RetrogeneDB ID: retro_ocun_1584

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018703:2526783..2527196(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C5orf49
• Ensembl ID: ENSOCUG00000026520
• Aliases: None
• Description: chromosome 5 open reading frame 49 [Source:HGNC Symbol;Acc:27028]

Sequence

>retro_ocun_1584
ATGGACCTGGCCGGCCTGGAGGGAGAAGAGGAGATAGCGGCGGCCACGCTGCGGGCCAGGCCGCGGCCGCTGCCCATCTC
TGCAATGTCGGCCTTCGGCTCCGTCCCGCCGCGTGCAGGGACCCCACGGAGCACGGCCACTACTGTCGCCGGGGCCAGAC
GGGGATTATTGCCCTTTGCGAATGCGTTTTTTAGAGGAAGCTTCATTACGATCAGAAATGGCACCGAAGCGGCGGAGCGC
ACACAGAAGCCCTGGGGCTCCACGCACACGAGGAGGAACCAGAGAGGCCCGTGGGCGTGCGACCCCGTCTCCGGGAGGCG
CACCTGCACACCAGTGGTGCAGCCACTGACCCCGCGCTTCCGCCTGCCAACCACCTGCAGGCTGGCGTCCACCGGGGAAG
GACCGCACCATCA

Alignment

ORF - retro_ocun_1584 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.44 %
• Parental protein coverage: 92.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MDQDGLEEEEEITAATLRARPRPLPISALSAFSYVPPRR-LDPKEYSYYYRQGQTGIISLYDCVFKRKLD
          MD..GLE.EEEI.AATLRARPRPLPISA.SAF..VPPR...DP.E...Y.R.GQTGII.L..CVF.RKL.
Retrocopy MDLAGLEGEEEIAAATLRARPRPLPISAMSAFGSVPPRA<RDPTEHGHYCRRGQTGIIALCECVF*RKLH

Parental  YNQKLHRDDREHTKGLGLHVNKEERERPVGV-LASSVYGRRIHQ-PVEPLNRDFR-RANHVQADFYRKND
          Y.QK.HR....HT..LGLH...EE.ERPVGV....S..G...HQ..V.PL...FR..ANH.QA...R...
Retrocopy YDQKWHRSGGAHTEALGLHAHEEEPERPVGV<ATPSPGGAPAHQ<VVQPLTPRFR<PANHLQAGVHRGRT

Parental  IPS
          .PS
Retrocopy APS

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	2.04 RPM
SRP017611_kidney	0.00 RPM	8.21 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_1584 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1584 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1584 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	ENSOCUG00000026520	1 retrocopy	retro_ocun_1584 ,