RetrogeneDB ID: retro_dnov_2122

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_49452:2153..2761(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000009769
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_2122
AACTACATATTTATGGGTGACTTTGTAGACAGAGATTATTATAGTTTGGAGACTTTCACTTATCTTCTTGCACTAACGGC
TAAATGGCCTGATCGTATTACACTCTTGCAAGGAAATCATGAAAGTAGACAGATAACACAAGTATGTGGATTTTATGATG
AGTGCCAAACCAAATATGGAAATGCGAATGCATGGAGATATTATACTAAAGTTTTTCACATGCTCACAGTAGCAGCTTTA
ATAGATGAGCAAATTTTGTGTGTTCATGGTGGTTTACCTTCCGATGTCAAAACACTGGATCAGATTCGAACTATTGAATG
GAATCAGGAAATTCCTCATAAAGTAACATGTTTTTGATCTGGTTTGGTCAGATCCTGAAGATGTAGACACTTGGGCAATC
AGTCCTCGAGGAGCAGATTGGCTTTTTGGAGCAAAGGTCACAAATGAATTTGTTCATATCAACAACTTAAAACTCATCTG
CAGAGCACACCAACTAGTGCATGAAGGCTATAAATTTATGTTTGACGAGAAGTTGGTAACAGTATGGTCTGCTCCTAACT
ATGGCTATCATTGTGGAAATAATTGCCTCCATCATGGTCTTCAAAGAT

Alignment

ORF - retro_dnov_2122 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.88 %
• Parental protein coverage: 73.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NYLFMGDYVDRGYYSVETVTLLVALKVRYRERITILRGNHESRQITQVYGFYDECLRKYGNAKVWKYFTD
          NY.FMGD.VDR.YYS.ET.T.L.AL......RIT.L.GNHESRQITQV.GFYDEC..KYGNA..W.Y.T.
Retrocopy NYIFMGDFVDRDYYSLETFTYLLALTAKWPDRITLLQGNHESRQITQVCGFYDECQTKYGNANAWRYYTK

Parental  LFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGP-MCDLLWSDPDDRGGWGISPRGAG
          .F..L...AL.D.QI.C.HGGL.....TLD.IR.....QE.PH......DL.WSDP.D...W.ISPRGA.
Retrocopy VFHMLTVAALIDEQILCVHGGLPSDVKTLDQIRTIEWNQEIPHKVT>VFDLVWSDPEDVDTWAISPRGAD

Parental  YTFGQDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQ-AAIMELDD
          ..FG......F.H.N.L.L..RAHQLV.EGY....D...VT..SAPNY.Y.CGN..A.IM...D
Retrocopy WLFGAKVTNEFVHINNLKLICRAHQLVHEGYKFMFDEKLVTVWSAPNYGYHCGNN>ASIMVFKD

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	2.92 RPM	76.62 RPM
SRP012922_cerebellum	3.30 RPM	115.89 RPM
SRP012922_heart	0.93 RPM	23.20 RPM
SRP012922_kidney	2.19 RPM	56.13 RPM
SRP012922_liver	1.08 RPM	36.53 RPM
SRP012922_lung	5.35 RPM	56.81 RPM
SRP012922_quadricep_muscle	2.08 RPM	51.41 RPM
SRP012922_spleen	2.98 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_2122 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,