RetrogeneDB ID: retro_dnov_5

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_160872:62..695(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000005974
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000006037
• Aliases: None
• Description: None

Sequence

>retro_dnov_5
TACAATGTCTCTTTGCTTTATGACCTTGAAAATCTCCCTGCATCCAAGGATTCAATTGTACATCAGGCTGGCATGTTGAA
ACGAAATTGTTTTGCCTCTGTCTTTGAGAAGTACTTCCAATTTCAAGAAGAGGGCAAGGAAGGCGAGAACAGGGCAGTTA
TCCATTATAGGGATGATGAAACCATGTATGTTGAGTCCAAAAAGGACAGAGTCACAGTAGTCTTCAGCACAGTGTTTAAA
GATGATGACGATGTGGTCATTGGAAAAGTGTTTATGCAGAAGTTCAAAGAAGGACGCAGAGCCAGCCACACAGCCCCACA
GGTCCTCTTCAGCCACAGGGAACCGCCTCTGGAGCTGAAAGACACACATGCTGCCGTGGGCGACAATATTGGCTATATTA
CCTTTGTGCTGTTCCCTCGCCACACCAACGCCAGTGCCCGAGACAACACCATCAACCTGATCCACACCTTTAGAGACTAC
CTGCACTACCATATCAAGTGCTCAAAGGCCTATATTCACACACGTATGCGGGCAAAAACATCTGACTTCCTTAAGGTGCT
GAACCGTGCACGCCCGGATGCTGAGAAAAAAGAAATGAAAACAATCACGGGGAAGACGTTTTCATCCCGCTAA

Alignment

ORF - retro_dnov_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.58 %
• Parental protein coverage: 67.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YNVSLLYDLENLPASKDSIVHQAGMLKRNCFASVFEKYFQFQEEGKEGENRAVIHYRDDETMYVESKKDR
          YNVSLLYDLENLPASKDSIVHQAGMLKRNCFASVFEKYFQFQEEGKEGENRAVIHYRDDETMYVESKKDR
Retrocopy YNVSLLYDLENLPASKDSIVHQAGMLKRNCFASVFEKYFQFQEEGKEGENRAVIHYRDDETMYVESKKDR

Parental  VTVVFSTVFKDDDDVVIGKVFMQEFKEGRRVSHTAPQVLFSHREPPLELKDTDAAVGDXXXXXXXXLFPR
          VTVVFSTVFKDDDDVVIGKVFMQ.FKEGRR.SHTAPQVLFSHREPPLELKDT.AAVGD........LFPR
Retrocopy VTVVFSTVFKDDDDVVIGKVFMQKFKEGRRASHTAPQVLFSHREPPLELKDTHAAVGDNIGYITFVLFPR

Parental  HTNASARDNTINLIHTFRDYLHYHIKCSKAYIHTRMRAKTSDFLKVLNRARPDAEKKEMKTIT
          HTNASARDNTINLIHTFRDYLHYHIKCSKAYIHTRMRAKTSDFLKVLNRARPDAEKKEMKTIT
Retrocopy HTNASARDNTINLIHTFRDYLHYHIKCSKAYIHTRMRAKTSDFLKVLNRARPDAEKKEMKTIT

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	123.68 RPM	84.01 RPM
SRP012922_cerebellum	44.13 RPM	27.63 RPM
SRP012922_heart	28.08 RPM	21.11 RPM
SRP012922_kidney	68.72 RPM	39.70 RPM
SRP012922_liver	28.79 RPM	24.00 RPM
SRP012922_lung	67.66 RPM	52.08 RPM
SRP012922_quadricep_muscle	28.56 RPM	19.56 RPM
SRP012922_spleen	115.03 RPM	89.62 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_5 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 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003197	2 retrocopies	retro_amel_1771, retro_amel_1846,
Canis familiaris	ENSCAFG00000014618	1 retrocopy	retro_cfam_513,
Choloepus hoffmanni	ENSCHOG00000010564	5 retrocopies	retro_chof_1845, retro_chof_2103, retro_chof_2226, retro_chof_2227, retro_chof_473,
Dasypus novemcinctus	ENSDNOG00000006037	1 retrocopy	retro_dnov_5 ,
Dipodomys ordii	ENSDORG00000016107	1 retrocopy	retro_dord_624,
Felis catus	ENSFCAG00000002370	1 retrocopy	retro_fcat_732,
Loxodonta africana	ENSLAFG00000007414	1 retrocopy	retro_lafr_593,
Myotis lucifugus	ENSMLUG00000004161	1 retrocopy	retro_mluc_390,
Mustela putorius furo	ENSMPUG00000016512	1 retrocopy	retro_mputfur_1294,
Mus musculus	ENSMUSG00000006304	1 retrocopy	retro_mmus_1556,
Oryctolagus cuniculus	ENSOCUG00000005516	1 retrocopy	retro_ocun_483,
Pteropus vampyrus	ENSPVAG00000017133	1 retrocopy	retro_pvam_1216,
Sorex araneus	ENSSARG00000003326	1 retrocopy	retro_sara_283,
Tarsius syrichta	ENSTSYG00000001037	1 retrocopy	retro_tsyr_557,