RetrogeneDB ID: retro_pabe_1685

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 19:59360086..59360398(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DESI2
• Ensembl ID: ENSPPYG00000000055
• Aliases: DESI2, DeSI-2, FAM152A, PPPDE1
• Description: Desumoylating isopeptidase 2 [Source:UniProtKB/Swiss-Prot;Acc:Q5R456]

Sequence

>retro_pabe_1685
TATTGGATGAACGAATATACCTCATCCATTGGAACTGGAGTTTTTCATTCAGGAATTGAAGTCTATGGCAGAGAATTTGC
TTATGGTGGCCGTCCTTACCCCTTTTCTGGAATATTTGAAATTTCCCCAGGAAATGCTTCTGAACTAGGAGAAACATTTA
AATTTAAAGAAGTTGTTGTTTTAGGGAGCACGGACTTCCTAGAAGATGATATAGAAAAAATTTTAGAAGAACTGGGAAAA
GAATACAAAGGCAATGTTTATCATTTAATGCATAAAAACTGCAATCATTTTTCTTCAGCTTTATCAGAGGTA

Alignment

ORF - retro_pabe_1685 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.23 %
• Parental protein coverage: 57.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YWMNEYTSSIGIGVFHSGIEVYGREFAYGGHPYPFSGIFEISPGNASELGETFKFKEAVVLGSTDFLEDD
          YWMNEYTSSIG.GVFHSGIEVYGREFAYGG.PYPFSGIFEISPGNASELGETFKFKE.VVLGSTDFLEDD
Retrocopy YWMNEYTSSIGTGVFHSGIEVYGREFAYGGRPYPFSGIFEISPGNASELGETFKFKEVVVLGSTDFLEDD

Parental  IEKIVEELGKEYKGNAYHLMHKNCNHFSSALSEI
          IEKI.EELGKEYKGN.YHLMHKNCNHFSSALSE.
Retrocopy IEKILEELGKEYKGNVYHLMHKNCNHFSSALSEV

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	6.25 RPM
SRP007412_cerebellum	0.12 RPM	25.17 RPM
SRP007412_heart	0.12 RPM	11.44 RPM
SRP007412_kidney	0.20 RPM	7.42 RPM
SRP007412_liver	0.09 RPM	6.82 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1685 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1685 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1685 has 0 orthologous retrocopies within eutheria group .

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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,