RetrogeneDB ID: retro_ggor_1562

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 21:20844633..20845129(+)
• Located in intron of: ENSGGOG00000005797

Retrocopy information

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

Parental gene information

• Parental gene symbol: EXOSC3
• Ensembl ID: ENSGGOG00000006970
• Aliases: None
• Description: None

Sequence

>retro_ggor_1562
TATATTCTAGTGAAAGGAGACCAGGTGACTGGCATAGTGACAGCTAAATCTGGAGATATATTCAGAGTTGATGTTGGAGG
GAGTGAGCCAGTTTCTTTGTCTTACTTGGCATTTGAAGGTGCAACTAAAAGAAACAGACCAAATGTGCAGGTTGGAGATC
TTATCTATGGCCAATTTGTGGTTGCTAATAAAGACATGGAACCAGAGATGGTCTGTATTGACAGCTATGGATGAGCCAAT
GGAAGGAATGTCATTGGACAGGATGGTCTGCTTTTTAAAGTGACTGGGCTTCATTAGAAAGCTGTTAGCTCTAGATCGTG
AAATCAAACAGGAAGTGGGAAAACTCTATCCACTGAAGATAGTATTTGGAATGAATGGAAGAATATGGGTTAAGGGAAAA
ACCGTCCAGCAGACTTTAATTTTGGCAAATGTTTTAGAAGCTTGTGAACACATGACATTAGATCAAAGAAAACAAATCTC
CAGATTGGCAGAAAGT

Alignment

ORF - retro_ggor_1562 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.9 %
• 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.FEGATKRNRPNVQVGDLIYGQFVVANKDMEPEM
Retrocopy YILVKGDQVTGIVTAKSGDIFRVDVGGSEPVSLSYLAFEGATKRNRPNVQVGDLIYGQFVVANKDMEPEM

Parental  VCIDSCGRANGMGVIGQDGLLFKVTLGL-IRKLLAPDCEIIQEVGKLYPLEIVFGMNGRIWVKAKTIQQT
          VCIDS.G.ANG..VIGQDGLLFKVT.GL.IRKLLA.D.EI.QEVGKLYPL.IVFGMNGRIWVK.KT.QQT
Retrocopy VCIDSYG*ANGRNVIGQDGLLFKVT-GL>IRKLLALDREIKQEVGKLYPLKIVFGMNGRIWVKGKTVQQT

Parental  LILANILEACEHMTSDQRKQIFSRLAES
          LILAN.LEACEHMT.DQRKQI.SRLAES
Retrocopy LILANVLEACEHMTLDQRKQI-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	0.05 RPM	10.98 RPM
SRP007412_cerebellum	0.12 RPM	11.31 RPM
SRP007412_heart	0.09 RPM	2.72 RPM
SRP007412_kidney	0.04 RPM	8.26 RPM
SRP007412_liver	0.03 RPM	7.41 RPM
SRP007412_testis	0.00 RPM	23.72 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1562 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1562 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2504
Pan troglodytes	retro_ptro_1455
Pongo abelii	retro_pabe_1843

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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,