RetrogeneDB ID: retro_ecab_60

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:35835317..35835752(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000004126
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000009152
• Aliases: None
• Description: None

Sequence

>retro_ecab_60
ATGAAACTCCTTGTGCTGGCTGTTCTGCTTACAGTGGGCGCTGGTGAGAGCGGCATCAGCCCGCGGGCAGTGTGGCAGTT
CCGCAGCATGATCCAGTGCACGATCCCCAACAGCAAACCCTATTTGGAATACAATGACTACGGCTGTTACTGTGGCCTGG
GTGGATCTGGCACTTCTGTGGATGAACTGGATGCGTGCTGCCAGGTACACGACAATTGCTACACTAAGGCCAAGGAACTG
AGCAGCTGTAGATTCCTCGTGGACAACCCCTACACTGAAAGCTACAAATTCTCATGCTCTGGCACTGAGGTCACCTGCAG
CGACAAAAACAACGCCTGTGAGGCCTTTATCTGTAACTGTGACCGAAGTGCTGCCATCTGCTTTTCAAAGGCCCCATACA
ACCTGGAGAACAAGAACCTGGACAGCAAGAGGTGT

Alignment

ORF - retro_ecab_60 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.86 %
• Parental protein coverage: 98.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKLLVLAVLLTVGAGENGISPRAVWQFRSMIQCTIPNSKPYLEFNDYGCYCGLGGSGTPVDELDACCQVH
          MKLLVLAVLLTVGAGE.GISPRAVWQFRSMIQCTIPNSKPYLE.NDYGCYCGLGGSGT.VDELDACCQVH
Retrocopy MKLLVLAVLLTVGAGESGISPRAVWQFRSMIQCTIPNSKPYLEYNDYGCYCGLGGSGTSVDELDACCQVH

Parental  DNCYTQAKELSSCRFLVDNPYTESYKFSCSGTEVTCSDKNNACEAFICNCDRNAAICFSKAPYNPENKNL
          DNCYT.AKELSSCRFLVDNPYTESYKFSCSGTEVTCSDKNNACEAFICNCDR.AAICFSKAPYN.ENKNL
Retrocopy DNCYTKAKELSSCRFLVDNPYTESYKFSCSGTEVTCSDKNNACEAFICNCDRSAAICFSKAPYNLENKNL

Parental  DSKRC
          DSKRC
Retrocopy DSKRC

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	0.00 RPM
SRP021940_cerebellum	0.00 RPM	0.16 RPM
SRP021940_embryo	0.03 RPM	1.36 RPM
SRP021940_placental_villous	0.00 RPM	0.05 RPM
SRP021940_synovial_membrane	0.00 RPM	0.00 RPM
SRP021940_testis	0.00 RPM	22.96 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_60 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_60 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_60 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000009152	1 retrocopy	retro_ecab_60 ,