RetrogeneDB ID: retro_ecab_493

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 2:64966280..64966995(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FADS1
• Ensembl ID: ENSECAG00000023280
• Aliases: None
• Description: fatty acid desaturase 1 [Source:HGNC Symbol;Acc:3574]

Sequence

>retro_ecab_493
GGTCAGCTGTCCTTCTTCAGCACCTCTACGTGGAACCACCTGCTACTTCATTTCCTCATTGGCCACCTGAAGGGGCCCCT
GCCTGTTAGTGGGACCACATGCACTTCCACCACCATGCCAAGCCCAGTTGCTTCCACTAGAAGGCAGACATCAACATGAA
CCCCTTCTTTGCCTTGGGGAAGATCCTCTCTGTGGAGCTTGGGAAACAAAAGAAAAAGCACATGCCATACAAACACCAGG
ACAAATGCTTCTTCCTGCTTGGGCCTCCAGCCTTGCTGCCTCTCTGCTTCCAGTGGGATATTTTCTATTTTGTTTTCAGT
GGACGAAGCGGATGGACTTGACCTGGATGATCACCTTCTACACCTGCATCTTCCTTGCTTATGTGTCATTATTGGGACTG
AAAGCCTTCCTGGACCTTTTCTTCATGGTCAGATTCCTAGAAAGCAATTGATTTGTGTGGGTGACACAAATGAACCACGT
CCCCATGTACATTGATCACAACCGGAACATGGAGTGGGTCTCCACCCAGCTCCAGGCAACACGCAACATCCACAAGTCTG
CTTTCAGTGACTGGTTCACTAGATATCTCAACTTCCAGACTGAGTACTGTCTGGAATGCCTCACCACAGTTACCACAAAG
CGATTCCCCTGGTGCAGTCCCTGTGTGCCAAGCATGGCAGAGACTACTAGTCCAAGCCCCTGCTCTCAGCCTTTG

Alignment

ORF - retro_ecab_493 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.29 %
• Parental protein coverage: 63.3 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GHLSVFSTSTWNHLLHHFVIGQLKG-APASWWNHLHFQHHAKPNCFRKDPDINMHPFFFALGKILSVELG
          G.LS.FSTSTWNHLL.HF.IG.LKG.APA..W.H.HF.HHAKP.CF....DINM.PFF.ALGKILSVELG
Retrocopy GQLSFFSTSTWNHLLLHFLIGHLKG<APAC*WDHMHFHHHAKPSCFH*KADINMNPFF-ALGKILSVELG

Parental  KQKKKYMPYNHQHKYFFLIGPPALLPLYFQWYIFYFVI-QRKKWVDLAWMVTFYVRIVLTYVPLLGLKGF
          KQKKK.MPY.HQ.K.FFL.GPPALLPL.FQW.IFYFV..Q..K..DL.WM.TFY..I.L.YV.LLGLK.F
Retrocopy KQKKKHMPYKHQDKCFFLLGPPALLPLCFQWDIFYFVF<QWTKRMDLTWMITFYTCIFLAYVSLLGLKAF

Parental  LGLFFMVRFLESNWFVWVTQMNHIPMHIDHDQNKDWFSTQLQATCNVHKSAFNDWFSGHLNFQIEHHL--
          L.LFFMVRFLESN.FVWVTQMNH.PM.IDH..N..W.STQLQAT.N.HKSAF.DWF...LNFQ.E..L..
Retrocopy LDLFFMVRFLESN*FVWVTQMNHVPMYIDHNRNMEWVSTQLQATRNIHKSAFSDWFTRYLNFQTEYCLEC

Parental  FPTMPRHNYHKVAPLVQSLCAKHGIQYQSKPL
          ..T..........P.V.S..........S.PL
Retrocopy LTTVTTKRFPWCSPCVPSMAETTSPSPCSQPL

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	8.56 RPM
SRP021940_cerebellum	0.00 RPM	56.61 RPM
SRP021940_embryo	0.03 RPM	208.42 RPM
SRP021940_placental_villous	0.00 RPM	6.78 RPM
SRP021940_synovial_membrane	0.03 RPM	36.54 RPM
SRP021940_testis	0.00 RPM	12.15 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_493 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_493 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_493 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
Ailuropoda melanoleuca	ENSAMEG00000016696	1 retrocopy	retro_amel_594,
Equus caballus	ENSECAG00000023280	1 retrocopy	retro_ecab_493 ,