RetrogeneDB ID: retro_pabe_2786

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:143578226..143578534(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL11
• Ensembl ID: ENSPPYG00000003025
• Aliases: None
• Description: mitochondrial ribosomal protein L11 [Source:HGNC Symbol;Acc:14042]

Sequence

>retro_pabe_2786
ATGTCGAAGCTCGGCCGGGCCACCGGGGGCCTCAGGAAGCCGGAGGTCGGCGGTGTGATCCAGACCATTGTGCGGGCAGG
CCTGGCCATGCCCGGGTCCCCCCGCTAGGCCCAGTGCTGGGTCAGAGAAGGGCTTCCATCAACCAATTTTGCAAGGAGTT
CAATGCGAGGACAAAGGACATCAAGGAAGGCATTCCTCTGCTTACCAAGATTTTTGTGAAGCCTGACGGGACATTTGAAA
TCAAGATTGGACAGCCCACTGTTTCCTACTTCGTGAAGGCAGCAGCTGGGATTGAAAAGGGGGCCCGG

Alignment

ORF - retro_pabe_2786 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.54 %
• Parental protein coverage: 53.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSKLGRATRGLRKPEVGGVIRAIVRAGLAM-PGPP-LGPALGQRGVSINQFCKEFNEKTKDIKEGIPLPT
          MSKLGRAT.GLRKPEVGGVI..IVRAGLAM.PGPP.LGP.LGQR..SINQFCKEFN..TKDIKEGIPL.T
Retrocopy MSKLGRATGGLRKPEVGGVIQTIVRAGLAM>PGPP>LGPVLGQRRASINQFCKEFNARTKDIKEGIPLLT

Parental  KILVKPDRTFEIKIGQPTVSYFLKAAAGIEKGAR
          KI.VKPD.TFEIKIGQPTVSYF.KAAAGIEKGAR
Retrocopy KIFVKPDGTFEIKIGQPTVSYFVKAAAGIEKGAR

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	14.15 RPM
SRP007412_cerebellum	0.00 RPM	18.12 RPM
SRP007412_heart	0.00 RPM	14.42 RPM
SRP007412_kidney	0.00 RPM	20.52 RPM
SRP007412_liver	0.00 RPM	18.27 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2786 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2786 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2786 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3390
Pan troglodytes	retro_ptro_2305
Gorilla gorilla	retro_ggor_2296

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012706	1 retrocopy	retro_cfam_761,
Callithrix jacchus	ENSCJAG00000001470	1 retrocopy	retro_cjac_803,
Dasypus novemcinctus	ENSDNOG00000004111	2 retrocopies	retro_dnov_1607, retro_dnov_566,
Echinops telfairi	ENSETEG00000015216	2 retrocopies	retro_etel_1754, retro_etel_333,
Homo sapiens	ENSG00000174547	1 retrocopy	retro_hsap_3390,
Gorilla gorilla	ENSGGOG00000001300	1 retrocopy	retro_ggor_2296,
Myotis lucifugus	ENSMLUG00000004047	1 retrocopy	retro_mluc_2131,
Mus musculus	ENSMUSG00000024902	1 retrocopy	retro_mmus_2118,
Nomascus leucogenys	ENSNLEG00000006111	1 retrocopy	retro_nleu_1705,
Otolemur garnettii	ENSOGAG00000010448	2 retrocopies	retro_ogar_1143, retro_ogar_3159,
Pongo abelii	ENSPPYG00000003025	1 retrocopy	retro_pabe_2786 ,
Pan troglodytes	ENSPTRG00000003924	1 retrocopy	retro_ptro_2305,
Ictidomys tridecemlineatus	ENSSTOG00000025971	1 retrocopy	retro_itri_941,
Tarsius syrichta	ENSTSYG00000008712	1 retrocopy	retro_tsyr_1095,
Tursiops truncatus	ENSTTRG00000002678	1 retrocopy	retro_ttru_431,