RetrogeneDB ID: retro_ptro_1384

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 19:62359288..62359609(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DESI2
• Ensembl ID: ENSPTRG00000002180
• Aliases: None
• Description: desumoylating isopeptidase 2 [Source:HGNC Symbol;Acc:24264]

Sequence

>retro_ptro_1384
TATGACACGTATTGGATGAAGGAATATACCTCATCCATTGGAATTGGAGTTTTTCATTCAGAAATTGAAGTCTATGGCAG
AGAATTTGCTTATGGTGGCCATCCTTACCCCTTTTCTGGAATATTTGAAATTTCCCCAGGAAATGCTTCTGAACTAGGAG
AAACATTTAAATTTAAAGAAGTTGTTGTTTTAGGGAGCACGGACTTCCTAGAAGATGATATAGAAAAAATTGTAGAAGAA
CTGGGAAAAGAATACAAAGGCAATGTTTATCATTTAATGTATAAAAACTGCAATCATTTTTCTTCAGCTTTATCAGAGGT
A

Alignment

ORF - retro_ptro_1384 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.59 %
• Parental protein coverage: 58.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FSQYWMNEYTSSIGIGVFHSGIEVYGREFAYGGHPYPFSGIFEISPGNASELGETFKFKEAVVLGSTDFL
          ...YWM.EYTSSIGIGVFHS.IEVYGREFAYGGHPYPFSGIFEISPGNASELGETFKFKE.VVLGSTDFL
Retrocopy YDTYWMKEYTSSIGIGVFHSEIEVYGREFAYGGHPYPFSGIFEISPGNASELGETFKFKEVVVLGSTDFL

Parental  EDDIEKIVEELGKEYKGNAYHLMHKNCNHFSSALSEI
          EDDIEKIVEELGKEYKGN.YHLM.KNCNHFSSALSE.
Retrocopy EDDIEKIVEELGKEYKGNVYHLMYKNCNHFSSALSEV

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	0.09 RPM	0.52 RPM
SRP007412_cerebellum	0.65 RPM	2.62 RPM
SRP007412_heart	0.44 RPM	2.59 RPM
SRP007412_kidney	0.16 RPM	1.46 RPM
SRP007412_liver	0.20 RPM	0.88 RPM
SRP007412_testis	8.01 RPM	25.71 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1384 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1384 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1384 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1493

---

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,