RetrogeneDB ID: retro_ecab_1011

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 9:50943517..50943967(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000018840
• Aliases: None
• Description: None

Sequence

>retro_ecab_1011
AGGGAGAAAGGAGCAGACAGTTTGTTTGAATGAATAACAGCTAAGAATTTCACAAAGCTAGGGAAAGAACTGGATTACAA
GTATATGAAGTCAATAGAACTCCTAATTACATCAATGCAAAAAGACCTTTGCCAAGGCATATAGTAGTAAAACTGGCAAA
AGTCAACAACAAAGATAAAGTATTAAAGGCAGCAAGGCAGAAGAGACTAATCTACAAAGGAATGCCTATCTAGCTTTCAG
TGGAATTCTCAGCAGAAACTACAGGCTAAGAGAGATTGGAATGTTATATTCAACATACTGAAAGACAAAAACTTTCAGCC
AAGAATACTCTATCCAGCAAAACTATGCTTTAAATATGATGGAGAAATAAAAGCTCTCCCAGATAAACAAAAGCTGAGGG
AGTTCATTGCCACTAGACCTCCCTTATGAGCAATGAGAAAGGATGCCCTC

Alignment

ORF - retro_ecab_1011 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.48 %
• Parental protein coverage: 75.88 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RQNRRESLFKEIITENFLNLGKGLE-IQVKEANRTPNYINVERPSPRHILVKLAKLVMKEYIMAEAARQK
          R.....SLF..I...NF..LGK.L...QV.E.NRTPNYIN..RP.PRHI.VKLAK...K......AARQK
Retrocopy REKGADSLFE*ITAKNFTKLGKELD<LQVYEVNRTPNYINAKRPLPRHIVVKLAKVNNKDKVL-KAARQK

Parental  KITYKGSPIRLSADFS-QTVQTRREWNDIIKILKYKNYPPRILYPVKLSFRYGREIKAFQDKQKLREFIT
          ...YKG.PI.LS..FS.Q..Q..R.WN.I..ILK.KN..PRILYP.KL.F.Y..EIKA..DKQKLREFI.
Retrocopy RLIYKGMPI*LSVEFS>QKLQAKRDWNVIFNILKDKNFQPRILYPAKLCFKYDGEIKALPDKQKLREFIA

Parental  TRPPLQEMMKTAL
          TRPPL..M.K.AL
Retrocopy TRPPL*AMRKDAL

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	0.03 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.00 RPM	0.00 RPM
SRP021940_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1011 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1011 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1011 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000018840	28 retrocopies	retro_ecab_1000, retro_ecab_1011 , retro_ecab_1045, retro_ecab_1062, retro_ecab_1076, retro_ecab_221, retro_ecab_243, retro_ecab_296, retro_ecab_322, retro_ecab_327, retro_ecab_424, retro_ecab_482, retro_ecab_498, retro_ecab_523, retro_ecab_545, retro_ecab_564, retro_ecab_571, retro_ecab_663, retro_ecab_718, retro_ecab_742, retro_ecab_763, retro_ecab_787, retro_ecab_790, retro_ecab_824, retro_ecab_902, retro_ecab_908, retro_ecab_928, retro_ecab_929,