RetrogeneDB ID: retro_ocun_1680

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018762:607107..607764(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000022587
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARL6IP6
• Ensembl ID: ENSOCUG00000013257
• Aliases: None
• Description: ADP-ribosylation-like factor 6 interacting protein 6 [Source:HGNC Symbol;Acc:24048]

Sequence

>retro_ocun_1680
AGTGGGAAGCGTTCGGCACTGCACCACAGTCGCCTTTGCACCCCGGTGCCCTTTGCGGCTCCACATACCCTGCCTTCTCT
CAGGGGGACAGTTGGGGTGAAGGCAAAGTCGACGACCAGGAGGGATGCAACCAAGTGGTCCGTGACTTGAGAGAGTTCTC
AGCTGGACCATCTTTGGAGTGCAAGAGAGGTTCTCTGTTCCCACCAGATGGAGATGGGTCACCGGTGCTGCCAGAGAAGC
TCAATGCATCTTCCTGGCTGCTGCGGGAAGCCAAACCCCATCTCAGCAGTGGCCGGTTCAGGTCCTTTCTATTCTATGTT
CACTGCTATTCGCCATCCTCCTCGCCTTTCTGCTCGCCATCGTCTACCTGGCTGTTAAAGAGTTGCATGCTGAGAATTTG
AAAAATGAAGATGGTGTAGACGCTGGGCTGTTAGGGTTCTGGATGCTGCTTATAATATCCCTAACTGCTGGATTCTCCTG
TTGCAGCTTTTCTTGGACAGTGACTTATTTGATTCTTTTGAACCAGGAATGTTTCCTCCTACTCCTCTTTCACCTGCCAG
GTTCAAGAAACGGACTGGACACTCCTTCCACATGGGCGACAGCATGGCAATTTTGAATGGCATTGTGGCTGCTCTTACTG
TAGCATGGTGCCTCATG

Alignment

ORF - retro_ocun_1680 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.82 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SGRRSAPRRRRLGTPVPFAAPQ-YSAFSQGDSWGVGEVDDEEGCTQVARDLRAEFSAGPSSESRRGSLFP
          SG.RSA....RL.TPVPFAAP..Y.AFSQGDSWG.G.VDD.EGC.QV.RDLR.EFSAGPS.E..RGSLFP
Retrocopy SGKRSALHHSRLCTPVPFAAPH<YPAFSQGDSWGEGKVDDQEGCNQVVRDLR-EFSAGPSLECKRGSLFP

Parental  PDGDGSPVLPEKRNG-IFPAAAGSRTSARQWPVQVLSILCALLFAILLAFLLAIVYLVVKELHAENLKNE
          PDGDGSPVLPEK.N..IF.AAAGS.T...QWPVQVLSILC.LLFAILLAFLLAIVYL.VKELHAENLKNE
Retrocopy PDGDGSPVLPEKLNA<IFLAAAGSQTPSQQWPVQVLSILCSLLFAILLAFLLAIVYLAVKELHAENLKNE

Parental  DGIDTGLLGFWTLLIISLTAGFSCCSFSWTVTY-FDSFEPGMFPPTPLSPARFKKLTGHSFHMGYSMAIL
          DG.D.GLLGFW.LLIISLTAGFSCCSFSWTVTY.FDSFEPGMFPPTPLSPARFKK.TGHSFHMG.SMAIL
Retrocopy DGVDAGLLGFWMLLIISLTAGFSCCSFSWTVTY<FDSFEPGMFPPTPLSPARFKKRTGHSFHMGDSMAIL

Parental  NGIVAALTVAWCLM
          NGIVAALTVAWCLM
Retrocopy NGIVAALTVAWCLM

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	6.68 RPM
SRP017611_kidney	0.00 RPM	10.64 RPM
SRP017611_liver	0.00 RPM	3.55 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1680 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1680 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1680 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Mustela putorius furo	ENSMPUG00000000415	1 retrocopy	retro_mputfur_75,
Oryctolagus cuniculus	ENSOCUG00000013257	3 retrocopies	retro_ocun_1649, retro_ocun_1680 , retro_ocun_1727,