RetrogeneDB ID: retro_ecab_606

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 23:31646049..31646255(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PET100
• Ensembl ID: ENSECAG00000008451
• Aliases: None
• Description: PET100 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:40038]

Sequence

>retro_ecab_606
TTTCAGATAATGCTGTAACTCATCTTCCCTGTGGCCATGTTCTGGATTGCTAACCAGGCTGAGTGGTTTGAGGACTAGTT
ACACCGCACAAGAGGGAGCTGTGGCCACCTAAGAAGGCGGCCTAGTCTCAGGAGCTAGAAGACTTCAAAGAGAGGAGACA
GAGGCAGCAGGAGCAGAAGCTCCTTCAAGCTGCCCGGTAGAACTCC

Alignment

ORF - retro_ecab_606 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.71 %
• Parental protein coverage: 90.79 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FRMTLYLTFPVAMFWIANQAEWFED-YVIQRKRELWPPEKEDQRQELEEFKERIRKQREEKLLRAARQSS
          F...L.L.FPVAMFWIANQAEWFED..V...KRELWPP.K....QELE.FKER...Q.E.KLL.AAR..S
Retrocopy FQIML*LIFPVAMFWIANQAEWFED<LVTPHKRELWPPKKAA*SQELEDFKERRQRQQEQKLLQAAR*NS

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	8.85 RPM
SRP021940_cerebellum	0.00 RPM	13.97 RPM
SRP021940_embryo	0.00 RPM	14.12 RPM
SRP021940_placental_villous	0.00 RPM	20.25 RPM
SRP021940_synovial_membrane	0.00 RPM	12.27 RPM
SRP021940_testis	0.00 RPM	42.84 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_606 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_606 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_606 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008524	2 retrocopies	retro_amel_591, retro_amel_878,
Equus caballus	ENSECAG00000008451	1 retrocopy	retro_ecab_606 ,
Felis catus	ENSFCAG00000023931	2 retrocopies	retro_fcat_1266, retro_fcat_1752,
Gorilla gorilla	ENSGGOG00000027594	1 retrocopy	retro_ggor_1905,
Pan troglodytes	ENSPTRG00000039245	1 retrocopy	retro_ptro_120,