RetrogeneDB ID: retro_ocun_1733

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018828:426673..427488(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000021399
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000017342
• Aliases: None
• Description: None

Sequence

>retro_ocun_1733
ATGCCAGGTGAGGACGAGGAGCAAACTATCGCAGAGGACCTGGTTGTGACCAAGTATAAGATGGGGGGCGACATCGCCAA
CCGGGTACTTCGGTCTTTGGTGGAGGCATCCAGCTCAGGTGTGTCCGTGCTGAGCCCGTGTGAGAAGGGTGATGCCATGA
TTATAGAAGAAACAGGGAAAATCTTCAAGAAGGAAAATAGATGAAAAAAGGTACTGCATTTCCTGCCACTATTTTAGTAA
ATAACTGTCTGTCACTGCTCCCCTTGGAAGAGTGATCAGGACTACATTCTCAAGGAAGGTGACTTGGTAACAATTGACCT
TGGGGTCCCTGTGGATGGCCTTATTGCTAATGTGGCTCACACTTTTGTGGTTGGTATAGCTCAGGGGACCCAACTAACAG
GGCGGAAAGCAGGTGTCATTAAGGCAGCTCACCTTTGTGCTGAAGCTGCCCTGCGCCTGGTCAAACCTGGAAATCAGAAC
ACACAGGTGACAGAAGCCTGGAACAAGGTTGCCCACTCATTTAACTGCATGCCAATGGAAGGCATGCTGTCACTCCAACT
GAAGCAACATGTCAACGATGAAGAGAAAACCATTATCCAGAATCCCACAGACCAGCAGAAGGACCAGGAAAAGCTGAATT
CGAGGTGCATGAAGTGTATGCCGTGGATGTCCTCGTCAGCTCAGGAGAGGACAAGGCCAAGAATGCAGGACAGGGAACCA
CCATTGAGAAACGAGACCCATCTAAACAATATGGCCTGAAAATGAAAACCTCGCGTGCCTTCCTCAGGGAGGTGGAAAGG
CGTTTTGATGCCCTT

Alignment

ORF - retro_ocun_1733 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.23 %
• Parental protein coverage: 70.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSGEDEQQEQTIAEDLVVTKYKMGGDIANRVLRSLVEASSSGVSVLSLCEKGDAMIMEETGKIFKANDS-
          M.GEDE..EQTIAEDLVVTKYKMGGDIANRVLRSLVEASSSGVSVLS.CEKGDAMI.EETGKIFK.....
Retrocopy MPGEDE--EQTIAEDLVVTKYKMGGDIANRVLRSLVEASSSGVSVLSPCEKGDAMIIEETGKIFKKENR<

Parental  VFTGIAFPTSISVNNCVCHFSPL-KSDQDYILKEGDLVKIDLGVHVDGFIANVAHTFVVGVAQGTQVTGR
          ...G.AFP..I.VNNC.....PL.KSDQDYILKEGDLV.IDLGV.VDG.IANVAHTFVVG.AQGTQ.TGR
Retrocopy MKKGTAFPATILVNNCL-SLLPL>KSDQDYILKEGDLVTIDLGVPVDGLIANVAHTFVVGIAQGTQLTGR

Parental  KADVIKAAHLCAEAALRLVKPGNQNTQVTEAWNKVAHSFNCTPIEGMLSHQLKQHVIDGEKTIIQNPTDQ
          KA.VIKAAHLCAEAALRLVKPGNQNTQVTEAWNKVAHSFNC.P.EGMLS.QLKQHV.D.EKTIIQNPTDQ
Retrocopy KAGVIKAAHLCAEAALRLVKPGNQNTQVTEAWNKVAHSFNCMPMEGMLSLQLKQHVNDEEKTIIQNPTDQ

Parental  QKKDHE-KAEFEVHEVYAVDVLVSSGEGKAKDAGQRTTIYKRDPSKQYGLKMKTSRAFFSEVERRFDAM
          Q.KD.E.KAEFEVHEVYAVDVLVSSGE.KAK.AGQ.TTI.KRDPSKQYGLKMKTSRAF..EVERRFDA.
Retrocopy Q-KDQE<KAEFEVHEVYAVDVLVSSGEDKAKNAGQGTTIEKRDPSKQYGLKMKTSRAFLREVERRFDAL

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	48.51 RPM
SRP017611_kidney	0.00 RPM	60.31 RPM
SRP017611_liver	0.00 RPM	23.89 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1733 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1733 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1733 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007181	2 retrocopies	retro_chof_1089, retro_chof_1847,
Homo sapiens	ENSG00000170515	6 retrocopies	retro_hsap_1930, retro_hsap_2413, retro_hsap_2868, retro_hsap_3646, retro_hsap_4191, retro_hsap_4895,
Macaca mulatta	ENSMMUG00000002164	2 retrocopies	retro_mmul_1168, retro_mmul_2631,
Mus musculus	ENSMUSG00000025364	1 retrocopy	retro_mmus_2803,
Oryctolagus cuniculus	ENSOCUG00000017342	1 retrocopy	retro_ocun_1733 ,
Sus scrofa	ENSSSCG00000000377	1 retrocopy	retro_sscr_338,
Sus scrofa	ENSSSCG00000022666	2 retrocopies	retro_sscr_1143, retro_sscr_337,
Tarsius syrichta	ENSTSYG00000006777	1 retrocopy	retro_tsyr_746,
Vicugna pacos	ENSVPAG00000009523	1 retrocopy	retro_vpac_2,