RetrogeneDB ID: retro_dnov_34

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_9170:48776..49541(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000000193
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PGAM2
• Ensembl ID: ENSDNOG00000024480
• Aliases: None
• Description: phosphoglycerate mutase 2 (muscle) [Source:HGNC Symbol;Acc:8889]

Sequence

>retro_dnov_34
ATGGCTGCCTACAAGTTGGTGCTGATCCGGCACGGCAAGAGCGCCTGGAACCTGGAGAACCGCTTCAGCGGTTGGTACGA
CGCCGACCTGAGCCCAGCGGGGCATGAGGAGGCGAAGCGCGGCGGGCAGGCGCTGCGAGATGCTGGCTATGAGTTTGACA
TCTGCTTCACCTCAGTGCAGAAGAGAGCAATCAGGACTCTGTGGACTGTGCTAGAAGCCATCGACCAGATGTGGCTGCCA
GTAGTGAGGACTTGGCGCCTCAATGAACGGCACTATGGGGGTCTGACTGGCCTCAATAAAGCAGAAACTGCTGCCAAGCA
TGGCGAAGCCCAAGTTAAAATCTGGAGGCGCTCCTATGATGTCTCACCACCACCGATGGAGCCAGATCATCCCTTCTACA
GCAACATCAGTAAGGATCGCAGGTATGCAGACCTCACTGAAGATCAGCTCCCCTCCTGTGAGAGTCTAAAGGACACTATT
GCCAGAGCCCTGCCTTTTTGGAATGAAGAAATTGTTCCCCAGATCAAGGAGGGGAAACGGGTATTGATTGCAGCACATGG
CAACAGTCTTCCGGGCATTGTCAAGCACCTGGAGGGTCTCACTGAAGAAGCTATCATGGAGCTGAACCTGCCCACTGGTA
TTCCCATTGTCTATGAGTTGGACAAGAACTTGAAGCCAATCAAACCTATGCAATTCCTAGGGGATGAAGAGACTGTACGG
AAGGCCATGGAAGCTGTGGCTGCCCAGGGCAAGGCTAAGAAGTAA

Alignment

ORF - retro_dnov_34 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.87 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATHRLVIVRHGESTWNQENRFCGWFDAELSEKGAEEARRGAQAIKDAGMEFDICYTSVLKRAIRTLWTI
          MA...LV..RHG.S.WN.ENRF.GW.DA.LS..G.EEA.RG.QA..DAG.EFDIC.TSV.KRAIRTLWT.
Retrocopy MAAYKLVLIRHGKSAWNLENRFSGWYDADLSPAGHEEAKRGGQALRDAGYEFDICFTSVQKRAIRTLWTV

Parental  LDGTDQMWLPVVRSWRLNERHYGGLTGLNKAETAAKHGEEQVKVWRRSFDVPPPPMDEKHPYYNAISKER
          L...DQMWLPVVR.WRLNERHYGGLTGLNKAETAAKHGE.QVK.WRRS.DV.PPPM...HP.Y..ISK.R
Retrocopy LEAIDQMWLPVVRTWRLNERHYGGLTGLNKAETAAKHGEAQVKIWRRSYDVSPPPMEPDHPFYSNISKDR

Parental  RYAGLKAGELPACESLKDTIARALPFWNDEIAPQIKAGKRVLIAAHGNSLRGIVKHLENMSDQAIMELNL
          RYA.L....LP.CESLKDTIARALPFWN.EI.PQIK.GKRVLIAAHGNSL.GIVKHLE.....AIMELNL
Retrocopy RYADLTEDQLPSCESLKDTIARALPFWNEEIVPQIKEGKRVLIAAHGNSLPGIVKHLEGLTEEAIMELNL

Parental  PTGIPIVYELDEKLKPTKPMRFLGDEETVRKAMEAVAAQGKAK
          PTGIPIVYELD..LKP.KPM.FLGDEETVRKAMEAVAAQGKAK
Retrocopy PTGIPIVYELDKNLKPIKPMQFLGDEETVRKAMEAVAAQGKAK

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	85.76 RPM	8.36 RPM
SRP012922_cerebellum	89.08 RPM	5.64 RPM
SRP012922_heart	52.44 RPM	2.09 RPM
SRP012922_kidney	57.22 RPM	3.29 RPM
SRP012922_liver	31.43 RPM	1.39 RPM
SRP012922_lung	23.06 RPM	2.14 RPM
SRP012922_quadricep_muscle	10.21 RPM	3583.71 RPM
SRP012922_spleen	32.28 RPM	2.29 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_34 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 7 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000024480	1 retrocopy	retro_dnov_34 ,
Macropus eugenii	ENSMEUG00000012920	8 retrocopies	retro_meug_1044, retro_meug_1303, retro_meug_1636, retro_meug_1838, retro_meug_202, retro_meug_2152, retro_meug_251, retro_meug_945,
Otolemur garnettii	ENSOGAG00000006713	1 retrocopy	retro_ogar_164,
Procavia capensis	ENSPCAG00000002181	1 retrocopy	retro_pcap_13,
Rattus norvegicus	ENSRNOG00000013532	1 retrocopy	retro_rnor_2889,
Tupaia belangeri	ENSTBEG00000004587	1 retrocopy	retro_tbel_3939,
Drosophila melanogaster	FBgn0014869	1 retrocopy	retro_dmel_57,