RetrogeneDB ID: retro_ocun_1086

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:25400519..25400979(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS7A
• Ensembl ID: ENSOCUG00000011187
• Aliases: None
• Description: COP9 signalosome subunit 7A [Source:HGNC Symbol;Acc:16758]

Sequence

>retro_ocun_1086
GGTGACAGGCAGAGCAGCAGAGTGTTCTTTGCCAAGTCCACTCAGAGGGCAGAACTGGCCCTATTCATCCACTAGGTATT
GAGGCCTCAGGTTCCTATGTGTTTTGGGGATGTGCTGCATAGATGAATGTTAGAGAGCTTACTGAGAGTATCTTTGCTTC
CACGTTCTTGCTGCTCACATTATTTCCTATGAGACATATGAAGAACTCCTTAGCTGAAGCCTGGAATCTTCCCCCACTCA
TAAATACTCAGAAGGATAAGCTTTGAGACCTATCAGTGATCACCATGGCTGTTTAAGTCAAATGCATCGCATGTGCAGTG
TTGCTGGAAACCCTGGCCCAGTATAACATGTGGCAGGTGGAAGACCTTGTGATAGAGGCTGAGAATCCAATGTCCTTCAT
TGTTCCCTGGCCCAGTGTGATCAGTGGCTGGATGGTGACTCCAGCATCTGGAAGAACATC

Alignment

ORF - retro_ocun_1086 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.21 %
• Parental protein coverage: 56. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GQNQEQFLLLAKSAKGAALATLIHQVL-EAPGVYVFGELLDMPNVRELAESDFASTFRLLTVFAYGTYAD
          G..Q......AKS...A.LA..IH.VL.EA.G.YVF.......NVREL.ES.FASTF.LLT.F.......
Retrocopy GDRQSSRVFFAKSTQRAELALFIH*VL<EASGSYVFWGCAA*MNVRELTESIFASTFLLLTLFPMRHMKN

Parental  YLAEARNLPPLTEAQKNKLRHLSVVTLAAKVKCIPYAVLLEALALRNVRQLEDLVIEAV-YADVLRGSLD
          .LAEA.NLPPL...QK.KL..LSV.T.A..VKCI..AVLLE.LA..N..Q.EDLVIEA.....VL..SL.
Retrocopy SLAEAWNLPPLINTQKDKL*DLSVITMAV*VKCIACAVLLETLAQYNMWQVEDLVIEAE<ESNVLHCSLA

Parental  QRNQRLEVDYSIGRDI
          Q..Q.L..D.SI...I
Retrocopy QCDQWLDGDSSIWKNI

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	92.72 RPM
SRP017611_kidney	0.00 RPM	74.40 RPM
SRP017611_liver	0.00 RPM	44.55 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1086 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1086 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1086 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000004634	1 retrocopy	retro_lafr_297,
Macropus eugenii	ENSMEUG00000010451	1 retrocopy	retro_meug_724,
Microcebus murinus	ENSMICG00000013661	1 retrocopy	retro_mmur_1458,
Oryctolagus cuniculus	ENSOCUG00000011187	1 retrocopy	retro_ocun_1086 ,
Oryctolagus cuniculus	ENSOCUG00000016918	1 retrocopy	retro_ocun_1194,
Ictidomys tridecemlineatus	ENSSTOG00000027250	1 retrocopy	retro_itri_538,