RetrogeneDB ID: retro_ocun_1727

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018825:695177..695835(-)
• Located in intron of: None

Retrocopy information

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

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_1727
AGTGGGAAGCGTTCGGCACTGCACTACAGTCGCCTTGGCACCCCGGTGCCCTTCGCGGCTCCACATACCCTGCCTTCTCT
CAGGGGGACAGTTGGGGTGAAAGGCGAAGTCGACGACCAGGAGGGATGCAACCAAGTGGCCCGCGACTTGAGAGAGTTCT
CGGCTGGACCATCTTTGGAGTGCAAGAGAGGTTCTCTGTTCCCACCAGATGGAGATGGGTCGCCGGTGCTGCCAGAGAAG
CTCAATGCATCTTCCTGGCTGCTGCGGGAAGCTGAACCCCATCTCAGCAATGGCTGGTTCAGGTCCTTTCTATTCTGTGT
TCGCTGCTGTTCGCCATCCTCCTTGCCTTTCTGCTCGCCATCGTCTACCTGGCCGTTAAAGAGTTGCGTGCTGAGAATTT
GAAAAATGAAGATTGTGTAGACGCTGGGCTGTTAGGGTTCTGGATGCTGCTTATAATATCCCTAACTGCTGGATTCTCCT
GTTGCAGCTTTTCTTGGACAGTGACTTATTTGATTCTTTTGAACCAGGAATGTTTCTTCCTACTCCTCTTTCACCTGCCA
CGTTCAAGAAACTGACTGGACACTCCTTCCACATGGGCGACAGCATGGCAATTTTGAATGGCATTGTAGCTGCTCTTACT
GTAGCGTGGTGCCTCATG

Alignment

ORF - retro_ocun_1727 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SGRRSAPRRRRLGTPVPFAAPQ-YSAFSQGDSWGV-GEVDDEEGCTQVARDLRAEFSAGPSSESRRGSLF
          SG.RSA....RLGTPVPFAAP..Y.AFSQGDSWG..GEVDD.EGC.QVARDLR.EFSAGPS.E..RGSLF
Retrocopy SGKRSALHYSRLGTPVPFAAPH<YPAFSQGDSWGE>GEVDDQEGCNQVARDLR-EFSAGPSLECKRGSLF

Parental  PPDGDGSPVLPEKRNG-IFPAAAGSRTSARQWPVQVLSILCALLFAILLAFLLAIVYLVVKELHAENLKN
          PPDGDGSPVLPEK.N..IF.AAAGS.T...QW.VQVLSILC.LLFAILLAFLLAIVYL.VKEL.AENLKN
Retrocopy PPDGDGSPVLPEKLNA<IFLAAAGS*TPSQQWLVQVLSILCSLLFAILLAFLLAIVYLAVKELRAENLKN

Parental  EDGIDTGLLGFWTLLIISLTAGFSCCSFSWTVTY-FDSFEPGMFPPTPLSPARFKKLTGHSFHMGYSMAI
          ED..D.GLLGFW.LLIISLTAGFSCCSFSWTVTY.FDSFEPGMF.PTPLSPA.FKKLTGHSFHMG.SMAI
Retrocopy EDCVDAGLLGFWMLLIISLTAGFSCCSFSWTVTY<FDSFEPGMFLPTPLSPATFKKLTGHSFHMGDSMAI

Parental  LNGIVAALTVAWCLM
          LNGIVAALTVAWCLM
Retrocopy LNGIVAALTVAWCLM

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_1727 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1727 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1727 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 ,