RetrogeneDB ID: retro_pabe_2586

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:192772411..192772741(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GAR1
• Ensembl ID: ENSPPYG00000014996
• Aliases: None
• Description: GAR1 ribonucleoprotein homolog (yeast) [Source:HGNC Symbol;Acc:14264]

Sequence

>retro_pabe_2586
AACAAAGGCCAAAGCCAAGGACCTCCAGAACGTGTAGTCTTAATAGGAGAGTTCCTGCATCCCTGTGAAGATGACATAGT
TTGTGAACATACTACAGATGAAAATAAGGTGCCTTATTTCAATGCTCCTGTTTACTTAGAAAACAAAGAACAAATTGGGA
AAGTGGATGAAATATTTGGACAACTTAGAGATTTTTATTTTTCCGTTAAAATGTCAGAAAACGGGAAGGCTTCATCCTTT
AAAAAACTCTAGAAGTTTTATATAGACCCATATAAGCTGCTGCCACTGCAGAGGTTTTTACCTCGACCTCCAGGTGAGAA
AGGACCTCCA

Alignment

ORF - retro_pabe_2586 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.64 %
• Parental protein coverage: 50.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NKGQDQGPPERVVLLGEFLHPCEDDIVCKCTTDENKVPYFNAPVYLENKEQIGKVDEIFGQLRDFYFSVK
          NKGQ.QGPPERVVL.GEFLHPCEDDIVC..TTDENKVPYFNAPVYLENKEQIGKVDEIFGQLRDFYFSVK
Retrocopy NKGQSQGPPERVVLIGEFLHPCEDDIVCEHTTDENKVPYFNAPVYLENKEQIGKVDEIFGQLRDFYFSVK

Parental  LSENMKASSFKKLQKFYIDPYKLLPLQRFLPRPPGEKGPP
          .SEN.KASSFKKL.KFYIDPYKLLPLQRFLPRPPGEKGPP
Retrocopy MSENGKASSFKKL*KFYIDPYKLLPLQRFLPRPPGEKGPP

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	0.00 RPM	6.41 RPM
SRP007412_cerebellum	0.00 RPM	5.11 RPM
SRP007412_heart	0.00 RPM	4.37 RPM
SRP007412_kidney	0.00 RPM	7.76 RPM
SRP007412_liver	0.00 RPM	6.79 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2586 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2586 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2586 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2119

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004605	2 retrocopies	retro_amel_1932, retro_amel_682,
Homo sapiens	ENSG00000109534	1 retrocopy	retro_hsap_3130,
Gorilla gorilla	ENSGGOG00000008681	1 retrocopy	retro_ggor_2144,
Myotis lucifugus	ENSMLUG00000003776	1 retrocopy	retro_mluc_1866,
Macaca mulatta	ENSMMUG00000021225	1 retrocopy	retro_mmul_1992,
Mustela putorius furo	ENSMPUG00000008615	2 retrocopies	retro_mputfur_1491, retro_mputfur_689,
Mus musculus	ENSMUSG00000028010	1 retrocopy	retro_mmus_2012,
Nomascus leucogenys	ENSNLEG00000016578	1 retrocopy	retro_nleu_2251,
Oryctolagus cuniculus	ENSOCUG00000003901	1 retrocopy	retro_ocun_414,
Otolemur garnettii	ENSOGAG00000004693	1 retrocopy	retro_ogar_1017,
Ochotona princeps	ENSOPRG00000012089	1 retrocopy	retro_opri_1168,
Pongo abelii	ENSPPYG00000014996	1 retrocopy	retro_pabe_2586 ,
Pan troglodytes	ENSPTRG00000016364	1 retrocopy	retro_ptro_2119,
Tarsius syrichta	ENSTSYG00000013668	2 retrocopies	retro_tsyr_355, retro_tsyr_613,
Tursiops truncatus	ENSTTRG00000016318	1 retrocopy	retro_ttru_1539,