RetrogeneDB ID: retro_dnov_1844

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_33:340128..340564(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2CA
• Ensembl ID: ENSDNOG00000013011
• Aliases: None
• Description: protein phosphatase 2, catalytic subunit, alpha isozyme [Source:HGNC Symbol;Acc:9299]

Sequence

>retro_dnov_1844
GCTAAGGAAATTTTAACAAAATAATCATATGTGCAAGTGGTTTTTTGCCCTCTTACAGGCTGTGGAGATGTTCATGGTCA
ATTTCATGATCTTATGGAACTCTTTAGAATTGGTGGGAAATCACCAGACACAAACTATCTATTCATGGGGGACTATGTTG
ACAGAGGTTATTATTCCAGTGGAGGCTGTGACTCCTCTTGTGGTATTAAAGGTGCATTATCCAGAATGCATTACAATATT
GAGAGGAAACAGTGAAAGCTGACAAATTACCCAAATACGTGGCTTTTATGATGAATGTCTATGAAAGTATGGAAATGCCA
ATGTGTGGAAATATTTCACAGATCTTTTTGATTATCTTCCACTTACAGCTTTAGCAGATGGACAGATATTCTGCCTCCAT
GGTGGCCTCTCTCCGTCCATAGATTCACTGTATCAC

Alignment

ORF - retro_dnov_1844 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.93 %
• Parental protein coverage: 52.73 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELFRIGGKSPDTNYLFMGDYVDRGYYS-VETVTLLVAL
          AKEILTK.S.VQ.V.CP.T.CGDVHGQFHDLMELFRIGGKSPDTNYLFMGDYVDRGYYS.VE.VT.LV.L
Retrocopy AKEILTK*SYVQVVFCPLTGCGDVHGQFHDLMELFRIGGKSPDTNYLFMGDYVDRGYYS>VEAVTPLVVL

Parental  KVRYRERITILRGNHESRQITQVYGFYDECLRKYGNAKVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPS
          KV.Y.E.ITILRGN.ES.QITQ..GFYDECL.KYGNA.VWKYFTDLFDYLPLTAL.DGQIFCLHGGLSPS
Retrocopy KVHYPECITILRGNSES*QITQIRGFYDECL*KYGNANVWKYFTDLFDYLPLTALADGQIFCLHGGLSPS

Parental  IDTLDH
          ID.L.H
Retrocopy IDSLYH

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	1.17 RPM	76.62 RPM
SRP012922_cerebellum	0.96 RPM	115.89 RPM
SRP012922_heart	0.70 RPM	23.20 RPM
SRP012922_kidney	0.82 RPM	56.13 RPM
SRP012922_liver	0.00 RPM	36.53 RPM
SRP012922_lung	1.83 RPM	56.81 RPM
SRP012922_quadricep_muscle	1.04 RPM	51.41 RPM
SRP012922_spleen	0.80 RPM	57.57 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_1844 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 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002653	1 retrocopy	retro_acar_69,
Bos taurus	ENSBTAG00000000469	1 retrocopy	retro_btau_1754,
Dasypus novemcinctus	ENSDNOG00000010906	1 retrocopy	retro_dnov_2211,
Dasypus novemcinctus	ENSDNOG00000013011	4 retrocopies	retro_dnov_1025, retro_dnov_1844 , retro_dnov_2100, retro_dnov_2122,
Echinops telfairi	ENSETEG00000007561	2 retrocopies	retro_etel_1233, retro_etel_659,
Felis catus	ENSFCAG00000029685	1 retrocopy	retro_fcat_1086,
Mustela putorius furo	ENSMPUG00000010169	1 retrocopy	retro_mputfur_633,
Sorex araneus	ENSSARG00000005447	3 retrocopies	retro_sara_296, retro_sara_385, retro_sara_715,
Sarcophilus harrisii	ENSSHAG00000016632	3 retrocopies	retro_shar_313, retro_shar_428, retro_shar_471,
Tursiops truncatus	ENSTTRG00000016859	1 retrocopy	retro_ttru_1584,