RetrogeneDB ID: retro_dnov_2390

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_70117:7303..7777(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000013707
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000009819
• Aliases: None
• Description: None

Sequence

>retro_dnov_2390
GCGAAGCCCAAGCTCCACTATCCAAACGGAAGAGGCTGGATGGAATCCATACGATGGGCTTTAGCTGCCGCTGGAGTTAA
GTTTGATGAAGAATTTTTAGAAACAAAAGAACAGTTGCTGCAGTTGCAGAATGGGAACCACCTGCTGTTCCAACAGGTGC
CAATGGTTGAAATTGACGGGATGAAGTTGGTGCAGACACGAAGCATTCTCCAGTACATAGCGGAGAAGCACCATCTCTTT
GGCAAGGACCTCAAGGAGAAAACCCTGATTGACATGTATGTGGAGGGGACCCTGAATCTGCTGGAACTGATTATCATGCA
TCCTTTCTTAAAACCAGACGATCAACAAAAGGAAGTGGTCACCATGACCCAGAAGGCTATCATTAGGTACTTTCCTGTGT
TTGAAAAGATTTTAAAGGATCATGGACAAACTTTTCTTGTTTGTAACCAGCTGAGCCTTGTGGATGTGATTCTA

Alignment

ORF - retro_dnov_2390 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.96 %
• Parental protein coverage: 87.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AKPILHYFNARGRMESIRWLLAAAGVEFEEKFIETPEDLDKLKSDGSLMFQQVPMVEIDGMKLAQTRAIL
          AKP.LHY.N.RG.MESIRW.LAAAGV.F.E.F.ET.E.L..L.....L.FQQVPMVEIDGMKL.QTR.IL
Retrocopy AKPKLHYPNGRGWMESIRWALAAAGVKFDEEFLETKEQLLQLQNGNHLLFQQVPMVEIDGMKLVQTRSIL

Parental  NYIASKYNLYGKDIKERALIDMYIEGVADLSEMILHLPLCPPEQKDDKIALIKDRTTNRYFPAFEKVLKS
          .YIA.K..L.GKD.KE..LIDMY.EG...L.E.I...P...P................RYFP.FEK.LK.
Retrocopy QYIAEKHHLFGKDLKEKTLIDMYVEGTLNLLELIIMHPFLKPDDQQKEVVTMTQKAIIRYFPVFEKILKD

Parental  HGQDYLVGNKLSRADIHL
          HGQ..LV.N.LS..D..L
Retrocopy HGQTFLVCNQLSLVDVIL

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	5.25 RPM	3.11 RPM
SRP012922_cerebellum	40.00 RPM	0.69 RPM
SRP012922_heart	14.85 RPM	0.00 RPM
SRP012922_kidney	11.77 RPM	59.96 RPM
SRP012922_liver	32.20 RPM	38.86 RPM
SRP012922_lung	5.65 RPM	0.61 RPM
SRP012922_quadricep_muscle	24.58 RPM	1.04 RPM
SRP012922_spleen	21.86 RPM	0.00 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_2390 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011287	1 retrocopy	retro_cjac_4055,
Dasypus novemcinctus	ENSDNOG00000009819	1 retrocopy	retro_dnov_2390 ,
Homo sapiens	ENSG00000182793	1 retrocopy	retro_hsap_2366,
Gorilla gorilla	ENSGGOG00000027587	1 retrocopy	retro_ggor_1797,
Microcebus murinus	ENSMICG00000002208	1 retrocopy	retro_mmur_350,
Otolemur garnettii	ENSOGAG00000003726	1 retrocopy	retro_ogar_345,
Pan troglodytes	ENSPTRG00000032453	1 retrocopy	retro_ptro_1732,
Tupaia belangeri	ENSTBEG00000001413	1 retrocopy	retro_tbel_2120,