RetrogeneDB ID: retro_ecab_237

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 10:34702976..34703478(-)
• 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_237
AGAAAAAAGAATAGTCTAAGGGACCACTGGGACAACAAGTGCATTAACATTCATATTATAGGTTTCCCAGAAGGAGAAGA
AAGAGACAAAGGGGCAAAGAATCTATTTGAAGGAATAATAGCTGAAAACTTTCCTAACCTAAGGAAGGAAACAGACATCA
AGGTACAGGAAGCACAGAGAACACCAAACAAGATAAACCCAAAGAGGCTCAAACCAAGACACATTATAAATAAAATGTCA
AGAATTAAAGAAAAAGAGAGAATCCTAAAAGCCATAATGGGCAACAAGTTACATACAAAGGAAATCCCATAAGGCTATCA
GCTGACTTCTCAGCAGAAACCTTATAAGCTAGAAGGGAGTAGCATGATATATTTAAAGTGCACAAAGGAAAGAACCTACA
GCCAAGGATACCCTACTGCCAAGTTTACCATTTGGAATGGAAGGAGAGACAAAGAGTTTCTTAGACAAGCAAAAAGTAAA
GGAGTTTATCACCAAGAAACCA

Alignment

ORF - retro_ecab_237 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.31 %
• Parental protein coverage: 68.46 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QNENSLRELWDNIKCTNIRFIGVPEGEERDKEA----ENRVAENFPNLKKETDIHIQEAQRTPKKISPKR
          ...NSLR..WDN.KC.NI..IG.PEGEERDK.A....E...AENFPNL.KETDI..QEAQRTP.KI.PKR
Retrocopy RKKNSLRDHWDN-KCINIHIIGFPEGEERDKGAKNLFEGIIAENFPNLRKETDIKVQEAQRTPNKINPKR

Parental  ATPRHIIIKISKMNDKERI-PRAARQKKISYKGTPIRLSVHFSTETLQARRDWNDIFKTLKDKNLQPRIL
          ..PRHII.K.S....KERI.P.........YKG.PIRLS..FS.ETL.ARR...DIFK..K.KNLQPRI.
Retrocopy LKPRHIINKMSRIKEKERI<PKSHNGQQVTYKGNPIRLSADFSAETL*ARRE*HDIFKVHKGKNLQPRIP

Parental  YPAKIFFRYE-GEIKSFPDNQKLRDFVATSP
          Y..........GE.KSF.D.QK...F....P
Retrocopy YCQVYHLEWK<GETKSFLDKQKVKEFITKKP

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_237 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_237 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_237 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,