RetrogeneDB ID: retro_ecab_520

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 2:69721891..69722242(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000014971
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MGST2
• Ensembl ID: ENSECAG00000019195
• Aliases: None
• Description: microsomal glutathione S-transferase 2 [Source:HGNC Symbol;Acc:7063]

Sequence

>retro_ecab_520
ATGGCTGGGAATTCAATCTTGCTGGCTGCTGTCTCTGTCTTCCCTGTCTGTCAGCAAAGTTATTTTGCTTTGCAGGTAGG
AAAGGCAAGATTAAAATACAAAATTATGCCCTTGGCAGTCTCTGGGTCACCAGAGTTTGACAGAATATTTCATGCACAAC
AAAACTATGGGGAGTTTTACCCCACAGTCGTGATTACATTGTGGATGGCCGGATGGTATTTCAATCAAGTTTTTGCTACT
TTTCTGGGTCAGCTGTACCTCTATGCCCATCACCAGTATATCTGGGGATATTCAGAAGCTGCTAACAAAAGGGTCACTGG
TTTCGGGTTGAGTCTGGGGATTTTGGCCGTT

Alignment

ORF - retro_ecab_520 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.2 %
• Parental protein coverage: 80.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGNSILLAAVSLLSACQQSYFAFQVGRARLKYKIMPPAVSGSPEFDRIFRAQQNSVEFYPAFMITLWMA
          MAGNSILLAAVS....CQQSYFA.QVG.ARLKYKIMP.AVSGSPEFDRIF.AQQN..EFYP...ITLWMA
Retrocopy MAGNSILLAAVSVFPVCQQSYFALQVGKARLKYKIMPLAVSGSPEFDRIFHAQQNYGEFYPTVVITLWMA

Parental  GWYFNQVFATCLGLLYIYARHQYFWGYSEAANKRMTGFRLGLGILAL
          GWYFNQVFAT.LG.LY.YA.HQY.WGYSEAANKR.TGF.L.LGILA.
Retrocopy GWYFNQVFATFLGQLYLYAHHQYIWGYSEAANKRVTGFGLSLGILAV

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	4.25 RPM
SRP021940_cerebellum	0.00 RPM	0.93 RPM
SRP021940_embryo	0.00 RPM	4.76 RPM
SRP021940_placental_villous	0.00 RPM	8.18 RPM
SRP021940_synovial_membrane	0.00 RPM	2.86 RPM
SRP021940_testis	0.00 RPM	2.05 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_520 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_520 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_520 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000019195	1 retrocopy	retro_ecab_520 ,
Vicugna pacos	ENSVPAG00000005209	1 retrocopy	retro_vpac_263,