RetrogeneDB ID: retro_ggor_2845

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 9:33654953..33655381(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAGE3
• Ensembl ID: ENSGGOG00000013507
• Aliases: None
• Description: None

Sequence

>retro_ggor_2845
ATGTGGGACGTGGATGCAGACGCAGGCGGAGGCGCCAACTGCGGGGATGGCCAGGGTGATCACAGCTGCCCCGGGGGTGC
GGACACCCCGGCAGCTCCGGCCAGCGGAGCTCCCCCACCGCACGCGTCAGGTCCTAGCAGAAACGCGGCGTCTGTGGCCA
GGGGCCAGGAATGCGGCCGCACATATTCACCCTCAGCGTGCCTTTCCCGACCCCTTTAGAGGCAGAAATTGCCCGTGGGT
CCCTGGCTCCAGATGCCGAACCCCACCAAAGGGTGGTTGGGAAGGATCTCACAGTGAGCGGCAGGATCCTGGCCGTCCGC
TGGAAAGCTGAAGACTGTCGCCTGCTCCGAATTTCCCTTATCAACTTTCTCAACCATCTTTCTCTGGTGGTGCGGACCCT
GCAGCACTTTGGGCCCCCAGTTTCCCGC

Alignment

ORF - retro_ggor_2845 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRDADADAGGGADGGDGRGGHSCRGGVDTAAAPAAGAPPAHAPGPGRDAASAARGS-GMRPHIFTLSVPF
          M.D.DADAGGGA..GDG.G.HSC.GG.DT.AAPA.GAPP.HA.GP.R.AAS.ARG..GMRPHIFTLSVPF
Retrocopy MWDVDADAGGGANCGDGQGDHSCPGGADTPAAPASGAPPPHASGPSRNAASVARGQ<GMRPHIFTLSVPF

Parental  PTPLEAEIAHGSLAPDAEPHQRVVGKDLTVSGRILVVRWKAEDCRLLRISVINFLDQLSLVVRTMQRFGP
          PTPLEAEIA.GSLAPDAEPHQRVVGKDLTVSGRIL.VRWKAEDCRLLRIS.INFL..LSLVVRT.Q.FGP
Retrocopy PTPLEAEIARGSLAPDAEPHQRVVGKDLTVSGRILAVRWKAEDCRLLRISLINFLNHLSLVVRTLQHFGP

Parental  PVSR
          PVSR
Retrocopy PVSR

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	3.21 RPM	10.12 RPM
SRP007412_cerebellum	10.13 RPM	8.00 RPM
SRP007412_heart	2.35 RPM	3.44 RPM
SRP007412_kidney	7.61 RPM	3.88 RPM
SRP007412_liver	6.07 RPM	6.36 RPM
SRP007412_testis	4.77 RPM	3.63 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_2845 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2845 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000024143	1 retrocopy	retro_dnov_244,
Dipodomys ordii	ENSDORG00000009093	1 retrocopy	retro_dord_448,
Homo sapiens	ENSG00000196976	1 retrocopy	retro_hsap_4244,
Gorilla gorilla	ENSGGOG00000013507	1 retrocopy	retro_ggor_2845 ,
Macaca mulatta	ENSMMUG00000007739	1 retrocopy	retro_mmul_1145,
Mus musculus	ENSMUSG00000015289	2 retrocopies	retro_mmus_1411, retro_mmus_1665,
Nomascus leucogenys	ENSNLEG00000014285	1 retrocopy	retro_nleu_1373,
Ochotona princeps	ENSOPRG00000003778	2 retrocopies	retro_opri_196, retro_opri_549,
Pongo abelii	ENSPPYG00000020881	1 retrocopy	retro_pabe_3394,
Rattus norvegicus	ENSRNOG00000037249	1 retrocopy	retro_rnor_595,
Sus scrofa	ENSSSCG00000025528	1 retrocopy	retro_sscr_94,