RetrogeneDB ID: retro_dnov_2232

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_57263:300..776(-)
• 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_2232
GCCACGGCAGCGGTCCCCACCTACACGTCACATGGCCTGGCCTGCTCAGCGAGCTGCTCGGTGGCCCTGGGCGCTGTCCA
CCACCTCGAGGGCCGCAGCAGAGCCAAGCCCTGGCCCTATGCCCGGGCGCTGGCCAACATCTACAGGTCCTGCCATGGGA
GGTTCCAAGGAGCTCTGGAAAGACCTCTGGCCAGGACCAGGTAGCCTGGTGCTGGAACGTCCGCAGGGGCTCAGCGAGAA
CCTGAACCCTCCCCTAGGCCTCTGGACTCCTGACTACGCCTTCAGGCAGGACTCAGCCCGGGGGCTGGAGGGCCCTCTTG
CTCTCACCAGTGCCAGCCAGCCCAGTCCCCTGAAGGTCAAGGAGTCCCAGGACCTCTGGCCTCAGTTGTTCCTGGTCACT
GATGGGGGGGCCACTTGGGGATGGGCAGAGCCCTGAGGACCACCTGAGCTCAACTGTGGTCGACTGATCTGTGCCT

Alignment

ORF - retro_dnov_2232 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.36 %
• Parental protein coverage: 59.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AVVAVPTDTLYGLACSASCSAALGAVYRLKGRCKAKPLAVCLGSVADVYRFCRVR-VP-KELLKDLLPGP
          A..AVPT.T..GLACSASCS.ALGAV..L.GR..AKP........A..YR.C..R.VP.KEL.KDL.PGP
Retrocopy ATAAVPTYTSHGLACSASCSVALGAVHHLEGRSRAKPWPYAR-ALANIYRSCHGR<VP<KELWKDLWPGP

Parental  VTLVMERSEELNKDLNPFTPLVGIRIPDHAFMQDLAQVFEGPLALTSANLSSQASSLNVKEFQDLWPHLS
          ..LV.ER...L...LN...P..G...PD.AF.QD.A...EGPLALTSA...SQ.S.L.VKE.QDLWP.L.
Retrocopy GSLVLERPQGLSENLN---PPLGLWTPDYAFRQDSARGLEGPLALTSA---SQPSPLKVKESQDLWPQLF

Parental  LIID-GGPLGDGQSPEYRLGSTVVDLSVP
          L..D.GGPLGDGQSPE..L.STVVD.SVP
Retrocopy LVTD>GGPLGDGQSPEDHLSSTVVD*SVP

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	0.00 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_2232 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,