RetrogeneDB ID: retro_ecab_111

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:103208900..103209236(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000004342
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000011446
• Aliases: None
• Description: None

Sequence

>retro_ecab_111
ATGGGAGATGAAAGAGGTGACAACTTTGAAGGTATGAGCACCGAACGCCTTAAACTGGAGTTAATGGAAGAAATCCATAT
GAGAAACTTAGTACAACTCTCAATACTTGAAATAGGAAACATGATTGTGGAACTCAATACTAGAAATAAACCCAGTAAGT
GGGAAATCCGTTATAAAACACAACTTGAACTGAATCATCAACTAGAAAAGCAAATTGCTACTCTCAAAGAGAAAATGGAA
ATGGTCCGTGGAAATCCTTCAGATAGACTATCTTCTATTCATCTCTATGAGCAAATGCCAGTGGAATCCTTAAATATACT
ACTTAAACAGCTAGAA

Alignment

ORF - retro_ecab_111 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.53 %
• Parental protein coverage: 99.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEEGKGDTFEGVSTDRLKPELLEEIHRKDIVQLSILEIREKIAELEAKLNTDDEGGEWKTRYETQLELND
          M....GD.FEG.ST.RLK.EL.EEIH....VQLSILEI...I.E....LNT......W..RY.TQLELN.
Retrocopy MGDERGDNFEGMSTERLKLELMEEIHMRNLVQLSILEIGNMIVE----LNTRNKPSKWEIRYKTQLELNH

Parental  QLEKQIVSLKEKMEKIRGNPADRLSSIRVYERMPVVSKRWLNKK
          QLEKQI..LKEKME..RGNP.DRLSSI..YE.MPV.S...L.K.
Retrocopy QLEKQIATLKEKMEMVRGNPSDRLSSIHLYEQMPVESLNILLKQ

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	0.06 RPM
SRP021940_cerebellum	0.00 RPM	0.00 RPM
SRP021940_embryo	0.00 RPM	0.23 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.00 RPM	0.00 RPM
SRP021940_testis	0.51 RPM	5.88 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_111 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_111 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_111 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Sus scrofa	retro_sscr_77

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004615	1 retrocopy	retro_amel_120,
Equus caballus	ENSECAG00000011446	1 retrocopy	retro_ecab_111 ,
Felis catus	ENSFCAG00000008786	1 retrocopy	retro_fcat_39,
Oryctolagus cuniculus	ENSOCUG00000026427	1 retrocopy	retro_ocun_406,
Otolemur garnettii	ENSOGAG00000010367	2 retrocopies	retro_ogar_1996, retro_ogar_957,
Sus scrofa	ENSSSCG00000026564	1 retrocopy	retro_sscr_77,