RetrogeneDB ID: retro_ecab_593

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 22:27181715..27181967(-)
• Located in intron of: ENSECAG00000014135

Retrocopy information

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

Parental gene information

• Parental gene symbol: MSRB2
• Ensembl ID: ENSECAG00000013072
• Aliases: None
• Description: methionine sulfoxide reductase B2 [Source:HGNC Symbol;Acc:17061]

Sequence

>retro_ecab_593
TCTCTCACCAAGAGTGAGCTGCGAAAGAAACGGACTCCAGAGCAACTTCTGTGTCAGGAGAGAGAAAGGAAGTGACCTGC
CTTTTGGTGGGATCTACCTGAGTCACAGGGAGTCAGGAGGGCATCACTGTGTGTGCTGTGACAGCCTCTCCTCAGTTCTG
AGAGAAAGCACGGCTCCGGCCCTCGATGGCCTTCCTTTTCTGAGGCTCATGGCACGTCTGGCTCTGCTGAAAGTAGCACT
GGGACCCAGAGA

Alignment

ORF - retro_ecab_593 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.6 %
• Parental protein coverage: 54.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SLAKSEWQKKLTPEQ-FYVTREKGTEPPFSGIYLNNEESGMYHCVCCDS-PLFSSEKKYSSGTGWPSFSE
          SL.KSE..KK.TPEQ.F.V.REKG...PF.GIYL...ESG..HCVCCDS.PL.SSE.K..SG..WPSFSE
Retrocopy SLTKSELRKKRTPEQ>FCVRREKGSDLPFGGIYLSHRESGGHHCVCCDS<PLLSSERKHGSGPRWPSFSE

Parental  AHGTSGSDESKTGILR
          AHGTSGS.ES.TG..R
Retrocopy AHGTSGSAESSTGTQR

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	2.13 RPM
SRP021940_cerebellum	0.00 RPM	2.44 RPM
SRP021940_embryo	0.00 RPM	4.25 RPM
SRP021940_placental_villous	0.00 RPM	1.54 RPM
SRP021940_synovial_membrane	0.03 RPM	1.89 RPM
SRP021940_testis	0.00 RPM	2.24 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_593 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_593 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_593 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_1147

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006388	1 retrocopy	retro_amel_505,
Canis familiaris	ENSCAFG00000004215	1 retrocopy	retro_cfam_1147,
Equus caballus	ENSECAG00000013072	1 retrocopy	retro_ecab_593 ,
Nomascus leucogenys	ENSNLEG00000012892	1 retrocopy	retro_nleu_2871,
Pongo abelii	ENSPPYG00000002148	1 retrocopy	retro_pabe_3127,
Sus scrofa	ENSSSCG00000011077	1 retrocopy	retro_sscr_218,