RetrogeneDB ID: retro_dnov_1639

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_2520:91334..91847(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUS1
• Ensembl ID: ENSDNOG00000001780
• Aliases: None
• Description: nuclear undecaprenyl pyrophosphate synthase 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:21042]

Sequence

>retro_dnov_1639
TCCCTGGAGAAGCTGCCGGTGCACATGGGCCTGGTGATCACTGAGGAGGAGCAGGAGCCCAGCTTCTCGGACATCGCAAG
CCTTGTGGTGTGGTGTATGGCCGTGGGCATCTCCTACATTAGCGTCTACGACCACCAAGGTATTTTCAAAAGAAATAATT
CCAGATTGATGGATGAAATTTTAAAACAACAGCAGGAACTTCTTGGCTTAGATTGTTCCAAATATTCACCAGAGTTTGCA
AATAGTAATGACAAAGATGATCAAGTTTTAGATTGCCAATCTGCAGTGATGGTGCTGTCCCCAGAAGATGGAAAAGCAGA
TCTTGTGAGAGCTGCACGTGACTTTTGTCAGTTAGTAGCCCAGCAGCAAAAGAGATCCACAGATTTGGATGTGGATATGT
TAAACAGTTTACTTAGTTCACGTGGTTTCCCTGATCCTGATTTAGTACTGAAGTTTGGTCCTGTGGACAGCACATTAGGC
TTTCTTCCCTGGCATATCAGATTGACTGAGATT

Alignment

ORF - retro_dnov_1639 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.42 %
• Parental protein coverage: 65.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLEKLPVHMGLVITEEEQEPSFSDIASLVVWCMAVGISYISVYDHQGIFKRNNSRLMDEILKQQQELLGL
          SLEKLPVHMGLVITEEEQEPSFSDIASLVVWCMAVGISYISVYDHQGIFKRNNSRLMDEILKQQQELLGL
Retrocopy SLEKLPVHMGLVITEEEQEPSFSDIASLVVWCMAVGISYISVYDHQGIFKRNNSRLMDEILKQQQELLGL

Parental  DCSKYSPEFANSNDKDDQVLDCQSAVMVLSPEDGKADIVRAARDFCQLVAQQQKRSTDLDVDMLNSLLSS
          DCSKYSPEFANSNDKDDQVLDCQSAVMVLSPEDGKAD.VRAARDFCQLVAQQQKRSTDLDVDMLNSLLSS
Retrocopy DCSKYSPEFANSNDKDDQVLDCQSAVMVLSPEDGKADLVRAARDFCQLVAQQQKRSTDLDVDMLNSLLSS

Parental  RGFPDPDLVLKFGPVDSTLGFLPWHIRLTEI
          RGFPDPDLVLKFGPVDSTLGFLPWHIRLTEI
Retrocopy RGFPDPDLVLKFGPVDSTLGFLPWHIRLTEI

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	5.83 RPM	8.95 RPM
SRP012922_cerebellum	1.37 RPM	2.61 RPM
SRP012922_heart	1.16 RPM	0.70 RPM
SRP012922_kidney	4.11 RPM	3.29 RPM
SRP012922_liver	2.79 RPM	1.24 RPM
SRP012922_lung	2.14 RPM	3.36 RPM
SRP012922_quadricep_muscle	0.87 RPM	1.56 RPM
SRP012922_spleen	2.86 RPM	3.09 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_1639 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000001780	1 retrocopy	retro_dnov_1639 ,
Erinaceus europaeus	ENSEEUG00000008948	1 retrocopy	retro_eeur_443,
Homo sapiens	ENSG00000153989	4 retrocopies	retro_hsap_1174, retro_hsap_1176, retro_hsap_1289, retro_hsap_4825,
Gorilla gorilla	ENSGGOG00000022321	4 retrocopies	retro_ggor_1012, retro_ggor_914, retro_ggor_915, retro_ggor_993,
Microcebus murinus	ENSMICG00000007831	1 retrocopy	retro_mmur_423,
Nomascus leucogenys	ENSNLEG00000013457	1 retrocopy	retro_nleu_2411,
Oryctolagus cuniculus	ENSOCUG00000011553	1 retrocopy	retro_ocun_1713,
Pongo abelii	ENSPPYG00000025886	1 retrocopy	retro_pabe_81,
Pan troglodytes	ENSPTRG00000018547	1 retrocopy	retro_ptro_808,
Tarsius syrichta	ENSTSYG00000003212	1 retrocopy	retro_tsyr_633,
Tursiops truncatus	ENSTTRG00000007352	2 retrocopies	retro_ttru_358, retro_ttru_684,