RetrogeneDB ID: retro_dnov_1333

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_18310:30487..31603(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2R5D
• Ensembl ID: ENSDNOG00000015445
• Aliases: None
• Description: protein phosphatase 2, regulatory subunit B', delta [Source:HGNC Symbol;Acc:9312]

Sequence

>retro_dnov_1333
CAGCCCCAGCCCTAGCCACCATTATCCAATAAATATCCCAGGAAGAGTACATCAACCCCCATACAGCTAAGGAAAATCAG
GTATTCAAGAGGACTCCAATTGTCAAGAAGGAGTGGTGGCAGAATTCCTCCCACTTCAATCTCAGCCAGAACCTGGAGCT
ACAAAAGCTTCCTGACTTGAAAGATTCCCCAACCCAGGAGCAGGAGGAGTTGTTTATCCAGAATCTCCACCAGTGCTGCA
TTCTCTTTGACTTTGTGTCAGACCCACTCAGTGACCTCAAATTCAAGGAAATAAGTCAGTCTGGACTCAACAAGATGGTG
GAGTACATCACCCATAGGCTTGATGTTGTCACCAAGACCATTTTCCCTGATGCTGGCACCATGCATTCAGTGAACCTCTT
CTGGACACTGCCTCCTTTGTCAAGTCTCTCTGAGGCAAAGTTTGACCAGAGACAGAAAAGCCCAGTCTGGAAGCTGCCAG
ACCACATCTCCAGTTTTTCTTCCTTGAGTCTCCTGTTTTCCAACCAAACAGAGCCAAGAAGTATACTGACCAAAAGTTTG
TCCTTGCTCTCCAGGTCCTGTTTGACAGTGAAGATTCTCAAGAGCAGGACTTCTTAAGACAATGTTACATCACCTCTGGG
GCAAGTTTTGGGGACACTCCCAGGCTTATATCCATTGGCAGATCAACTACATCTGCCACAGGTTCATCTGTGAGACAGAG
CGTCACAATTGGATTGCTGAGCTCCTGGAGATCCTGGGCAGCTTCTTCAGTGGCTTTGCCCTGTCGCTGAAGGACGAGCA
CAAGATGTTCCTCATCTGCACACTGCTTCCCCTCACAAAGTAAAGTCCCTGAGGTTCTATCAGCCTCATTTGGCATACTG
TGTGGGACAGTTCCTGGAGAGGGAGAGCAGTCTAACTGAGGCAGCGATAGTGGGATTTCTCAAGCTCCTGGCCTAAGACC
CATAGCCCCAAGGAGGTGATGTTCCTGAATGAGCTGGAGGAGATTCTGGATATCATTGAACCTTCAGAGCTCAGCAGAGT
GATGGAACCACTCTTCTGCCAGCTTGCCAAGTGTATCTCCAGCCCCCATTTCCAAGTGGCAGAGCGTTCTCTTTTC

Alignment

ORF - retro_dnov_1333 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.23 %
• Parental protein coverage: 67.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  QPQPQPPSSNKRPSNSTPPPTQLSKIKYSGGPQ-IVKKERRQSSSRFNLSKNRELQKLPALKXXXXXXXX
          QPQP.PP.SNK.P..ST..P.QL.KI.YS.G.Q.IVKKE..Q.SS.FNLS.N.ELQKLP.LK........
Retrocopy QPQP*PPLSNKYPRKSTSTPIQLRKIRYSRGLQ<IVKKEWWQNSSHFNLSQNLELQKLPDLKDSPTQEQE

Parental  XXXXXXXXXCCVLFDFVSDPLSDLKFKEVKRAGLNEMVEYITHSRDVVTEAIYPEAVTMFSVNLFRTLPP
          .........CC.LFDFVSDPLSDLKFKE....GLN.MVEYITH..DVVT..I.P.A.TM.SVNLF.TLPP
Retrocopy ELFIQNLHQCCILFDFVSDPLSDLKFKEISQSGLNKMVEYITHRLDVVTKTIFPDAGTMHSVNLFWTLPP

Parental  SSNPTGAEFD-PEEDEPTLEAAWPHLQLVYEFFLRFLESPDFQPNIAKKYIDQKFVLALLDLFDSEDPRE
          .S....A.FD.PE...P.LEAA.PHLQ....FFL...ESP.FQPN.AKKY.DQKFVLAL..LFDSED..E
Retrocopy LSSLSEAKFD<PETEKPSLEAARPHLQF---FFL---ESPVFQPNRAKKYTDQKFVLALQVLFDSEDSQE

Parental  RDF-LKTILHRIYGKFLG-LRAYIRRQINHIFYRFIYETEHHNGIAELLEILGSIINGFALPLKEEHKMF
          .DF.LKT.LH...GKF.G...AYI..QIN.I..RFI.ETE.HN.IAELLEILGS...GFAL.LK.EHKMF
Retrocopy QDF<LKTMLHHLWGKFWGHSQAYIHWQINYICHRFICETERHNWIAELLEILGSFFSGFALSLKDEHKMF

Parental  LIRVLLPL-HKVKSLSVYHPQLAYCVVQFLEKESSLTEPVIVGLLKF-WPKTHSPKEVMFLNELEEILDV
          LI..LLPL.HKVKSL..Y.P.LAYCV.QFLE.ESSLTE..IVG.LK..WPKTHSPKEVMFLNELEEILD.
Retrocopy LICTLLPL<HKVKSLRFYQPHLAYCVGQFLERESSLTEAAIVGFLKL>WPKTHSPKEVMFLNELEEILDI

Parental  IEPSEFSKVMEPLFRQLAKCVSSPHFQVAERALY
          IEPSE.S.VMEPLF.QLAKC.SSPHFQVAER.L.
Retrocopy IEPSELSRVMEPLFCQLAKCISSPHFQVAERSLF

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	0.19 RPM	76.23 RPM
SRP012922_cerebellum	0.41 RPM	44.13 RPM
SRP012922_heart	0.00 RPM	4.87 RPM
SRP012922_kidney	0.00 RPM	16.98 RPM
SRP012922_liver	0.00 RPM	12.07 RPM
SRP012922_lung	0.00 RPM	25.35 RPM
SRP012922_quadricep_muscle	0.00 RPM	13.85 RPM
SRP012922_spleen	0.00 RPM	34.80 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_1333 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000015445	1 retrocopy	retro_dnov_1333 ,
Monodelphis domestica	ENSMODG00000019007	1 retrocopy	retro_mdom_798,
Pongo abelii	ENSPPYG00000016625	1 retrocopy	retro_pabe_1434,