RetrogeneDB ID: retro_dnov_872

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_116778:4814..5695(+)
• Located in intron of: None

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_872
ATGGTGGATATAGATAAACTCAACTTCCACAACATCATCCAATGGCTGCTAGAAGACAGAGAGTCTAATCCTGGTTAGAA
TGTCCAGCTACAGGAGAACGAAATTAGAGAACTGTACTTAAAGTCTTCTGAGATCTTTCTCAGTCAATCTATCCTACCAG
AACTTGAAGCATTACTCAAAATTTTTGGTGATATCCATGGGCAATACTATAATTTGCTTAGACTTTTTGAGTATGGTGGT
TTTTCACCAGGAAGCAACTATCTGTTTCTTGGGGACTATGTAGACAGAGGGAAGCAGTCCTTGGAGACTATCTGCCTCTT
CTTGGCCAATAAAATCAAATATCCTGAGAATTTTTTCCTTCTCCACGGAAACCACGAATGTGCCAGCATCAATAGAATTT
ATGGATTTTGTGATGAATGTAAAAGAAGATACAACACTAAGCAATGGAAAACTTTCACAGAATGCTTTTACTGTTTACTG
ATAGCAGCCATCATGGATGAGAAAATATTCTGCTGTTATGGAGGTTTATCACCACATCTTCAATCTATGGCACAGATTTG
ACAAATTATGTGACCAAATGATGTACCAGATCAAGGTCTTCTTTGTGATCTTTTGTGGTCTGACCCCAATAAAGATGTCT
TAGGCTGGGGAGAAAATGACAGAAGAGTGGCCTTCACATTTGGTGCAGAAGTGGTTGCAAAATGTCTTCATAAGCATGAT
TTGGATCTTATATGTAGAACCCATCAGGTGGTTGAAGATGGCCATGAATTTTTTGCCAAGAAGCAGTTGGTCACTCTGTT
TTCTGCACCCAATTACTGTAGAGAGTTGACAATGCAGGTTCCACGATGAGTGTGGATGAAACGCTAATGTGCTTTTTTCA
G

Alignment

ORF - retro_dnov_872 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.68 %
• Parental protein coverage: 87.46 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADIDKLNIDSIIQRLLEVRGSKPGKNVQLQENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYY
          M.DIDKLN...IIQ.LLE.R.S.PG.NVQLQENEIR.L.LKS.EIFLSQ.IL.ELEA.LKI.GDIHGQYY
Retrocopy MVDIDKLNFHNIIQWLLEDRESNPG*NVQLQENEIRELYLKSSEIFLSQSILPELEALLKIFGDIHGQYY

Parental  DLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAFII-YPENFFLPRGFFECASINRIYGFXXXX
          .LLRLFEYGGF.P.SNYLFLGDYVDRGKQSLETICL.LA..I.YPENFFL..G..ECASINRIYGF....
Retrocopy NLLRLFEYGGFSPGSNYLFLGDYVDRGKQSLETICLFLANKIKYPENFFLLHGNHECASINRIYGFCDEC

Parental  KRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPD
          KRRYN.K.WKTFT.CF.CL.IAAI.DEKIFCC.GGLSP.LQSM.QI..IM.P.DVPDQGLLCDLLWSDP.
Retrocopy KRRYNTKQWKTFTECFYCLLIAAIMDEKIFCCYGGLSPHLQSMAQI*QIM*PNDVPDQGLLCDLLWSDPN

Parental  KDVLGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEF-DNA
          KDVLGWGENDR.V.FTFGAEVVAK.LHKHDLDLICR.HQVVEDG.EFFAK.QLVTLFSAPNYC.E..DNA
Retrocopy KDVLGWGENDRRVAFTFGAEVVAKCLHKHDLDLICRTHQVVEDGHEFFAKKQLVTLFSAPNYCREL<DNA

Parental  GAMMSVDETLMCSFQ
          G..MSVDETLMC.FQ
Retrocopy GSTMSVDETLMCFFQ

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	0.00 RPM	56.91 RPM
SRP012922_heart	0.23 RPM	15.08 RPM
SRP012922_kidney	0.00 RPM	20.26 RPM
SRP012922_liver	0.00 RPM	32.20 RPM
SRP012922_lung	0.00 RPM	39.71 RPM
SRP012922_quadricep_muscle	0.00 RPM	31.67 RPM
SRP012922_spleen	0.00 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_872 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,