RetrogeneDB ID: retro_dnov_539

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_5917:217836..218370(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DESI2
• Ensembl ID: ENSDNOG00000003484
• Aliases: None
• Description: desumoylating isopeptidase 2 [Source:HGNC Symbol;Acc:24264]

Sequence

>retro_dnov_539
TGGGTAAATGAATGCACTTCATCCATTGGAACTGGAGTTCTTCATTCAGGAATTGAAGGATATAGCAGAGAATTTGCTTA
TGGTGGCCATCCTTACCCCTTTTCTGAATATTTGTAATTTCCCCAGGAAATGCTTCCAAACTAGGAGAAACATTTAAATT
TAAAGAAGCTGTTGTTTTGGGGAGCATTGACTTCCTAGAAGATGATCTAGAAGAAATTGTAGAACTGGGAAAAGAATACA
AAGGCAATACCTATCATTGGGTGCATGAAAACTGCAATCACTTTTCTTCAGTTTTATCAGAGATTCTTTGTGGAAAGGAG
ATTCCTCACTGGATCAATCGACTTGCCTAGGTTAGCTCCTGTATACCCTTTCTACAGAGTTGCCTCCCAAAGGAGTGGCT
TCTTTCAGCAGCCCTCCGGTCTACTGTGAGCTAAGAGCTCCAGGATGAACTGGAGGAAGTGGAGAGATGCTGCCACACCA
GCTTCCATAGCAAGTACTGCAGCAGGCTCCATACCTGGGTGTCACACTAAACTA

Alignment

ORF - retro_dnov_539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.48 %
• Parental protein coverage: 93.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WMNEYTSSIGIGVFHSGIEVYGREFAYGGHPYPFSG-IFEISPGNASELGETFKFKEAVVLGRTDFLEDD
          W.NE.TSSIG.GV.HSGIE.Y.REFAYGGHPYPFS..IF.ISPGNAS.LGETFKFKEAVVLG..DFLEDD
Retrocopy WVNECTSSIGTGVLHSGIEGYSREFAYGGHPYPFSE<IFVISPGNASKLGETFKFKEAVVLGSIDFLEDD

Parental  IEKIVEELGKEYKGNAYHLMHKNCNHFSSALSEILCGKEIPRWINRLAYFSSCIPFLQSCLPKEWLTPGA
          .E.IVE.LGKEYKGN.YH..H.NCNHFSS.LSEILCGKEIP.WINRLA..SSCIPFLQSCLPKEWL...A
Retrocopy LEEIVE-LGKEYKGNTYHWVHENCNHFSSVLSEILCGKEIPHWINRLA*VSSCIPFLQSCLPKEWLLSAA

Parental  LQSSFNQEIQEELEEA-GEAAA-SDAATSTADSRPGRHTKL
          L.S....E.Q.ELEE....AA.....A...A.S.PG.HTKL
Retrocopy LRSTVS*ELQDELEEV>RDAATPASIASTAAGSIPGCHTKL

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
SRP012922_ascending_colon	0.19 RPM	2.92 RPM
SRP012922_cerebellum	0.00 RPM	6.46 RPM
SRP012922_heart	0.00 RPM	3.02 RPM
SRP012922_kidney	0.00 RPM	1.64 RPM
SRP012922_liver	0.00 RPM	4.49 RPM
SRP012922_lung	0.00 RPM	2.75 RPM
SRP012922_quadricep_muscle	0.00 RPM	4.67 RPM
SRP012922_spleen	0.00 RPM	4.12 RPM

ChIP-Seq

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST

Dasypus novemcinctus was not studied using EST data.

TSS

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab

retro_dnov_539 was not experimentally validated.

Homology

Retrocopy orthology:

Dasypus novemcinctus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,