RetrogeneDB ID: retro_ecab_555

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 20:35025869..35026331(-)
• Located in intron of: ENSECAG00000009741

Retrocopy information

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

Parental gene information

• Parental gene symbol: C10orf82
• Ensembl ID: ENSECAG00000000731
• Aliases: None
• Description: chromosome 10 open reading frame 82 [Source:HGNC Symbol;Acc:28500]

Sequence

>retro_ecab_555
ATGGAGTCTTCCAAGACCTTCATGAGACAGCTGCCAATCACACCAGGCTACAGTGGCTTCGTGCCATACCTTAGCTGCGA
GGGAACCTCCAGCAAGGACAACATGTCCCACTGTCTGAAAACCTTCCAGGAGATCACACAGCGATATAAAGACCAGAGGG
AGGAATTTCACTGCTCGGTCGCCGCTGCCCCAAAACTGAAGCCCATCTGCTCTGAGGAGACGGTCCTGCGGGCCCTGCAC
CAGTACGAACGGCAGTACCACCCCACGAGTCTGGAATGCAAGTACATAAAGAAACCTCTCCAGGAGCCTCCGATCCCTGG
CTGGGCGGGCTACCTGCCGAGAGCCAGGGTCACTGAATTAGGCTGCGCCACACGGTACACTGTCATGGCCAGAAATTGCT
ACAAGGACTTCCTGGACATCACAGAGCAGGCCAAGAGAGTGCACCTGAAGCCATATGAGGAG

Alignment

ORF - retro_ecab_555 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.75 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MESSKTFMRQLPITPGYCGFVPYLSCEGTSSENNMSHCLKTFQEITQRYKDQLEEFHCSVAAAPKLKPIC
          MESSKTFMRQLPITPGY.GFVPYLSCEGTSS..NMSHCLKTFQEITQRYKDQ.EEFHCSVAAAPKLKPIC
Retrocopy MESSKTFMRQLPITPGYSGFVPYLSCEGTSSKDNMSHCLKTFQEITQRYKDQREEFHCSVAAAPKLKPIC

Parental  SEETVLRALHQYERQYHPTSLECKYVKKPLQEPPIPGWAGYLPRARVTELGCATRYTVMARNCYKDFLDI
          SEETVLRALHQYERQYHPTSLECKY.KKPLQEPPIPGWAGYLPRARVTELGCATRYTVMARNCYKDFLDI
Retrocopy SEETVLRALHQYERQYHPTSLECKYIKKPLQEPPIPGWAGYLPRARVTELGCATRYTVMARNCYKDFLDI

Parental  TEQAKRVHLKPYEE
          TEQAKRVHLKPYEE
Retrocopy TEQAKRVHLKPYEE

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	0.12 RPM	1.42 RPM
SRP021940_cerebellum	0.21 RPM	0.05 RPM
SRP021940_embryo	0.23 RPM	1.07 RPM
SRP021940_placental_villous	0.00 RPM	0.29 RPM
SRP021940_synovial_membrane	0.14 RPM	0.88 RPM
SRP021940_testis	0.19 RPM	49.24 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_555 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_555 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_555 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000000731	1 retrocopy	retro_ecab_555 ,