RetrogeneDB ID: retro_pabe_1843

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 21:33446457..33446953(+)
• Located in intron of: ENSPPYG00000011361

Retrocopy information

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

Parental gene information

• Parental gene symbol: EXOSC3
• Ensembl ID: ENSPPYG00000019055
• Aliases: None
• Description: exosome component 3 [Source:HGNC Symbol;Acc:17944]

Sequence

>retro_pabe_1843
TATATTCTAGTGAAAGGAGACCAGGTGACTGGCATAGTGACAGCTAAATCTGGAGATATATTCAGAGTTGATGTTGGAGG
GAGTGAGCCAGTTTCTTTGTCTTACTTGGCATTTGAAGGTGCAACTAAAAGAAACAGACCAAATGTGCAGGTTGGAGATC
TCATCTATGGCCAATTTGTGTTTGCTAATAAAGACATGGAACCAAAGATGGTCTGTATTGACAGCTATGGATGAGCCAAT
GGAAGGAATGTCATTGGACAGGATGGTCTGCTTTTTAAAGTGACTGGGCTTCATTAGAAAGCTGTTAGCTCCAGATCGTG
AAATCAAACAGGAAGTAGGAAAACTCTATCCACTGAAGATAGTATTTGGAATGAATGGAAGAATATGGGTTAAGGGAAAA
ACCATCCAGCAGACTTTAATTTTGGCAAATATTTTAGAAGCTTGTGAACACATGACATTAGATCAAAGAAAACAAATCTC
CAGATTGGCAGAAAGT

Alignment

ORF - retro_pabe_1843 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 60.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANKDMEPEM
          Y..VKGD.V.GIVTAKSGDIF.VDVGGSEP.SLSYL.FEGATKRNRPNVQVGDLIYGQFV.ANKDMEP.M
Retrocopy YILVKGDQVTGIVTAKSGDIFRVDVGGSEPVSLSYLAFEGATKRNRPNVQVGDLIYGQFVFANKDMEPKM

Parental  VCIDSCGRANGMGVIGQDGLLFKVTLGL-IRKLLAPDCEIIQEVGKLYPLEIVFGMNGRIWVKAKTIQQT
          VCIDS.G.ANG..VIGQDGLLFKVT.GL.IRKLLAPD.EI.QEVGKLYPL.IVFGMNGRIWVK.KTIQQT
Retrocopy VCIDSYG*ANGRNVIGQDGLLFKVT-GL>IRKLLAPDREIKQEVGKLYPLKIVFGMNGRIWVKGKTIQQT

Parental  LILANILEACEHMTSDQRKQIFSRLAES
          LILANILEACEHMT.DQRKQI.SRLAES
Retrocopy LILANILEACEHMTLDQRKQI-SRLAES

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	0.28 RPM	3.70 RPM
SRP007412_cerebellum	0.73 RPM	2.92 RPM
SRP007412_heart	0.06 RPM	2.68 RPM
SRP007412_kidney	0.13 RPM	4.54 RPM
SRP007412_liver	0.03 RPM	4.38 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1843 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1843 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1843 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2504
Pan troglodytes	retro_ptro_1455
Gorilla gorilla	retro_ggor_1562

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000107371	1 retrocopy	retro_hsap_2504,
Gorilla gorilla	ENSGGOG00000006970	1 retrocopy	retro_ggor_1562,
Nomascus leucogenys	ENSNLEG00000003529	1 retrocopy	retro_nleu_1434,
Ornithorhynchus anatinus	ENSOANG00000000886	1 retrocopy	retro_oana_13,
Pongo abelii	ENSPPYG00000019055	1 retrocopy	retro_pabe_1843 ,
Pan troglodytes	ENSPTRG00000020952	1 retrocopy	retro_ptro_1455,