RetrogeneDB ID: retro_ocun_611

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:50308293..50308693(+)
• Located in intron of: ENSOCUG00000003778

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARL6
• Ensembl ID: ENSOCUG00000029293
• Aliases: None
• Description: ADP-ribosylation factor-like 6 [Source:HGNC Symbol;Acc:13210]

Sequence

>retro_ocun_611
TCAGTAGAGAAATTCAAATCATCCAGTTTATTTTTTACAGTGCTTGACACGTAAGCTCAAGGAGGATACAGAAATCTCTG
GGAACACTGGTATAAAGAAGGACAAGCCATTATCTTTGTCATTGATAGTAGTGGTAAGTTAAGAATGGTTGTGGCCAAAG
AAGAACTTGATTACTCTTCTGAATCATGCAGATATTAAACATCATCGAATTCCAATCTTACTCTTTACAAACAAAATGGA
TCTTAGAGATGCAGTGACCTCTGTGAAAGTGTCTCAGTTGCTGTGTTTAGAGAACATAAAAAATAAACCATGACACATTT
GTGCTAGTGATGCCATAAAAGGAGAAGGCTTGCAGGAAGGTGTAGACTGGCTTCAAGATCAGACCCAGGCTGTAAAGACG

Alignment

ORF - retro_ocun_611 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.57 %
• Parental protein coverage: 71.51 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDKLRMVVAKEELD-TLLNHPDIKHRR
          ..EKFKSSSL.FTV.D...QG.YRNLWEH.YKEGQAIIFVIDSS.KLRMVVAKEELD.TLLNH.DIKH.R
Retrocopy SVEKFKSSSLFFTVLDT*AQGGYRNLWEHWYKEGQAIIFVIDSSGKLRMVVAKEELD>TLLNHADIKHHR

Parental  IPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQIQAVKT
          IPIL.F.NKMDLRDAVTSVKVSQLLCLENIK.KP.HICASDAIKGEGLQEGVDWLQDQ.QAVKT
Retrocopy IPILLFTNKMDLRDAVTSVKVSQLLCLENIKNKP*HICASDAIKGEGLQEGVDWLQDQTQAVKT

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	0.17 RPM	12.75 RPM
SRP017611_kidney	0.41 RPM	9.83 RPM
SRP017611_liver	0.46 RPM	0.62 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_611 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_611 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_611 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
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 ,
Rattus norvegicus	ENSRNOG00000001689	1 retrocopy	retro_rnor_2142,