RetrogeneDB ID: retro_ecab_833

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 5:45007234..45007506(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000017627
• Aliases: None
• Description: None

Sequence

>retro_ecab_833
CAGAACCAGCAGCAGTGCCAGCCCCCTCCCAAGTGCCTTCCCAAGTGCCCCCAAAAATGTCCACCTAAGTGCCCCCCCAG
TACCCAGCCCCGTGTCCCCCTCCAGTCTCCTCCTGCTGTGACCCCAGCTCTGGGGGCTGCCGCAGCTCTGGGGGAGGGGG
CTGCTGCCTGAGCCACCACAGGTCCCATCTCTTCCACCGGCGGTGGCACCAGAGCCCCGACTGCTGTGAGGGTGAGCCCT
CGGGGGGCTCCGGCTGCTACGGCAGCTCTGGG

Alignment

ORF - retro_ecab_833 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.04 %
• Parental protein coverage: 82.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QPPPKCSPKCSPKCTPKCPPKCPPKCPP-QCPAPCPPPVSSCCGPSSGGCCSSGGGGCCLSHHRRRRSHR
          Q....C.P...PKC.PKCP.KCPPKCPP.Q.PAPCPPPVSSCC.PSSGGC.SSGGGGCCLSHHR....HR
Retrocopy QNQQQCQPP--PKCLPKCPQKCPPKCPP<QYPAPCPPPVSSCCDPSSGGCRSSGGGGCCLSHHRSHLFHR

Parental  RRQQSSDCCNSGSGQQSGGSSCCHESG
          R..QS.DCC....G..SGGS.C...SG
Retrocopy RWHQSPDCC---EGEPSGGSGCYGSSG

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	0.05 RPM	0.00 RPM
SRP021940_embryo	0.05 RPM	0.00 RPM
SRP021940_placental_villous	0.00 RPM	0.05 RPM
SRP021940_synovial_membrane	0.00 RPM	0.00 RPM
SRP021940_testis	0.00 RPM	0.13 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_833 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_833 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_833 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	ENSECAG00000017627	1 retrocopy	retro_ecab_833 ,