RetrogeneDB ID: retro_ocun_1942

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:84862045..84862480(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000028097
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARL8B
• Ensembl ID: ENSOCUG00000014090
• Aliases: None
• Description: ADP-ribosylation factor-like 8B [Source:HGNC Symbol;Acc:25564]

Sequence

>retro_ocun_1942
TCAAGTCAGTTCAGTGAAGACATGATACCCACTGTGGGCTTCAACATGAGGAAAGTCACGAAAGGTAACGTCACCATAAA
GATCTGGGACATAGGAGGACAGCCCCGCTTCCGGAGCATGTGGGAACGATACTGCAGGGGAGTCAACGCTATTGTTTATA
TGATAGATGCTGCAGATCGTGAGAAAATAGAGGCCTCCCGAAATGAGCTACACAATCTTCTAGACAAACCACAGTTACAA
GGAATCCCAGTGCTAGTACTTGGAAACAAGAGAGATCTCCCCAGTGCCTTGGATGAGAAACAGCTAATTGAAAAAATGAA
TCTGTCTGCTATTCAGGATAGAGAAATCTGCTGCTATTCAATTTCTTGCAAAGAAAAGGATAACATAGATATCACACTTC
AGTGGCTTATTCAACATTCAAAATCGAGAAGAAGC

Alignment

ORF - retro_ocun_1942 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.62 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGQFSEDMIPTVGFNMRKVTKGNVTIKIWDIGGQPRFRSMWERYCRGVNAIVYMIDAADREKIEASRNEL
          S.QFSEDMIPTVGFNMRKVTKGNVTIKIWDIGGQPRFRSMWERYCRGVNAIVYMIDAADREKIEASRNEL
Retrocopy SSQFSEDMIPTVGFNMRKVTKGNVTIKIWDIGGQPRFRSMWERYCRGVNAIVYMIDAADREKIEASRNEL

Parental  HNLLDKPQLQGIPVLVLGNKRDLPNALDEKQLIEKMNLSAIQDREICCYSISCKEKDNIDITLQWLIQHS
          HNLLDKPQLQGIPVLVLGNKRDLP.ALDEKQLIEKMNLSAIQDREICCYSISCKEKDNIDITLQWLIQHS
Retrocopy HNLLDKPQLQGIPVLVLGNKRDLPSALDEKQLIEKMNLSAIQDREICCYSISCKEKDNIDITLQWLIQHS

Parental  KSRRS
          KSRRS
Retrocopy KSRRS

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	3.64 RPM	29.08 RPM
SRP017611_kidney	3.45 RPM	21.18 RPM
SRP017611_liver	1.39 RPM	13.41 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1942 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1942 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1942 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007757	2 retrocopies	retro_chof_1196, retro_chof_2630,
Callithrix jacchus	ENSCJAG00000015842	2 retrocopies	retro_cjac_1120, retro_cjac_470,
Homo sapiens	ENSG00000134108	1 retrocopy	retro_hsap_361,
Gallus gallus	ENSGALG00000008314	1 retrocopy	retro_ggal_25,
Gorilla gorilla	ENSGGOG00000004952	1 retrocopy	retro_ggor_373,
Microcebus murinus	ENSMICG00000000244	2 retrocopies	retro_mmur_1220, retro_mmur_1239,
Mustela putorius furo	ENSMPUG00000017035	2 retrocopies	retro_mputfur_1390, retro_mputfur_541,
Oryctolagus cuniculus	ENSOCUG00000000824	4 retrocopies	retro_ocun_1007, retro_ocun_1502, retro_ocun_1868, retro_ocun_987,
Oryctolagus cuniculus	ENSOCUG00000014090	2 retrocopies	retro_ocun_1942 , retro_ocun_751,
Oryctolagus cuniculus	ENSOCUG00000023009	1 retrocopy	retro_ocun_1404,
Oryctolagus cuniculus	ENSOCUG00000023198	1 retrocopy	retro_ocun_132,
Oryctolagus cuniculus	ENSOCUG00000023645	2 retrocopies	retro_ocun_1137, retro_ocun_247,
Pongo abelii	ENSPPYG00000013694	1 retrocopy	retro_pabe_343,
Tarsius syrichta	ENSTSYG00000001724	1 retrocopy	retro_tsyr_2150,
Vicugna pacos	ENSVPAG00000012114	2 retrocopies	retro_vpac_495, retro_vpac_519,