RetrogeneDB ID: retro_dnov_54

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_1059:18604..19421(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTPLAD1
• Ensembl ID: ENSDNOG00000001687
• Aliases: None
• Description: protein tyrosine phosphatase-like A domain containing 1 [Source:HGNC Symbol;Acc:24175]

Sequence

>retro_dnov_54
TGGGAGTGACTCACCAAGCAGGAGAAGCATCCACTGTTTTTGGCCCCTGACTTTGATAGCTGGCTAGATGAGTCTGACGA
GGAAATGGAACTCAGAGCCAAGGAAGAAGAATGCCTAAATAAACTCAGACTTGAAAGCGAAGGCTCCCCTGAAACTCTTG
CAAGCTTGAAGAAAGGATACCTGTTCATGCATAATTTGGTACAGTTTTTGGGATCCTCGTGTATCTTTGTTAATTGGACT
GTGCGATTCTTTATCTTGGGAAAGAGTCCTTCTCTGACGCTTTAGACACCCTGGCTGACATGATGCATTTCTGCCAGATG
GTGGCAGCTGTGGAAACTATCAATGCAGTGATTGGAGTCACTAATTCACCAGTATTGCCTCCCTTTAGCTAGCCTCTTGG
AAGAAATTTCATTTTGTTTATCATCCTTGGCACCATGGAAGAAATGCAAAACAGTGCTGTGGTTTTCTTTGTGTTTTATC
TGTGGAGCACAACTGAAATTTTGGTTTTCCCCTTTACATGCTTTCCTGCATTGATCTGGATTGGAAAGTGCTCACATGGC
GTCACTACACTGTGTGGATTCCCTTATATCCTCTGCGATGTTTGAGCGAAGCTGTCACAGAGATCCAGTCCATTCCAATA
GTCAATGAAACAGGAAGATTCAGTTTCACATTGCCATATGCAATGAAAATCAAATTTCGATTTTCCTTTTTTCTTCAGAT
TTAACTTATAATGTCATTTTTAGGGTTATACATAAATTTCTGTCAACTTTATAAACAGCGCAGGCAGATTTATGGACAAA
AAATGAAAAAGATTCAC

Alignment

ORF - retro_dnov_54 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.91 %
• Parental protein coverage: 75.41 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WERLTKQEKRPLFLAPDFDRWLDESDAEMELRAKEEERLNKLRLESEGSPETLASLKKGYLFMYNFVQFL
          WE.LTKQEK.PLFLAPDFD.WLDESD.EMELRAKEEE.LNKLRLESEGSPETLASLKKGYLFM.N.VQFL
Retrocopy WE*LTKQEKHPLFLAPDFDSWLDESDEEMELRAKEEECLNKLRLESEGSPETLASLKKGYLFMHNLVQFL

Parental  GFSWIFVNLTVRFFILGK-ESFYDTFHTLADMMYFCQMLAAVETINAAIGVTNSPLLPSLIQLLGRNFIL
          G.S.IFVN.TVRFFILGK.ESF.D...TLADMM.FCQM.AAVETINA.IGVTNSP.LP.....LGRNFIL
Retrocopy GSSCIFVNWTVRFFILGK<ESFSDALDTLADMMHFCQMVAAVETINAVIGVTNSPVLPPFS*PLGRNFIL

Parental  FIIFGTMEEMQNSAMVFFVFYLWSAIEI-FRYPFYMLSCIDMDWKVLTWLRYTVWIPLYPLGCLSEAVSV
          FII.GTMEEMQNSA.VFFVFYLWS..EI.F..P.YMLSCID.DWKVLTW..YTVWIPLYPL.CLSEAV..
Retrocopy FIILGTMEEMQNSAVVFFVFYLWSTTEI<FGFPLYMLSCIDLDWKVLTWRHYTVWIPLYPLRCLSEAVTE

Parental  IQSIPIFNETGRFSFTLPYPMKIKVRFSFFLQIYLIMSFLGLYINFRHLYKQRRRRYGQKKKKIH
          IQSIPI.NETGRFSFTLPY.MKIK.RFSFFLQI.LIMSFLGLYINF..LYKQRR..YGQK.KKIH
Retrocopy IQSIPIVNETGRFSFTLPYAMKIKFRFSFFLQI*LIMSFLGLYINFCQLYKQRRQIYGQKMKKIH

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	44.73 RPM
SRP012922_cerebellum	0.00 RPM	57.60 RPM
SRP012922_heart	0.00 RPM	13.69 RPM
SRP012922_kidney	0.00 RPM	62.15 RPM
SRP012922_liver	0.00 RPM	177.56 RPM
SRP012922_lung	0.00 RPM	28.56 RPM
SRP012922_quadricep_muscle	0.00 RPM	10.04 RPM
SRP012922_spleen	0.00 RPM	48.30 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_54 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000001687	2 retrocopies	retro_dnov_352, retro_dnov_54 ,
Myotis lucifugus	ENSMLUG00000015087	1 retrocopy	retro_mluc_71,