RetrogeneDB ID: retro_dnov_1700

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_270029:202..661(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP6C
• Ensembl ID: ENSDNOG00000015319
• Aliases: None
• Description: protein phosphatase 6, catalytic subunit [Source:HGNC Symbol;Acc:9323]

Sequence

>retro_dnov_1700
ATGGCGCCACTAGACTTGGACAAGTATGTGGAGACAGCATGTCTATGCAAGTACATGCCGAAGGGACGCCTTAAAGCGGT
GATGTGACTATGTTTGTGACTTCCTTTCAGAAGAGTCAAATGTTCAGCCAGTATCAAACTAGTAACAGTGTGTGGAGACA
CACACGGGACAGTATTATGACCTCTGTGAACTACTCAGAACTGGAGGTCAGGTTCTTGACACAAACTACGTATTTATGGG
TGACTTTGTAGACAGAGGTTATTCTAGCTGGGAGACTTTCACTTACCTTCTTGCACTAAAGACTAAATAGCCTGATCGGA
TTATGCTCTCACAAGGAAATCATGAGAGGAGACAGAAAACCAAGTACACAGATTTTACGATGCGTGCCAAACCAAACATG
GAAACGCCAATGCCTGGAGACATTGTACCAACGTTTCTGATGTGCTCACAGTAGCTGCT

Alignment

ORF - retro_dnov_1700 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.43 %
• Parental protein coverage: 50.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAPLDLDKYVEIARLCKYLPE-NDLKRLCDYVCDLLLEESNVQPVST-PVTVCGDIHG-QFYDLCELFRT
          MAPLDLDKYVE.A.LCKY.P....LKR.CDYVCD.L.EESNVQPVS...VTVCGD.HG.Q.YDLCEL.RT
Retrocopy MAPLDLDKYVETACLCKYMPK>DALKR*CDYVCDFLSEESNVQPVSN<LVTVCGDTHG>QYYDLCELLRT

Parental  GGQVPDTNYIFMGDFVDRGYYSLETFTYLLALKAKWPDRITLLRGNHESRQIT-QVYGFYDECQTKYGNA
          GGQV.DTNY.FMGDFVDRGY.S.ETFTYLLALK.K.PDRI.L..GNHE.RQ.T.QV..FYD.CQTK.GNA
Retrocopy GGQVLDTNYVFMGDFVDRGYSSWETFTYLLALKTK*PDRIMLSQGNHERRQKT<QVHRFYDACQTKHGNA

Parental  NAWRYCTKVFDMLTVAA
          NAWR.CT.V.D.LTVAA
Retrocopy NAWRHCTNVSDVLTVAA

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	27.03 RPM
SRP012922_cerebellum	0.00 RPM	15.40 RPM
SRP012922_heart	0.23 RPM	8.82 RPM
SRP012922_kidney	0.00 RPM	13.96 RPM
SRP012922_liver	0.00 RPM	9.75 RPM
SRP012922_lung	0.00 RPM	31.61 RPM
SRP012922_quadricep_muscle	0.00 RPM	13.67 RPM
SRP012922_spleen	0.23 RPM	24.61 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_1700 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012357	3 retrocopies	retro_chof_1759, retro_chof_183, retro_chof_608,
Dasypus novemcinctus	ENSDNOG00000015319	1 retrocopy	retro_dnov_1700 ,
Erinaceus europaeus	ENSEEUG00000010197	1 retrocopy	retro_eeur_706,
Macaca mulatta	ENSMMUG00000020549	1 retrocopy	retro_mmul_698,
Rattus norvegicus	ENSRNOG00000015145	1 retrocopy	retro_rnor_2074,
Sarcophilus harrisii	ENSSHAG00000008282	1 retrocopy	retro_shar_146,
Sus scrofa	ENSSSCG00000005600	1 retrocopy	retro_sscr_243,