RetrogeneDB ID: retro_dnov_9

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_61730:9423..9900(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000018877
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000018281
• Aliases: None
• Description: None

Sequence

>retro_dnov_9
ATGTCGGACACTGCAGTAGCTGACACTCGGCGCCTTAACTCGAAGCCGCAGGACCTGACCGGCGCTTACGGGCCGCCAAG
TAACTTCCTGGAGATCGACATTTTTAATCCACAGACGGTGGGCGTGGGCCGCGCGCGCTTCACCACCTATGAGGTTCGCA
TGCGGACAAACCTACCTATCTTCAAGCTGAAGGAGTCTTGTGTGCGGCGGCGCTACAGTGATTTTGAGTGGCTAAAAAAT
GAGCTTGAGCGAGATAGTAAGATTGTAGTACCGCCACTGCCTGGGAAAGCCTTGAAGCGGCAGCTCCCTTTCCGAGGGGA
CGAAGGGATCTTTGAGGAATCCTTCATTGAAGAAAGGAGGCAGGGTCTCGAACAGTTTATTAACAAAATTGCTGGGCACC
CACTGGCTCAGAACGAACGCTGCCTACACATGTTCCTGCAGGAGGAGGCAACTGACAGGAACTATGTCCCTGGGAAG

Alignment

ORF - retro_dnov_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.26 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NLPIFKLKE-CVRR-YSDFEWLKNEXXXXXXIVVPPLPGKALKRQLPFRGDEGIFEESFIEERRQGLEQF
          NLPIFKLKE.CVRR.YSDFEWLKNE......IVVPPLPGKALKRQLPFRGDEGIFEESFIEERRQGLEQF
Retrocopy NLPIFKLKESCVRRRYSDFEWLKNELERDSKIVVPPLPGKALKRQLPFRGDEGIFEESFIEERRQGLEQF

Parental  INKIAGHPLAQNERCLHMFLQEEAIDRNYVPGK
          INKIAGHPLAQNERCLHMFLQEEA.DRNYVPGK
Retrocopy INKIAGHPLAQNERCLHMFLQEEATDRNYVPGK

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	8.17 RPM	2.33 RPM
SRP012922_cerebellum	11.96 RPM	4.26 RPM
SRP012922_heart	2.32 RPM	1.39 RPM
SRP012922_kidney	7.39 RPM	6.57 RPM
SRP012922_liver	2.48 RPM	0.00 RPM
SRP012922_lung	8.86 RPM	2.60 RPM
SRP012922_quadricep_muscle	4.33 RPM	1.38 RPM
SRP012922_spleen	8.58 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_9 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007871	1 retrocopy	retro_btau_1080,
Dasypus novemcinctus	ENSDNOG00000018281	1 retrocopy	retro_dnov_9 ,
Oryctolagus cuniculus	ENSOCUG00000014919	1 retrocopy	retro_ocun_1286,
Otolemur garnettii	ENSOGAG00000008973	1 retrocopy	retro_ogar_2565,
Rattus norvegicus	ENSRNOG00000004036	2 retrocopies	retro_rnor_1751, retro_rnor_501,
Sorex araneus	ENSSARG00000001830	1 retrocopy	retro_sara_452,