RetrogeneDB ID: retro_ocun_311

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:138536076..138536427(+)
• Located in intron of: ENSOCUG00000021262

Retrocopy information

• Ensembl ID: ENSOCUG00000005752
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GABARAP
• Ensembl ID: ENSOCUG00000006997
• Aliases: None
• Description: GABA(A) receptor-associated protein (GABARAP), mRNA [Source:RefSeq mRNA;Acc:NM_001082142]

Sequence

>retro_ocun_311
ATGAAGTTCGTGTACAAGGAGGAGCATCCGTTCGAGAAGCGCCGCTCTGAGGGCGAGAAGATCAGAAAGAAATACACGGA
CCGGGTCCCGGTGATAGTAGAAAAGGCTCCCAAAGCTCGGATAGGAGACATGGACAAAAAAAAATACCTGGTGCCTTCTG
ATCTCACAGTTGGTCAGTTCTACTTCCTGATCCGGAAGCGAATTCATCTCCAAGCTGAGGATGCCTTGTTTTTCTTTGTC
AACAACGTCATTCCACCCACCAGTGCCACCATGGGTCAGCTCTACCAGGAGCACCATGAAGAGGACTTCTTTCTGTACAT
TGCCTACAGTGACGAAAGTGTCTACGGCCTG

Alignment

ORF - retro_ocun_311 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.44 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKFVYKEEHPFEKRRSEGEKIRKKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHL
          MKFVYKEEHPFEKRRSEGEKIRKKY.DRVPVIVEKAPKARIGD.DKKKYLVPSDLTVGQFYFLIRKRIHL
Retrocopy MKFVYKEEHPFEKRRSEGEKIRKKYTDRVPVIVEKAPKARIGDMDKKKYLVPSDLTVGQFYFLIRKRIHL

Parental  RAEDALFFFVNNVIPPTSATMGQLYQEHHEEDFFLYIAYSDESVYGL
          .AEDALFFFVNNVIPPTSATMGQLYQEHHEEDFFLYIAYSDESVYGL
Retrocopy QAEDALFFFVNNVIPPTSATMGQLYQEHHEEDFFLYIAYSDESVYGL

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	0.39 RPM	180.74 RPM
SRP017611_kidney	0.30 RPM	317.96 RPM
SRP017611_liver	0.31 RPM	108.68 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_311 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_311 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_311 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000012473	1 retrocopy	retro_cint_25,
Callithrix jacchus	ENSCJAG00000016655	2 retrocopies	retro_cjac_2851, retro_cjac_3820,
Gorilla gorilla	ENSGGOG00000013770	1 retrocopy	retro_ggor_821,
Loxodonta africana	ENSLAFG00000000744	1 retrocopy	retro_lafr_61,
Macaca mulatta	ENSMMUG00000010545	1 retrocopy	retro_mmul_155,
Mus musculus	ENSMUSG00000018567	1 retrocopy	retro_mmus_3107,
Nomascus leucogenys	ENSNLEG00000008049	2 retrocopies	retro_nleu_1670, retro_nleu_4,
Oryctolagus cuniculus	ENSOCUG00000006997	1 retrocopy	retro_ocun_311 ,
Oryctolagus cuniculus	ENSOCUG00000016834	3 retrocopies	retro_ocun_1380, retro_ocun_496, retro_ocun_697,
Oryctolagus cuniculus	ENSOCUG00000022970	4 retrocopies	retro_ocun_1155, retro_ocun_572, retro_ocun_731, retro_ocun_784,
Pongo abelii	ENSPPYG00000007901	1 retrocopy	retro_pabe_122,
Pan troglodytes	ENSPTRG00000034115	1 retrocopy	retro_ptro_60,
Rattus norvegicus	ENSRNOG00000017417	2 retrocopies	retro_rnor_1818, retro_rnor_2093,
Sus scrofa	ENSSSCG00000017936	1 retrocopy	retro_sscr_163,
Drosophila melanogaster	FBgn0052672	1 retrocopy	retro_dmel_23,