RetrogeneDB ID: retro_dnov_2675

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_97333:4189..4763(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DERL3
• Ensembl ID: ENSDNOG00000011041
• Aliases: None
• Description: derlin 3 [Source:HGNC Symbol;Acc:14236]

Sequence

>retro_dnov_2675
GAGTACCTGCAGATTGCACCAGTCAGCCATGCCTATACCACCACCTACATCCTCACTACCACCACTGTGCAGTTAGAATT
GATCACACCTTTTCAGTTACACTTCAATCCTGAATCAATCTTTAAACACTTTCAAATATGGAGATTAATCACTAATTTCT
TATTCTTTAGGCCAGTTGGATTCAATTTTTAATTCTAATATGATTTTTCTATATTATTACTGTCAAATGCCAGAAGAAGG
CTCTTTCCAAGGTCAAACAGCAGACTTTGTGTTTTTGTTCCTTTTTGGTGGATTCCTAATGACCCTTTATGATTTGTTTG
TGAGTTTAGTTTTCTTGGGTCAGACCTTTACAATAATGCTTGCACATGTGGATCTAAAGGCACCCATAAATCCACATGAA
CTTCTTCGGCCTTCTCAACTCACAAGCCCTCTTCTGCCCTGGGTACTCATGAGCTTTTCCTTATTATTGGGGAACTCAAT
GTGGACCTCTTGGGTATTGAAGTTGGGTACAAATATTTTTTGTTGGAAGATGTATTTCCCAAGTCAATCTGGTAGAATAA
GAATTCTGAAAACA

Alignment

ORF - retro_dnov_2675 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.29 %
• Parental protein coverage: 97.97 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  EFLQVPAVTRVYTAACVLTTAAVQLELLSPFQLYFNPHLVFRKFQIWRLITNFLFFGPLGFSFFF-NMLF
          E.LQ...V...YT....LTT..VQLEL..PFQL.FNP...F..FQIWRLITNFLFF.P.GF.F.F.NM.F
Retrocopy EYLQIAPVSHAYTTTYILTTTTVQLELITPFQLHFNPESIFKHFQIWRLITNFLFFRPVGFNF*F>NMIF

Parental  VFRYCRMLEEGSFRGRTADFVFMFLFGGFLMILLGFLGSLF-FLGQAL-MAMLVYVWSRRSPQIRVNFFG
          ...YC.M.EEGSF.G.TADFVF.FLFGGFLM.L.....SL..FLG..L........W..R.P.I..NFFG
Retrocopy LYYYCQMPEEGSFQGQTADFVFLFLFGGFLMTLYDLFVSLV<FLGSDL<LQ*CLHMWI*RHP*IHMNFFG

Parental  LLTFQA-PFLPWALMGFSM-LLGNSILVDLLGIAVGHIYYFLEDV-FPNQPGGKRLLLT
          LL..QA.P.LPW.LM.FS....G....VDLLGI.VG..Y..LEDV.FP.Q.G..R.L.T
Retrocopy LLNSQA<PLLPWVLMSFSL<IIGE-LNVDLLGIEVGYKYFLLEDV>FPSQSGRIRILKT

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	9.14 RPM
SRP012922_cerebellum	0.00 RPM	0.27 RPM
SRP012922_heart	0.00 RPM	0.00 RPM
SRP012922_kidney	0.00 RPM	0.55 RPM
SRP012922_liver	0.00 RPM	0.62 RPM
SRP012922_lung	0.00 RPM	5.65 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.17 RPM
SRP012922_spleen	0.00 RPM	57.00 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_2675 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000011041	2 retrocopies	retro_dnov_2070, retro_dnov_2675 ,
Sus scrofa	ENSSSCG00000010069	1 retrocopy	retro_sscr_865,