RetrogeneDB ID: retro_ocun_79

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 18:4669689..4670226(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000024510
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ARL5B
• Ensembl ID: ENSOCUG00000014876
• Aliases: None
• Description: ADP-ribosylation factor-like 5B [Source:HGNC Symbol;Acc:23052]

Sequence

>retro_ocun_79
ATGGGAATTCTCTTCACCAGGGTATGGAGACTGTTCAATAACCAGGAGCACAAAGTTATAATTGTTGGGCTGGATAATGC
TGGGAAAACTACCATCCTTTACCAATTTTCTATGAATGAAGTTGTACACACATCCCCTACAATAGGAAGTAATGTAGAAG
AGATAGTGATTAATAATACACGTTTCCTAATGTGGGATATTGGTGGCCAAGAATCTCTTTGTTCTTCCTGGAACACTTAC
TATACTAACACAGAGTTTGTAATAGTTGTTGTGGACAGTACAGATAGAGAGAGGATATATGTAACTAGAGAAGAACTCTA
TAAAATGTTAGCACATGAGGACTTAAGGAAAGCTGGTTTGCTGATTTTTGCTAATAAGCAAGATGTTAAAGAATGCATGA
CTGTAGCAGAAATCTCTCAGTTTTTGAAGCTGACTTCTATCAAAGATCACCAGTGGCATATCCAGGCCTGCTGTGCTCTT
ACTGGAGAGGGATTATGTCAAGGACTTGAATGGATGATGTCCCGACTTAAGATTAGA

Alignment

ORF - retro_ocun_79 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.89 %
• Parental protein coverage: 99.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGLIFAKLWSLFCNQEHKVIIVGLDNAGKTTILYQFLMNEVVHTSPTIGSNVEEIVVKNTHFLMWDIGGQ
          MG..F...W.LF.NQEHKVIIVGLDNAGKTTILYQF.MNEVVHTSPTIGSNVEEIV..NT.FLMWDIGGQ
Retrocopy MGILFTRVWRLFNNQEHKVIIVGLDNAGKTTILYQFSMNEVVHTSPTIGSNVEEIVINNTRFLMWDIGGQ

Parental  ESLRSSWNTYYSNTEFIILVVDSIDRERLAITKEELYRMLAHEDLRKAAVLIFANKQDMKGCMTAAEISK
          ESL.SSWNTYY.NTEF.I.VVDS.DRER...T.EELY.MLAHEDLRKA..LIFANKQD.K.CMT.AEIS.
Retrocopy ESLCSSWNTYYTNTEFVIVVVDSTDRERIYVTREELYKMLAHEDLRKAGLLIFANKQDVKECMTVAEISQ

Parental  YLTLSSIKDHPWHIQSCCALTGEGLCQGLEWMTSRIGVR
          .L.L.SIKDH.WHIQ.CCALTGEGLCQGLEWM.SR...R
Retrocopy FLKLTSIKDHQWHIQACCALTGEGLCQGLEWMMSRLKIR

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	2.65 RPM	3.59 RPM
SRP017611_kidney	5.47 RPM	3.34 RPM
SRP017611_liver	2.00 RPM	1.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_79 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_79 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_79 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005856	2 retrocopies	retro_cpor_558, retro_cpor_747,
Macaca mulatta	ENSMMUG00000007453	3 retrocopies	retro_mmul_614, retro_mmul_726, retro_mmul_743,
Oryctolagus cuniculus	ENSOCUG00000002217	5 retrocopies	retro_ocun_1608, retro_ocun_399, retro_ocun_400, retro_ocun_465, retro_ocun_847,
Oryctolagus cuniculus	ENSOCUG00000014876	1 retrocopy	retro_ocun_79 ,
Oryctolagus cuniculus	ENSOCUG00000029293	1 retrocopy	retro_ocun_611,
Ictidomys tridecemlineatus	ENSSTOG00000027859	1 retrocopy	retro_itri_580,