RetrogeneDB ID: retro_dnov_1666

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_25996:1063..1277(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000025130
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000005868
• Aliases: None
• Description: None

Sequence

>retro_dnov_1666
GCATCCGCCACTGCCATGGGAGTGAAGATGGATACCATCTCCCCCTGGAGACGGGCGCACCTTTCCCAAGTGCGGCCAGA
CCTGCGTGGTGCACTACACGGGGATGCTTGAAGATGGAAAGAAATTTGATTCCTCTCAGGACAGAAACAAGCCCTTTAAA
TTTACACTAGGCAAGCAGGAGGTGATCCGAGGCTGGGAAGAAGGGGTTGCCCAG

Alignment

ORF - retro_dnov_1666 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.28 %
• Parental protein coverage: 73.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ASAAAMGVQVETISP-GDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFTLGKQEVIRGWEEGV
          ASA.AMGV...TISP.GDGRTFPK.GQTCVVHYTGMLEDGKKFDSS.DRNKPFKFTLGKQEVIRGWEEGV
Retrocopy ASATAMGVKMDTISP>GDGRTFPKCGQTCVVHYTGMLEDGKKFDSSQDRNKPFKFTLGKQEVIRGWEEGV

Parental  AQ
          AQ
Retrocopy AQ

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	24.31 RPM	31.89 RPM
SRP012922_cerebellum	10.31 RPM	14.57 RPM
SRP012922_heart	8.82 RPM	10.67 RPM
SRP012922_kidney	14.24 RPM	12.32 RPM
SRP012922_liver	7.28 RPM	11.15 RPM
SRP012922_lung	26.88 RPM	27.49 RPM
SRP012922_quadricep_muscle	10.39 RPM	10.56 RPM
SRP012922_spleen	31.48 RPM	38.92 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_1666 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 15 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008303	4 retrocopies	retro_btau_1220, retro_btau_1265, retro_btau_128, retro_btau_1760,
Ciona savignyi	ENSCSAVG00000006859	1 retrocopy	retro_csav_11,
Dasypus novemcinctus	ENSDNOG00000004678	1 retrocopy	retro_dnov_1280,
Dasypus novemcinctus	ENSDNOG00000005868	16 retrocopies	retro_dnov_1289, retro_dnov_1577, retro_dnov_1666 , retro_dnov_2236, retro_dnov_228, retro_dnov_2404, retro_dnov_2418, retro_dnov_2544, retro_dnov_2589, retro_dnov_263, retro_dnov_584, retro_dnov_621, retro_dnov_670, retro_dnov_684, retro_dnov_707, retro_dnov_937,
Dasypus novemcinctus	ENSDNOG00000011244	1 retrocopy	retro_dnov_894,
Homo sapiens	ENSG00000088832	1 retrocopy	retro_hsap_1198,
Gorilla gorilla	ENSGGOG00000001729	3 retrocopies	retro_ggor_1494, retro_ggor_2344, retro_ggor_933,
Macaca mulatta	ENSMMUG00000015996	1 retrocopy	retro_mmul_10,
Monodelphis domestica	ENSMODG00000019554	2 retrocopies	retro_mdom_151, retro_mdom_733,
Mus musculus	ENSMUSG00000032966	1 retrocopy	retro_mmus_1293,
Procavia capensis	ENSPCAG00000008816	2 retrocopies	retro_pcap_289, retro_pcap_37,
Rattus norvegicus	ENSRNOG00000008822	1 retrocopy	retro_rnor_453,
Sus scrofa	ENSSSCG00000007188	1 retrocopy	retro_sscr_98,
Tursiops truncatus	ENSTTRG00000003547	3 retrocopies	retro_ttru_1227, retro_ttru_802, retro_ttru_904,
Vicugna pacos	ENSVPAG00000011511	1 retrocopy	retro_vpac_171,