RetrogeneDB ID: retro_dnov_420

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_4544:178212..178558(+)
• Located in intron of: ENSDNOG00000006938

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000017624
• Aliases: None
• Description: None

Sequence

>retro_dnov_420
GAAGTACAGAATGTGTTAGAAAGATTTCGAACTGACATTAAACAAGGCTCTTCTTGCAAAGAGAAAAAGATTGGAAATGT
TTACCAAGGCTTCTCTCAAAACCAGTAACCAGAAAATTGGACATGTTTGGAAAGCACAACAAGAGCAAAGGCAAAACTTA
ACCAAGAATATTCTCAGCAGTTTCTGACTCTGTTTCAGCAGTGGGATACAGATGTGCAGAAAGCTGAGGAACAAAAAGAA
AATTGGCTAGTACGTTCTGACAGCAAACAAAAGGTTTTTCAATAATCTAGAATTGTTTAGAGGTAGAGAATGAAAATAAT
GAAGCAGGTTGTGTGAGCAGTTCCTA

Alignment

ORF - retro_dnov_420 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.17 %
• Parental protein coverage: 62.16 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  EVHNMLERFGADI-NKTLLAKRKRLEVYTKASLKTSNQKIEHFWKVQQEQRQ-KLNQEYSQQFLTLFQQW
          EV.N.LERF..DI.NK.LLAKRKRLE..TKASLKTSNQKI.H.WK.QQEQRQ.KLNQEYSQQFLTLFQQW
Retrocopy EVQNVLERFRTDI>NKALLAKRKRLEMFTKASLKTSNQKIGHVWKAQQEQRQ<KLNQEYSQQFLTLFQQW

Parental  EVDVQKAEEQEE-KLANIFRQQ-QKIFQQSRIVQSQRLKAIKQ-LYEQFV
          ..DVQKAEEQ.E.KLA..F.QQ.QK.FQ.SRIV...R.K..KQ.L.EQF.
Retrocopy DTDVQKAEEQKE<KLASTF*QQ>QKVFQ*SRIV*R*RMKIMKQ>LCEQFL

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	0.00 RPM	1.36 RPM
SRP012922_cerebellum	0.00 RPM	13.06 RPM
SRP012922_heart	0.00 RPM	0.70 RPM
SRP012922_kidney	0.00 RPM	0.55 RPM
SRP012922_liver	0.00 RPM	0.00 RPM
SRP012922_lung	0.00 RPM	1.83 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.00 RPM
SRP012922_spleen	0.00 RPM	2.75 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_420 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 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013389	2 retrocopies	retro_chof_1384, retro_chof_2693,
Callithrix jacchus	ENSCJAG00000001658	1 retrocopy	retro_cjac_2710,
Cavia porcellus	ENSCPOG00000001202	1 retrocopy	retro_cpor_686,
Dasypus novemcinctus	ENSDNOG00000017387	2 retrocopies	retro_dnov_2623, retro_dnov_739,
Dasypus novemcinctus	ENSDNOG00000017624	3 retrocopies	retro_dnov_2294, retro_dnov_2402, retro_dnov_420 ,
Echinops telfairi	ENSETEG00000007664	1 retrocopy	retro_etel_1510,
Myotis lucifugus	ENSMLUG00000010711	2 retrocopies	retro_mluc_1098, retro_mluc_1839,
Mus musculus	ENSMUSG00000067764	1 retrocopy	retro_mmus_1085,
Mus musculus	ENSMUSG00000072479	1 retrocopy	retro_mmus_1782,
Otolemur garnettii	ENSOGAG00000024543	1 retrocopy	retro_ogar_633,
Rattus norvegicus	ENSRNOG00000017224	1 retrocopy	retro_rnor_1728,
Ictidomys tridecemlineatus	ENSSTOG00000001853	1 retrocopy	retro_itri_931,