RetrogeneDB ID: retro_ocun_1404

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 8:28909939..28910162(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARL8A
• Ensembl ID: ENSOCUG00000023009
• Aliases: None
• Description: ADP-ribosylation factor-like 8A [Source:HGNC Symbol;Acc:25192]

Sequence

>retro_ocun_1404
ATACCCTGGGTGGGTTTCAACACGAGAAAAGTCACCCAGGTAACGTCACAATAAAGACCCGGGACGTGGGGGACAGCCTC
GATTCTGGAACACGTGGGAATGATACCGCAGGGGAGTCAGCGCTATGGTTTACGTGATAGATGCTGCAAAGCTTGAAAAG
ATAGAAGCCTCCCCAAACGAGCTGTATAATCTTCTAGATAAACCACAGGAACAAGGAACCCCT

Alignment

ORF - retro_ocun_1404 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.13 %
• Parental protein coverage: 59.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IPTVGFNMRKITK-GNVTIKLWDIG-GQPRFRSMWERYCRGVSAIVYMVDAADQEKIEASKNELHNLLDK
          IP.VGFN.RK.T..GNVTIK..D.G.GQPRF...WE.Y.RGVSA.VY..DAA..EKIEAS.NEL.NLLDK
Retrocopy IPWVGFNTRKVTQ<GNVTIKTRDVG<GQPRFWNTWE*YRRGVSAMVYVIDAAKLEKIEASPNELYNLLDK

Parental  PQLQGIP
          PQ.QG.P
Retrocopy PQEQGTP

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	31.02 RPM
SRP017611_kidney	0.00 RPM	3.55 RPM
SRP017611_liver	0.00 RPM	0.77 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1404 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1404 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1404 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Meleagris gallopavo	ENSMGAG00000001081	1 retrocopy	retro_mgal_18,
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,
Ictidomys tridecemlineatus	ENSSTOG00000013990	1 retrocopy	retro_itri_659,