RetrogeneDB ID: retro_ecab_484

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 2:31139846..31140362(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000006639
• Aliases: None
• Description: None

Sequence

>retro_ecab_484
AGAGAACTGACACTAAAAAGAAATGAAGAAAGTCTCCAAGAAATATCCAACTCAATTAGGAAATGCAACATGAGAATTAT
AGGTATTCGAGAAGGAGAAGAGAAGGAGAATGTAGGAGAAAGCCTGTTCAAAGAAACAGCAGAGAACTTCCCAAACCTGG
GGAAGGAGATGGAAATCCACGTGAAAAAGGCTACCAGACTTCCTAAATACGTCAATGTAAAAAGACCTACTGCAAGGCAT
ATAGTAGTGAAACTCGCAAAGTTGAATGACAAAAAATACTAAGGGCAGCAAGGCAGAAGAAAACAACTTAGAAAGGAACC
GCTATCAGGCTTTCAGTGGATTTCTCTGCAGAAACCTTACAGGCTAAGAGGGACTGGAATGACATATTCAAATCTTTGAA
AGACAGAAAATTTCAGCCAAGAATACTCTATCCAGCAAAAAATATCCTTCAGATATGATGGAGAAATAAAAACTTTCCCA
GATAAACGAAAGCTAAGGGAGTTCATAGCCACAAGA

Alignment

ORF - retro_ecab_484 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.71 %
• Parental protein coverage: 67.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KEKKIQKEGENFQETTDSMRKCNIRIIRIPEGDEKENGTESVLKGIIAENFPDLENETETRVEEAFRSPR
          .E.......E..QE...S.RKCN.RII.I.EG.EKEN..ES..K...AENFP.L..E.E..V..A.R.P.
Retrocopy RELTLKRNEESLQEISNSIRKCNMRIIGIREGEEKENVGESLFKET-AENFPNLGKEMEIHVKKATRLPK

Parental  YVNVKRTTARHIVVKLAKLND-ERILRAARQKKITYKGTPLRLSVDFSVETLQAWRDWNDILKTLKDNNL
          YVNVKR.TARHIVVKLAKLND...ILRAARQKK.T.KGT..RLSVDFS.ETLQA.RDWNDI.K.LKD...
Retrocopy YVNVKRPTARHIVVKLAKLND<QKILRAARQKKTT*KGTAIRLSVDFSAETLQAKRDWNDIFKSLKDRKF

Parental  QPRILYPA-KISFRYEGE-KSFLDKQKLRDFTAMR
          QPRILYPA.KISFRY.GE.K.F.DK.KLR.F.A.R
Retrocopy QPRILYPA>KISFRYDGEIKTFPDKRKLREFIATR

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	0.03 RPM	0.03 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.00 RPM	0.05 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_484 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_484 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_484 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000005242	2 retrocopies	retro_ecab_192, retro_ecab_934,
Equus caballus	ENSECAG00000006639	4 retrocopies	retro_ecab_274, retro_ecab_484 , retro_ecab_671, retro_ecab_689,