RetrogeneDB ID: retro_ocun_119

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:86635609..86636152(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000005663
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000029741
• Aliases: None
• Description: None

Sequence

>retro_ocun_119
ATGAACACACTGCTGTCGCGGGCAAACTCGCTGTTTGCCTTCTCGCTGAGCGTGATGGCGGCAGTCACCCTGGGCTGCTT
CGTCACCACCGCATTCAAAGACAGGTGCGTGCCGGTGCAGCTGCAGGTCTCCCGGATCATGCTAAAAAATGTAGAAGACT
TCACTGGACCCAGACAAAGAAGCGACCTGGGATTCATCACATTTCATATAACTGCTGATCTGGAGAAGACGTTTGACTGG
AATGTTAAGCAGTTGTTTCTTTATTTATCAGCAGAATATTCAACAAAAAATAATGCTGTGAACCAGGTGGTCCTCTGGGA
CAAGATTGTTCTGAGAGGTGACAATCCGAAGCTGAGGGTGAAAGATGTGAAAGCGAAGTATTTTTTCTTTGATGATGGAA
ATGGTCTCAAGGGAAACCGGAATGTCACTTTGACCCTATCTTGGAATGTTGTACCAATTGCTGGAATTCTACCTCTTGTG
ACAGGATCAGGACATGTGTCTGTCCCATTTCCAGATGCATATGAAATAATGAAGAGTTACTAA

Alignment

ORF - retro_ocun_119 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.44 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNTVLSRANSLFAFSLSVMAALTFGCFITTAFKDRSVPVRLHVSRIMLKNVEDFTGPRERSDLGFITFDI
          MNT.LSRANSLFAFSLSVMAA.T.GCF.TTAFKDR.VPV.L.VSRIMLKNVEDFTGPR.RSDLGFITF.I
Retrocopy MNTLLSRANSLFAFSLSVMAAVTLGCFVTTAFKDRCVPVQLQVSRIMLKNVEDFTGPRQRSDLGFITFHI

Parental  TADLENIFDWNVKQLFLYLSAEYSTKNNALNQVVLWDKIVLRGDNPKLLLKDMKTKYFFFDDGNGLKGNR
          TADLE..FDWNVKQLFLYLSAEYSTKNNA.NQVVLWDKIVLRGDNPKL..KD.K.KYFFFDDGNGLKGNR
Retrocopy TADLEKTFDWNVKQLFLYLSAEYSTKNNAVNQVVLWDKIVLRGDNPKLRVKDVKAKYFFFDDGNGLKGNR

Parental  NVTLTLSWNVVPNAGILPLVTGSGHVSVPFPDTYEITKSY
          NVTLTLSWNVVP.AGILPLVTGSGHVSVPFPD.YEI.KSY
Retrocopy NVTLTLSWNVVPIAGILPLVTGSGHVSVPFPDAYEIMKSY

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	1.66 RPM	11.76 RPM
SRP017611_kidney	0.00 RPM	22.91 RPM
SRP017611_liver	0.00 RPM	20.27 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_119 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_119 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_119 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000001987	2 retrocopies	retro_mmur_1595, retro_mmur_731,
Oryctolagus cuniculus	ENSOCUG00000029741	1 retrocopy	retro_ocun_119 ,
Otolemur garnettii	ENSOGAG00000003825	1 retrocopy	retro_ogar_1710,
Pongo abelii	ENSPPYG00000015218	1 retrocopy	retro_pabe_138,
Sarcophilus harrisii	ENSSHAG00000015012	1 retrocopy	retro_shar_481,
Ictidomys tridecemlineatus	ENSSTOG00000013678	1 retrocopy	retro_itri_57,