RetrogeneDB ID: retro_dnov_525

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_5720:432625..433499(-)
• Located in intron of: ENSDNOG00000003834

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1CA
• Ensembl ID: ENSDNOG00000007986
• Aliases: None
• Description: protein phosphatase 1, catalytic subunit, alpha isozyme [Source:HGNC Symbol;Acc:9281]

Sequence

>retro_dnov_525
ATGGCAGATAAAGATAAACTCAGCATCAACAGCGTCATCCAACAGTATTCTGGAAGTGAAAGGGTCCAAGTGTGGTTAAA
ATGTCCAGCCACAGGAGAATGAAATCAGAAGACGGTGCTTAAAGTGTTGTGAGACTTTCTCAGTCAGCCTATCCTACTAG
AACTTGAGGCACCACTCAAAATATGTGGTGATATCCATGGGCAATACTATGGTTTGCTTTGACTTTTTGAGTACAGTGGA
GTTTCACGAGAAAGCAACTACCTATTTCTCGGGGACTGTTTGGACAGAGGGAAGCGGTCATTGGAGACTATCTGCCTCTT
ACTGACCTACAAAATCATATATCCCAAGAATTTTTTTCTCTCAGGAAACCATGAATGTGCCAGCATCAATAGAATTTCTG
GATTTTATGAATGTAAAAGAAGATACAACATTAAACTATGCAAAACTTTCATAGTGGCTTGAACTCTTTACCAATATCAG
GCATTGTGGATGAGAAAATACTCTGCTGTCATGGAAGTTTGTCATCAGATCTTCAGTCTGTGGAGCAGATTCACCAAATT
ATGTGACCAACTGATATAACGGATCAAAGTCTTCTTTGTGATCTTTTGTGGTCTGACCCCAATAAAGATGTCTTAGGCTG
GGGTGAAAATGACATAGGAGTGTCCTTCACATCTGGTGCAGAAGTGGTTCCAAAATTTCTCCACAAGTATGATTTGGATC
TTATATGTAGAACCCATCATGTGGTTGAAGATGGCTATGAGTTTTTTGCCAAGAGTCAGTTGTCACTCTGTTTTCTGCAC
CCAGTTATTGTGGAGAGTTTGACAATGCAAGTGCCATGATGAGTGTGGATGAAACACTAATTTGTTCTTTTCAG

Alignment

ORF - retro_dnov_525 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.51 %
• Parental protein coverage: 87.46 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MADIDKLNIDSIIQR-LLEVRGSKPGKNVQLQENEIRGLCLKSREIF-LSQPILLELEAPLKICGDIHGQ
          MAD.DKL.I.S.IQ...LEV.GSK.G.NVQ.QENEIR..CLK..E.F.LSQPILLELEAPLKICGDIHGQ
Retrocopy MADKDKLSINSVIQQ>ILEVKGSKCG*NVQPQENEIRRRCLKCCETF<LSQPILLELEAPLKICGDIHGQ

Parental  YYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAF-IIYPENFFLPRGFFECASINRIYGFXX
          YY.LL.LFEY.G...ESNYLFLGD..DRGK.SLETICLLL...IIYP.NFFL..G..ECASINRI.GF..
Retrocopy YYGLL*LFEYSGVSRESNYLFLGDCLDRGKRSLETICLLLTYKIIYPKNFFLS-GNHECASINRISGFYE

Parental  XXKRRYNIKLWKTFTDC-FNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWS
          ..KRRYNIKL.KTF.....N.LPI..IVDEKI.CCHG.LS.DLQS.EQI..IM.PTD..DQ.LLCDLLWS
Retrocopy C-KRRYNIKLCKTFIVA<LNSLPISGIVDEKILCCHGSLSSDLQSVEQIHQIM*PTDITDQSLLCDLLWS

Parental  DPDKDVLGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQL-VTLFSAPNYCGEF
          DP.KDVLGWGEND.GVSFT.GAEVV.KFLHK.DLDLICR.H.VVEDGYEFFAK.QL.VTLFSAP.YCGEF
Retrocopy DPNKDVLGWGENDIGVSFTSGAEVVPKFLHKYDLDLICRTHHVVEDGYEFFAKSQL<VTLFSAPSYCGEF

Parental  DNAGAMMSVDETLMCSFQ
          DNA.AMMSVDETL.CSFQ
Retrocopy DNASAMMSVDETLICSFQ

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	77.40 RPM
SRP012922_cerebellum	0.14 RPM	56.91 RPM
SRP012922_heart	0.00 RPM	15.08 RPM
SRP012922_kidney	0.00 RPM	20.26 RPM
SRP012922_liver	0.15 RPM	32.20 RPM
SRP012922_lung	0.00 RPM	39.71 RPM
SRP012922_quadricep_muscle	0.00 RPM	31.67 RPM
SRP012922_spleen	0.11 RPM	45.78 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_525 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 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000004542	1 retrocopy	retro_cint_3,
Callithrix jacchus	ENSCJAG00000000983	1 retrocopy	retro_cjac_923,
Dasypus novemcinctus	ENSDNOG00000007986	3 retrocopies	retro_dnov_2565, retro_dnov_525 , retro_dnov_872,
Macropus eugenii	ENSMEUG00000005323	1 retrocopy	retro_meug_1748,
Drosophila melanogaster	FBgn0003134	5 retrocopies	retro_dmel_21, retro_dmel_37, retro_dmel_42, retro_dmel_48, retro_dmel_81,