKEA

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	0.00 RPM	0.00 RPM
SRP021940_embryo	0.00 RPM	0.00 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.00 RPM	0.00 RPM
SRP021940_testis	0.00 RPM	0.06 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_925 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_925 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_925 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000009821	7 retrocopies	retro_ecab_137, retro_ecab_142, retro_ecab_237, retro_ecab_394, retro_ecab_643, retro_ecab_731, retro_ecab_925 ,