RetrogeneDB ID: retro_ecab_436

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 18:58321242..58321496(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF1
• Ensembl ID: ENSECAG00000012516
• Aliases: None
• Description: eukaryotic translation initiation factor 1 [Source:HGNC Symbol;Acc:3249]

Sequence

>retro_ecab_436
GATTACATCCATATAAGAATTCAACAGAGAAATGGCGGGAAGACTCTTACTACTGTCCATCGGATTATTGATGATTGTGA
TAAAAGGAAACTAGCGAAGGCATTTAAGGAGAAATTTGTCGCCATAGGACTGTAACTGAGCATCCAGAATATGGAGAAGT
AATTCACCTATAAGGCAACCAGCACAAGAACATATGCTAGGTCCTGGTAGAGATTGGGCTGGCTGAGGATGACCAGCTGA
ATGTTCATGGGTTT

Alignment

ORF - retro_ecab_436 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.42 %
• Parental protein coverage: 75.22 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DYIHIRIQQRNGRKTLTTVQGIADDYDKKKLVKAFKKKFACNG-TVIEHPEYGEVIQLQGDQRKNICQFL
          DYIHIRIQQRNG.KTLTTV..I.DD.DK.KL.KAFK.KF...G.TV.EHPEYGEVI.L.G.Q.KNIC..L
Retrocopy DYIHIRIQQRNGGKTLTTVHRIIDDCDKRKLAKAFKEKFVAIG<TVTEHPEYGEVIHL*GNQHKNIC*VL

Parental  VEIGLAKEDQLKVHGF
          VEIGLA..DQL.VHGF
Retrocopy VEIGLAEDDQLNVHGF

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	0.06 RPM	118.12 RPM
SRP021940_cerebellum	0.00 RPM	146.14 RPM
SRP021940_embryo	0.08 RPM	66.54 RPM
SRP021940_placental_villous	0.05 RPM	163.91 RPM
SRP021940_synovial_membrane	0.00 RPM	83.65 RPM
SRP021940_testis	0.06 RPM	247.20 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_436 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_436 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_436 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000013853	4 retrocopies	retro_dord_349, retro_dord_350, retro_dord_663, retro_dord_753,
Equus caballus	ENSECAG00000012516	1 retrocopy	retro_ecab_436 ,
Rattus norvegicus	ENSRNOG00000032769	1 retrocopy	retro_rnor_520,
Rattus norvegicus	ENSRNOG00000033765	15 retrocopies	retro_rnor_1088, retro_rnor_1347, retro_rnor_1518, retro_rnor_1744, retro_rnor_1971, retro_rnor_2067, retro_rnor_2171, retro_rnor_2203, retro_rnor_2532, retro_rnor_2548, retro_rnor_2579, retro_rnor_45, retro_rnor_532, retro_rnor_571, retro_rnor_65,
Sorex araneus	ENSSARG00000006287	1 retrocopy	retro_sara_36,
Sarcophilus harrisii	ENSSHAG00000005729	1 retrocopy	retro_shar_42,