RetrogeneDB ID: retro_ecab_731

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 3:94406127..94406764(+)
• 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_731
TCACTAGAGGGACTCAATAGCAGAGTAGATGATACAGAAGAATGGATCAGTAAACTGAAGGACAGACTATAGGAAATCAC
CCAAGTTGAACAAGCAAAAGAGAAAATTACAAAGAATGAGAAGAGTTGAAGGGAACTCTGGGACATTATCAAGCCTACTA
ACATTCATATTATAGGTGTCCCAGAAGGAGAAGAGAGAGACAAAGGGGCAGAGAATCTATTTGAAGAAATAATAGCTGAA
AACTTTCCTAACCTAAGGAAGGAAATAGACATTCAAGTACAGTAAGCACAGAGAGCACCAAACAAGATAAACCCAAAGAG
GCCCACACCAAGACACATTATAATTAAAATCTCCAAAATTAAAGATATAGAATCCTAAAGGCAGCAAGAGAAGTAAAACA
CGTGACATACAAAGGAAAGCCCATAAGGCTATCAGCAGACATCTCAGCCAAAACCCTACGGCTGGAAGAGAGTGGCATGA
CTTATGTAAAGTGCTGACAGGAAAAAACCTACAGCCAAGAATACTCTATCCAGCAAGGTTATCATTCAGATCGGAAGGAG
AGATAAAGAGTTTCCCAGACAAGCAAAAATTAAACGAGTTTGTCACCAAGAATTCAGTTCTAAAAGAAATGTTGAAG

Alignment

ORF - retro_ecab_731 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.57 %
• Parental protein coverage: 87.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SLERLNSRVSDTHEQMSEIDERLEEISQAEQKKEKRIRQNENSLRELWDNIKCTNIRFIGVPEGEERDKE
          SLE.LNSRV.DT.E..S....RL.EI.Q.EQ.KEK.I..NE.S.RELWD.IK.TNI..IGVPEGEERDK.
Retrocopy SLEGLNSRVDDTEEWISKLKDRL*EITQVEQAKEK-ITKNEKS*RELWDIIKPTNIHIIGVPEGEERDKG

Parental  A----ENRVAENFPNLKKETDIHIQEAQRTPKKISPKRATPRHIIIKISKMNDKER-IPRAARQKKISYK
          A....E...AENFPNL.KE.DI..Q.AQR.P.KI.PKR.TPRHIIIKISK..D.E.....A...K...YK
Retrocopy AENLFEEIIAENFPNLRKEIDIQVQ*AQRAPNKINPKRPTPRHIIIKISKIKDIES<LKAAREVKHVTYK

Parental  GTPIRLSVHFSTETLQ-ARRDWNDIFKTLKDKNLQPRILYPAKIFFRYEGEIKSFPDNQKLRDFVATSPP
          G.PIRLS...S..TL..A.R.W.D..K.L..KNLQPRILYPA...FR.EGEIKSFPD.QKL..FV.....
Retrocopy GKPIRLSADISAKTLR<AGREWHDLCKVLTGKNLQPRILYPARLSFRSEGEIKSFPDKQKLNEFVTKNSV

Parental  LQEILK
          L.E.LK
Retrocopy LKEMLK

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_731 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_731 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_731 has 0 orthologous retrocopies within eutheria group .

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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,