RetrogeneDB ID: retro_pabe_122

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:87032093..87032435(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000006780
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: GABARAP
• Ensembl ID: ENSPPYG00000007901
• Aliases: None
• Description: GABA(A) receptor-associated protein [Source:HGNC Symbol;Acc:4067]

Sequence

>retro_pabe_122
TACAAGGAGGTCCATCCCTCTGAGTATCGGAAAAGGGAAGGAGAAAAGATCCGGAAGAAATACCCGGACAGGATCCCCGT
GATTGTAGAGAAGGCTCCAAAAGCCAGGGTGCCTCATCTGGACAAGAGGAAGTACCTAGTGCCCTCCGACCTTACCGATG
GCCAGTTCTACTTCTTAATCCGGAAGAGAATCCACCTGAGACCTGAGGACGCCTTATTCTTCTTTGTCAACAACACTATC
CCTCCCACTAGTGCCACCATGGGCCAACTGTATGAGGACAGTCATGAGGAAGATGATTTTCTGTATGTGGCCTACAGTAA
TGAGAGTATCCATGGGAAATGA

Alignment

ORF - retro_pabe_122 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.25 %
• Parental protein coverage: 95.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YKEEHPFEKRRSEGEKIRKKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHLRAED
          YKE.HP.E.R..EGEKIRKKYPDR.PVIVEKAPKAR...LDK.KYLVPSDLT.GQFYFLIRKRIHLR.ED
Retrocopy YKEVHPSEYRKREGEKIRKKYPDRIPVIVEKAPKARVPHLDKRKYLVPSDLTDGQFYFLIRKRIHLRPED

Parental  ALFFFVNNVIPPTSATMGQLYQEHHEEDFFLYIAYSDESVYG
          ALFFFVNN.IPPTSATMGQLY...HEED.FLY.AYS.ES..G
Retrocopy ALFFFVNNTIPPTSATMGQLYEDSHEEDDFLYVAYSNESIHG

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
SRP007412_brain_prefrontal_cortex	24.00 RPM	160.12 RPM
SRP007412_cerebellum	9.12 RPM	95.34 RPM
SRP007412_heart	3.85 RPM	52.32 RPM
SRP007412_kidney	12.43 RPM	162.75 RPM
SRP007412_liver	6.76 RPM	124.21 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_122 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_122 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_122 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_2235

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 25 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	ENSPPYG00000007565	2 retrocopies	retro_pabe_3368, retro_pabe_372,
Pongo abelii	ENSPPYG00000007628	7 retrocopies	retro_pabe_1280, retro_pabe_1566, retro_pabe_245, retro_pabe_3157, retro_pabe_3158, retro_pabe_940, retro_pabe_978,
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,