RetrogeneDB ID: retro_ocun_1365

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:83246164..83246463(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HAGH
• Ensembl ID: ENSOCUG00000024657
• Aliases: None
• Description: hydroxyacylglutathione hydrolase [Source:HGNC Symbol;Acc:4805]

Sequence

>retro_ocun_1365
TTATTGCTTGCCCTGATGGACAGCTACACGTACCTGGTCATGGATGATGATGCCAAGGAGGACACCATTGCAGACCTGAG
TGCAGCCCCAGAAGGTTCTAGACACAGAAAGCACAGGGTGAAGCTGACCACAGTGCTCACCACCCACCATTCCTGGGACC
ACCCTGGTGGGAAATAGAAACTGGTCAAGCAAGAGCTGGGACTGCCGGTGTACAAGGGCAATGATCTGATCCAGCCCTGA
CACACAAGCTCACACACTTGTCCATGTTGCAGGTGGCATCTCTCAACATCAAATGCCTG

Alignment

ORF - retro_ocun_1365 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.86 %
• Parental protein coverage: 57.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLPALTDNYMYLVIDDDTKEAAIVDPVQPQKVLDTVRKHGVKLTTVLTTHHHWDHAGGNEKLLKLEPGLK
          LL.AL.D.Y.YLV..DD...................RKH.VKLTTVLTTHH.WDH.GG..KL.K.E.GL.
Retrocopy LLLALMDSYTYLVM-DDDAKEDTIADLSAAPEGSRHRKHRVKLTTVLTTHHSWDHPGGK*KLVKQELGLP

Parental  VYGGDDRI-GALTHKVTHLSTLQVGSLSVKCL
          VY.G.D.I..ALTHK.THLS.LQV.SL..KCL
Retrocopy VYKGNDLI<PALTHKLTHLSMLQVASLNIKCL

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	23.57 RPM
SRP017611_kidney	0.00 RPM	51.08 RPM
SRP017611_liver	0.00 RPM	50.87 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1365 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1365 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1365 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	ENSOCUG00000024657	1 retrocopy	retro_ocun_1365 ,