RetrogeneDB ID: retro_dnov_352

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_3903:17176..18071(-)
• Located in intron of: ENSDNOG00000011751

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_352
ATGGAGAACCAGGTGCTGACACCACATGTATACTGGGCTCAGTGATACTGCAAGTTGTATCTGTGCGTGGAGCTGAGCGA
CATTCAGAATCCTGCTGTCAGCATCACTGAAAATGTTCTACATTTTAAAGCTCAGGGACATAGTGCCAAAGGAGACAACA
TCTACATATTTCACCTGGAGTTCGTTGAACTTGTGAAGCCAGAGCTGGTTTACAAACTGACCCAGAGGCAGGTAAACATT
ACAGTACAGAAGGTGAGTCAGTGGTGGAACGACTCACCAAGCAGGAGAAATGTCCACTGTTTTTGGCCCCTGATTTGATC
ACTGGCTAGACAAGCCTAATACGGAAATGGAGCTCAGAGCCAAGGAACAAGAATGCCTAAATAAACTCAGACTTGAAAGT
GAGCCTCCCCTGAAACTCTTGCAAGCTTGAAGAAAGGACACCTGCTCATGGATAATTTTGTAAAGTTCTTGGGATTCTCC
TGGATCCTTGTTAACTTGACTGTGCCATTCTTTATCTTGGGAAAAGCATCCTTCTATGACATATTTCACACCCTGGCTGA
CAGTTGTATTTCTGCCAGATGCTGGCAGCCATGGAAACTGTCAATACAGCAATTAGAATCACTAACTCACCAGTATTGCC
TTCTCTTATCCAACTTCTTGGAAGAAATTTCTTTCTGTTTATAATCTTAGGCACCATGGAAAAAATGTGAAACAGTATTG
TGGTTTTCTTTGTGTTTTATCTGTGGAGCACTATTAAATTTTCAGGTACCCCGTTTACATGCTTTCCTGCCTTTGATATG
GATTGGAAAGTGCCCACAGGCTTCCCTACCGCGTGCGTATTCCCATATACCCTGTAGGCTGTTCAGCTCAAGCTGTTTCA
GTGATCCAGTCCATT

Alignment

ORF - retro_dnov_352 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.9 %
• Parental protein coverage: 83.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MENQVLTPHVYWAQRHRELYLRVELSDVQNPAISITENVLHFKAQGHGAKGDNVYEFHLEFFDLVKPELV
          MENQVLTPHVYWAQ....LYL.VELSD.QNPA.SITENVLHFKAQGH.AKGDN.Y.FHLEF..LVKPELV
Retrocopy MENQVLTPHVYWAQ*YCKLYLCVELSDIQNPAVSITENVLHFKAQGHSAKGDNIYIFHLEFVELVKPELV

Parental  YKLTQRQVNITVQKKVSQWW-ERLTKQEKRPLFLAPD-FDRWLDESDAEMELRAKEEERLNKLRLESE-G
          YKLTQRQVNITVQK.VSQWW.ERLTKQEK.PLFLAPD.FD.WLD....EMELRAKE.E.LNKLRLESE..
Retrocopy YKLTQRQVNITVQK-VSQWW<ERLTKQEKCPLFLAPD<FDHWLDKPNTEMELRAKEQECLNKLRLESE<A

Parental  SPETLASLKKGYLFMYNFVQFLGFSWIFVNLTVRFFILGKESFYDTFHTLAD-MMYFCQMLAAVETINAA
          SPETLASLKKG.L.M.NFV.FLGFSWI.VNLTV.FFILGK.SFYD.FHTLAD...YFCQMLAA.ET.N.A
Retrocopy SPETLASLKKGHLLMDNFVKFLGFSWILVNLTVPFFILGKASFYDIFHTLAD<QLYFCQMLAAMETVNTA

Parental  IGVTNSPLLPSLIQLLGRNFILFIIFGTMEEMQNSAMVFFVFYLWSAIE-IFRYPFYMLSCI-DMDWKVL
          I..TNSP.LPSLIQLLGRNF.LFII.GTME.M.NS..VFFVFYLWS.I..IFRYP.YMLSC..DMDWKV.
Retrocopy IRITNSPVLPSLIQLLGRNFFLFIILGTMEKM*NSIVVFFVFYLWSTIK<IFRYPVYMLSCL>DMDWKVP

Parental  TW-LRYTVWIPLYPLGCLSEAVSVIQSI
          T..L.Y.V.IP.YP.GC...AVSVIQSI
Retrocopy TG<LPYRVRIPIYPVGCSAQAVSVIQSI

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	0.14 RPM	57.60 RPM
SRP012922_heart	0.23 RPM	13.69 RPM
SRP012922_kidney	0.27 RPM	62.15 RPM
SRP012922_liver	0.00 RPM	177.56 RPM
SRP012922_lung	0.00 RPM	28.56 RPM
SRP012922_quadricep_muscle	0.35 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_352 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,