RetrogeneDB ID: retro_rnor_2093

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:190528383..190528731(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gabarap
• Ensembl ID: ENSRNOG00000017417
• Aliases: None
• Description: Gamma-aminobutyric acid receptor-associated protein [Source:UniProtKB/Swiss-Prot;Acc:P60517]

Sequence

>retro_rnor_2093
ATGAAGTTTGTGTACAAAGAAGAGCATCCGTGAGAGAAGCACCGCTCTGGGGGCGAGAAAATCCGAAAGAAATACCCAGA
CCGGGTCCCGGGATAGTGAAAAAGCTCCCAAAGCTTGGATAGGGGACCTGGACAAAAAGAAATACTGGTGCCTTCTGATC
TTACAGTTGGTCAATTCTACTTCTTGATCCAGAAGCGAATTCATCTCCGTGCTGAAGATGCCTTGTTTTTCTTTGTCAAC
AATGTCATTCCACCCACTAGTGCCATGATGGGTCAGCTGTACCAGGAACACCGTGAAGAAGACTTCTTCCTATACATTGC
CTACAGTGATGAAAGTGTCTGGTCTGTG

Alignment

ORF - retro_rnor_2093 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.33 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MKFVYKEEHPFEKRRSEGEKIRKKYPDRV-PVIV-EKAPKARIGDLDKKKY-LVPSDLTVGQFYFLIRKR
          MKFVYKEEHP.EK.RS.GEKIRKKYPDRV.P.IV.EKAPKA.IGDLDKKKY.LVPSDLTVGQFYFLI.KR
Retrocopy MKFVYKEEHP*EKHRSGGEKIRKKYPDRV<PGIV<EKAPKAWIGDLDKKKY<LVPSDLTVGQFYFLIQKR

Parental  IHLRAEDALFFFVNNVIPPTSATMGQLYQEHHEEDFFLYIAYSDESVYGL
          IHLRAEDALFFFVNNVIPPTSA.MGQLYQEH.EEDFFLYIAYSDESV...
Retrocopy IHLRAEDALFFFVNNVIPPTSAMMGQLYQEHREEDFFLYIAYSDESVWSV

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	74.84 RPM
SRP017611_kidney	0.00 RPM	190.92 RPM
SRP017611_liver	0.00 RPM	96.69 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2093 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2093 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2093 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 22 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,
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 ,
Rattus norvegicus	ENSRNOG00000017905	5 retrocopies	retro_rnor_1240, retro_rnor_1739, retro_rnor_1865, retro_rnor_1868, retro_rnor_2033,
Rattus norvegicus	ENSRNOG00000019425	1 retrocopy	retro_rnor_57,
Sus scrofa	ENSSSCG00000017936	1 retrocopy	retro_sscr_163,
Drosophila melanogaster	FBgn0052672	1 retrocopy	retro_dmel_23,