RetrogeneDB ID: retro_dnov_1774

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_29459:16230..16829(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YRDC
• Ensembl ID: ENSDNOG00000009111
• Aliases: None
• Description: yrdC domain containing (E. coli) [Source:HGNC Symbol;Acc:28905]

Sequence

>retro_dnov_1774
GAGGTGCACGCTGGCACTATGGTAGTGACCCCCACTGACATGTTGTATAGCCTGGCCTGCTCAGCAGTCTGCTCGGAGGC
ACTGGACACTGTCTGTGGCCTCAAGTGCCACAACAAAGCCGAGTCGCTGGTCATATGCCTAGGCTGCATGACGGCCATCT
ACAGGCACAGCCATGTGAGGGTTCCCAAGGAGCTCCTAAAAGAACTCTTGCCAAGACCATTTACCCTGGTGATGGAATGT
TCAGAGACGCTCAACAAGGACCTGAACCCCTTCACTCCTCTTGTAGGCACCTGGATTCCTGACCATGCCTTCATGGAGGA
CTTGGCCCAGGTGTTTGAGGGACCTCTTGCTCTCACCAGCACCAACCTCAGCTCCCAGTCAGTGAGTTCCAGGACCTCTA
GCCTCAGTTGTCTCTGGTCATTGATTTGGGGGTGGGGATATTTGGGGATGGGCACAGCCCTGAGTGCCACCTTAGCTCAA
CTGTGGTTGACTTATCTGTACCTAGAGAGTTTGGCATCATTCATCCAGGCTGTGCCCTGGAAAGTACTACAGCCATCCTT
CAATAGAAGTATAGACTATTCCCTACAGATGGATCCTGC

Alignment

ORF - retro_dnov_1774 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.16 %
• Parental protein coverage: 72.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ELRAGAVVAVPTDTLYGLACSASCSAALGAVYRLKGRCKAKPLAVCLGSVADVYRFCRVRVPKELLKDLL
          E..AG..V..PTD.LY.LACSA.CS.AL..V..LK...KA..L..CLG.....YR...VRVPKELLK.LL
Retrocopy EVHAGTMVVTPTDMLYSLACSAVCSEALDTVCGLKCHNKAESLVICLGCMTAIYRHSHVRVPKELLKELL

Parental  PGPVTLVMERSEELNKDLNPFTPLVGIRIPDHAFMQDLAQVFEGPLALTSANLSSQASSLNVKEFQDLWP
          P.P.TLVME.SE.LNKDLNPFTPLVG..IPDHAFM.DLAQVFEGPLALTS.NLSSQ..S........LW.
Retrocopy PRPFTLVMECSETLNKDLNPFTPLVGTWIPDHAFMEDLAQVFEGPLALTSTNLSSQSVSSRTSSLSCLW-

Parental  HLSLIIDGGPL-GDGQSPEYRLGSTVVDLSVPGKFGIIRPGCALESTTAILQQKYGLLPLDGSC
          ..SLI...G.L.GDG.SPE..L.STVVDLSVP..FGII.PGCALESTTAILQ.KY.L.P.DGSC
Retrocopy --SLIWGWGYL<GDGHSPECHLSSTVVDLSVPREFGIIHPGCALESTTAILQ*KYRLFPTDGSC

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	6.03 RPM
SRP012922_cerebellum	0.00 RPM	13.61 RPM
SRP012922_heart	0.00 RPM	3.71 RPM
SRP012922_kidney	0.00 RPM	10.68 RPM
SRP012922_liver	0.00 RPM	4.95 RPM
SRP012922_lung	0.00 RPM	8.40 RPM
SRP012922_quadricep_muscle	0.00 RPM	3.29 RPM
SRP012922_spleen	0.11 RPM	9.16 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_1774 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 16 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001173	1 retrocopy	retro_amel_350,
Dasypus novemcinctus	ENSDNOG00000009111	2 retrocopies	retro_dnov_1774 , retro_dnov_2232,
Equus caballus	ENSECAG00000022522	1 retrocopy	retro_ecab_534,
Felis catus	ENSFCAG00000011018	1 retrocopy	retro_fcat_375,
Homo sapiens	ENSG00000196449	2 retrocopies	retro_hsap_4199, retro_hsap_4289,
Gorilla gorilla	ENSGGOG00000007619	1 retrocopy	retro_ggor_2866,
Macropus eugenii	ENSMEUG00000005068	1 retrocopy	retro_meug_452,
Microcebus murinus	ENSMICG00000011953	1 retrocopy	retro_mmur_188,
Myotis lucifugus	ENSMLUG00000000955	1 retrocopy	retro_mluc_367,
Macaca mulatta	ENSMMUG00000005372	2 retrocopies	retro_mmul_1206, retro_mmul_1662,
Nomascus leucogenys	ENSNLEG00000011665	2 retrocopies	retro_nleu_1045, retro_nleu_1046,
Otolemur garnettii	ENSOGAG00000030474	2 retrocopies	retro_ogar_1107, retro_ogar_2342,
Pongo abelii	ENSPPYG00000001523	1 retrocopy	retro_pabe_3495,
Pan troglodytes	ENSPTRG00000000557	4 retrocopies	retro_ptro_2850, retro_ptro_2906, retro_ptro_2907, retro_ptro_2999,
Tupaia belangeri	ENSTBEG00000008863	1 retrocopy	retro_tbel_1817,
Tarsius syrichta	ENSTSYG00000005555	3 retrocopies	retro_tsyr_1108, retro_tsyr_1420, retro_tsyr_874,