RetrogeneDB ID: retro_ggor_1493

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 19:54885579..54885921(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPPDE1
• Ensembl ID: ENSGGOG00000009797
• Aliases: None
• Description: None

Sequence

>retro_ggor_1493
CAGTTAGTGGTGCTCAACGTGTATGACATGTATTGGATGAAGGAATATACCTCATCCATTGGAATTGGAGTTTTTCATTC
AGAAATTGAAGTCTATGGCAGAGAATTTGCTTATGGTGGCCATCCTTACCCCTTTTCTGGAATATTTGAAATTTCCCCAG
GAAATGCTTCTGAACTAGGAGAAACATTTAAATTTAAAGAAGTTGTTGTTTTAGGGAGCACGGACTTCCTAGAAGATGAT
ATAGAAAAAATTGTAGAAGAACTGGGAAAAGAATACAAAGGCAATGTTTACCATTTAATGCATAAAAACTGCAATCATTT
TTCTTCAGCTTTATCAGAGGTA

Alignment

ORF - retro_ggor_1493 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.57 %
• Parental protein coverage: 58.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QLKVCNTFECYYWMNEYTSSIGIGVFHSGIEVYGREFAYGGHPYPFSGIFEISPGNASELGETFKFKEAV
          QL.V.N....Y.WM.EYTSSIGIGVFHS.IEVYGREFAYGGHPYPFSGIFEISPGNASELGETFKFKE.V
Retrocopy QLVVLNVYDMY-WMKEYTSSIGIGVFHSEIEVYGREFAYGGHPYPFSGIFEISPGNASELGETFKFKEVV

Parental  VLGSTDFLEDDIEKIVEELGKEYKGNAYHLMHKNCNHFSSALSEI
          VLGSTDFLEDDIEKIVEELGKEYKGN.YHLMHKNCNHFSSALSE.
Retrocopy VLGSTDFLEDDIEKIVEELGKEYKGNVYHLMHKNCNHFSSALSEV

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	0.19 RPM	5.27 RPM
SRP007412_cerebellum	0.55 RPM	14.03 RPM
SRP007412_heart	0.13 RPM	4.66 RPM
SRP007412_kidney	0.04 RPM	12.39 RPM
SRP007412_liver	0.18 RPM	14.22 RPM
SRP007412_testis	5.08 RPM	148.35 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_1493 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1493 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1384

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000016	1 retrocopy	retro_chof_2439,
Dasypus novemcinctus	ENSDNOG00000003484	3 retrocopies	retro_dnov_1042, retro_dnov_2533, retro_dnov_539,
Erinaceus europaeus	ENSEEUG00000009507	2 retrocopies	retro_eeur_394, retro_eeur_470,
Homo sapiens	ENSG00000121644	1 retrocopy	retro_hsap_2071,
Gorilla gorilla	ENSGGOG00000009797	1 retrocopy	retro_ggor_1493 ,
Nomascus leucogenys	ENSNLEG00000004019	1 retrocopy	retro_nleu_2734,
Ochotona princeps	ENSOPRG00000015368	2 retrocopies	retro_opri_1007, retro_opri_963,
Pongo abelii	ENSPPYG00000000055	1 retrocopy	retro_pabe_1685,
Pan troglodytes	ENSPTRG00000002180	1 retrocopy	retro_ptro_1384,
Sus scrofa	ENSSSCG00000010876	1 retrocopy	retro_sscr_388,
Drosophila melanogaster	FBgn0033551	1 retrocopy	retro_dmel_30,