RetrogeneDB ID: retro_dnov_697

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_956:801958..802380(+)
• Located in intron of: ENSDNOG00000014090

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000018728
• Aliases: None
• Description: None

Sequence

>retro_dnov_697
GCTCTAGGCATGATTTTGGACCTGGAGCCTGATGAAGAGCTGGAAGACAACCCCAAGCAGAGCGACCTGATTGAGCAGGC
AGCTGAGATGCTGTATGGATTAATCCACACCCGCTACATCCTCACCAACCGCGGCATCACCCAGATGTTGGAAAAATACA
CCAGGGAAACTTTGGCTGCTGTCCCCGTGTGTACTGTGAGAACCAGCCAATGCTTCCCATTGGCCTGTCGGATATCCCAG
GCGAGGCCATGGTGAAGCTCTACTGTCCCAAGTGCATAGACGTGTACACACCCAAGGTGTCGAGGCACCACCACACAGAC
GGCGCCTACTTCGGCGCTGGATTCCTACACATGCTCTTCATGGTGCACCCCGAGTACCCGCCCAAGCGGCCTGCCAGCCA
GTTTGTGCCCAGGCTCTCTGGT

Alignment

ORF - retro_dnov_697 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.32 %
• Parental protein coverage: 66.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ALDMILDLEPDE-LED-PNQSDLIEQAAEMLYGLI-ARYILTNRGIAQMLEKY-QQGDFGYCPRVYCENQ
          AL.MILDLEPDE.LED.P.QSDLIEQAAEMLYGLI..RYILTNRGI.QMLEKY..QG.FG.CPRVYCENQ
Retrocopy ALGMILDLEPDEELEDNPKQSDLIEQAAEMLYGLIHTRYILTNRGITQMLEKY<HQGNFGCCPRVYCENQ

Parental  PMLPIGLSDIPGEAMVKLYCPKCMDVYTPKSSRHHHTDGAYFGTGFPHMLFMVHPEYRPKRPANQFVPRL
          PMLPIGLSDIPGEAMVKLYCPKC.DVYTPK.SRHHHTDGAYFG.GF.HMLFMVHPEY.PKRPA.QFVPRL
Retrocopy PMLPIGLSDIPGEAMVKLYCPKCIDVYTPKVSRHHHTDGAYFGAGFLHMLFMVHPEYPPKRPASQFVPRL

Parental  YG
          .G
Retrocopy SG

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	17.89 RPM	49.59 RPM
SRP012922_cerebellum	14.02 RPM	40.83 RPM
SRP012922_heart	10.21 RPM	25.99 RPM
SRP012922_kidney	26.56 RPM	58.87 RPM
SRP012922_liver	10.06 RPM	27.71 RPM
SRP012922_lung	20.77 RPM	47.04 RPM
SRP012922_quadricep_muscle	14.02 RPM	32.19 RPM
SRP012922_spleen	17.97 RPM	60.32 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_697 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 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005751	1 retrocopy	retro_acar_107,
Bos taurus	ENSBTAG00000008837	1 retrocopy	retro_btau_885,
Callithrix jacchus	ENSCJAG00000002996	1 retrocopy	retro_cjac_2700,
Dasypus novemcinctus	ENSDNOG00000018728	1 retrocopy	retro_dnov_697 ,
Dipodomys ordii	ENSDORG00000014179	1 retrocopy	retro_dord_45,
Erinaceus europaeus	ENSEEUG00000006417	2 retrocopies	retro_eeur_331, retro_eeur_555,
Echinops telfairi	ENSETEG00000015168	3 retrocopies	retro_etel_225, retro_etel_271, retro_etel_769,
Felis catus	ENSFCAG00000007642	2 retrocopies	retro_fcat_1749, retro_fcat_206,
Macropus eugenii	ENSMEUG00000004095	10 retrocopies	retro_meug_1158, retro_meug_1316, retro_meug_1598, retro_meug_187, retro_meug_1939, retro_meug_40, retro_meug_525, retro_meug_528, retro_meug_751, retro_meug_752,
Monodelphis domestica	ENSMODG00000015287	4 retrocopies	retro_mdom_1433, retro_mdom_1558, retro_mdom_704, retro_mdom_936,
Mustela putorius furo	ENSMPUG00000011129	1 retrocopy	retro_mputfur_154,
Oryctolagus cuniculus	ENSOCUG00000023483	2 retrocopies	retro_ocun_1477, retro_ocun_362,
Ochotona princeps	ENSOPRG00000012138	1 retrocopy	retro_opri_970,
Sarcophilus harrisii	ENSSHAG00000001478	2 retrocopies	retro_shar_672, retro_shar_693,
Sus scrofa	ENSSSCG00000001414	1 retrocopy	retro_sscr_538,
Tursiops truncatus	ENSTTRG00000014103	2 retrocopies	retro_ttru_1595, retro_ttru_1740,