RetrogeneDB ID: retro_ocun_1431

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 8:101081761..101082334(+)
• Located in intron of: ENSOCUG00000024119

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPDYA
• Ensembl ID: ENSOCUG00000021734
• Aliases: None
• Description: speedy/RINGO cell cycle regulator family member A [Source:HGNC Symbol;Acc:30613]

Sequence

>retro_ocun_1431
ATGAGGCACAATCAGATGTGTTGTGAGACACCACCTACTGTCACTATTCATGTAAAATCAGGACCAAGTAGATCACATCT
ACCCAAAAAATCCATTAATCTGAAGCGTCCTATTTTTAAAGATAGTTGGCAAGCATCTGAAAAAAATGCACATAATAACA
ACAAATCTAAACGTCCCAAAGGTCCTTGCCTAGTTATACGGCGTCAGGAAATGACTGCTTTCTTTAAATTATTTGATGAC
GATTTAATTCAAGATTTCTTGTGGATGGACTGCTGCTGTAAAATTGCAGACAAGTATCTTTTGGCTATGACCTTTGTTTA
TTTCAAGAGGGCTAAATTTGCTATAAATGAACATACCAGGATAAATTTCTTTATTGCTTTGTACCTGGCTAACACAGTTG
AAGAAGATGAAGAAGAGTCCAAGTATGAAATTTTTCCCTGGGCTTTAGGGAAAAACTGGAGAAAATTGTTCCCTAATTTC
TTAAAGTTAAGGGACCAGCTCTGGGATAGAATTGACTATAGGGCTATTGTAAGCAGGCGATGCTGTGAGGAGCCAATGAC
CATCCATCAAACA

Alignment

ORF - retro_ocun_1431 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.34 %
• Parental protein coverage: 61.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRHNQMCCETPPTVTIHVKSGPSRSHQPKKSMNLKRPIFKDSWQASEKNAHNSNKSKRPKGPCLVIRRQE
          MRHNQMCCETPPTVTIHVKSGPSRSH.PKKS.NLKRPIFKDSWQASEKNAHN.NKSKRPKGPCLVIRRQE
Retrocopy MRHNQMCCETPPTVTIHVKSGPSRSHLPKKSINLKRPIFKDSWQASEKNAHNNNKSKRPKGPCLVIRRQE

Parental  MTAFFKLFDDDLIQDFLWMDCCCKIADKYLLAMTFVYFKRAKFAINEHTRINFFIALYLANTVEEDEEES
          MTAFFKLFDDDLIQDFLWMDCCCKIADKYLLAMTFVYFKRAKFAINEHTRINFFIALYLANTVEEDEEES
Retrocopy MTAFFKLFDDDLIQDFLWMDCCCKIADKYLLAMTFVYFKRAKFAINEHTRINFFIALYLANTVEEDEEES

Parental  KYEIFPWALGKNWRKLFPNFLKLRDQLWDRIDYRAIVSRRCCEEVMAIAPT
          KYEIFPWALGKNWRKLFPNFLKLRDQLWDRIDYRAIVSRRCCEE.M.I..T
Retrocopy KYEIFPWALGKNWRKLFPNFLKLRDQLWDRIDYRAIVSRRCCEEPMTIHQT

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
SRP017611_brain	0.00 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1431 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1431 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1431 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
Oryctolagus cuniculus	ENSOCUG00000021734	1 retrocopy	retro_ocun_1431 ,