RetrogeneDB ID: retro_dnov_275

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_322:164107..164385(+)
• Located in intron of: ENSDNOG00000023882

Retrocopy information

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

Parental gene information

• Parental gene symbol: BLOC1S6
• Ensembl ID: ENSDNOG00000019785
• Aliases: None
• Description: biogenesis of lysosomal organelles complex-1, subunit 6, pallidin [Source:HGNC Symbol;Acc:8549]

Sequence

>retro_dnov_275
CCTGACAGCCTGGGGATGGGGAAGACACTGCCAGGTTTAAGTGACACTTCTACAGATGAAAGATTAATAGAGGACTTGAT
GTAGAAGACAAAACTGTAGAGCAACTGGCAGAAGGATTGCTTTCTCACCATTTGCCAGATCTGCAGGGATCAAAACAAGT
CCTCGAGGAACTCACACAGAACCAGGTTGTATTATTAGACACACTGGAATGAGAGATTTCAGAATTTGAAGAATGCCATT
CTATGTTGGATAGTAATACTTTATTTGCTGAAGCTAAG

Alignment

ORF - retro_dnov_275 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.53 %
• Parental protein coverage: 53.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PDGLGTGKTLPGLNDTSPDEGLVEDLT-VEDKAVEQLAEGLLSHYLPDLQRSKQALQELTQNQVVLLDTL
          PD.LG.GKTLPGL.DTS.DE.L.EDL..VEDK.VEQLAEGLLSH.LPDLQ.SKQ.L.ELTQNQVVLLDTL
Retrocopy PDSLGMGKTLPGLSDTSTDERLIEDLM<VEDKTVEQLAEGLLSHHLPDLQGSKQVLEELTQNQVVLLDTL

Parental  RQEISKFKECHSM-DXXXXFTEAK
          ..EIS.F.ECHSM.D....F.EAK
Retrocopy E*EISEFEECHSMLDSNTLFAEAK

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	26.84 RPM
SRP012922_cerebellum	0.14 RPM	7.70 RPM
SRP012922_heart	0.00 RPM	4.41 RPM
SRP012922_kidney	0.00 RPM	4.38 RPM
SRP012922_liver	0.00 RPM	4.80 RPM
SRP012922_lung	0.00 RPM	16.04 RPM
SRP012922_quadricep_muscle	0.00 RPM	5.02 RPM
SRP012922_spleen	0.23 RPM	17.51 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_275 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 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012059	7 retrocopies	retro_chof_1342, retro_chof_20, retro_chof_2054, retro_chof_2102, retro_chof_211, retro_chof_248, retro_chof_600,
Dasypus novemcinctus	ENSDNOG00000019785	5 retrocopies	retro_dnov_1687, retro_dnov_1885, retro_dnov_2009, retro_dnov_2411, retro_dnov_275 ,
Echinops telfairi	ENSETEG00000007378	1 retrocopy	retro_etel_404,
Gorilla gorilla	ENSGGOG00000013892	1 retrocopy	retro_ggor_2983,
Macropus eugenii	ENSMEUG00000012636	1 retrocopy	retro_meug_778,
Microcebus murinus	ENSMICG00000005595	1 retrocopy	retro_mmur_1610,
Monodelphis domestica	ENSMODG00000017628	2 retrocopies	retro_mdom_1673, retro_mdom_561,
Oryctolagus cuniculus	ENSOCUG00000017351	1 retrocopy	retro_ocun_1575,
Otolemur garnettii	ENSOGAG00000013706	1 retrocopy	retro_ogar_206,
Ochotona princeps	ENSOPRG00000007310	1 retrocopy	retro_opri_574,
Pan troglodytes	ENSPTRG00000007038	1 retrocopy	retro_ptro_2949,