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


Retrocopy-Parental alignment summary:






>retro_dnov_352
ATGGAGAACCAGGTGCTGACACCACATGTATACTGGGCTCAGTGATACTGCAAGTTGTATCTGTGCGTGGAGCTGAGCGA
CATTCAGAATCCTGCTGTCAGCATCACTGAAAATGTTCTACATTTTAAAGCTCAGGGACATAGTGCCAAAGGAGACAACA
TCTACATATTTCACCTGGAGTTCGTTGAACTTGTGAAGCCAGAGCTGGTTTACAAACTGACCCAGAGGCAGGTAAACATT
ACAGTACAGAAGGTGAGTCAGTGGTGGAACGACTCACCAAGCAGGAGAAATGTCCACTGTTTTTGGCCCCTGATTTGATC
ACTGGCTAGACAAGCCTAATACGGAAATGGAGCTCAGAGCCAAGGAACAAGAATGCCTAAATAAACTCAGACTTGAAAGT
GAGCCTCCCCTGAAACTCTTGCAAGCTTGAAGAAAGGACACCTGCTCATGGATAATTTTGTAAAGTTCTTGGGATTCTCC
TGGATCCTTGTTAACTTGACTGTGCCATTCTTTATCTTGGGAAAAGCATCCTTCTATGACATATTTCACACCCTGGCTGA
CAGTTGTATTTCTGCCAGATGCTGGCAGCCATGGAAACTGTCAATACAGCAATTAGAATCACTAACTCACCAGTATTGCC
TTCTCTTATCCAACTTCTTGGAAGAAATTTCTTTCTGTTTATAATCTTAGGCACCATGGAAAAAATGTGAAACAGTATTG
TGGTTTTCTTTGTGTTTTATCTGTGGAGCACTATTAAATTTTCAGGTACCCCGTTTACATGCTTTCCTGCCTTTGATATG
GATTGGAAAGTGCCCACAGGCTTCCCTACCGCGTGCGTATTCCCATATACCCTGTAGGCTGTTCAGCTCAAGCTGTTTCA
GTGATCCAGTCCATT

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:

ParentalMENQVLTPHVYWAQRHRELYLRVELSDVQNPAISITENVLHFKAQGHGAKGDNVYEFHLEFFDLVKPELV
MENQVLTPHVYWAQ....LYL.VELSD.QNPA.SITENVLHFKAQGH.AKGDN.Y.FHLEF..LVKPELV
RetrocopyMENQVLTPHVYWAQ*YCKLYLCVELSDIQNPAVSITENVLHFKAQGHSAKGDNIYIFHLEFVELVKPELV
ParentalYKLTQRQVNITVQKKVSQWW-ERLTKQEKRPLFLAPD-FDRWLDESDAEMELRAKEEERLNKLRLESE-G
YKLTQRQVNITVQK.VSQWW.ERLTKQEK.PLFLAPD.FD.WLD....EMELRAKE.E.LNKLRLESE..
RetrocopyYKLTQRQVNITVQK-VSQWW<ERLTKQEKCPLFLAPD<FDHWLDKPNTEMELRAKEQECLNKLRLESE<A
ParentalSPETLASLKKGYLFMYNFVQFLGFSWIFVNLTVRFFILGKESFYDTFHTLAD-MMYFCQMLAAVETINAA
SPETLASLKKG.L.M.NFV.FLGFSWI.VNLTV.FFILGK.SFYD.FHTLAD...YFCQMLAA.ET.N.A
RetrocopySPETLASLKKGHLLMDNFVKFLGFSWILVNLTVPFFILGKASFYDIFHTLAD<QLYFCQMLAAMETVNTA
ParentalIGVTNSPLLPSLIQLLGRNFILFIIFGTMEEMQNSAMVFFVFYLWSAIE-IFRYPFYMLSCI-DMDWKVL
I..TNSP.LPSLIQLLGRNF.LFII.GTME.M.NS..VFFVFYLWS.I..IFRYP.YMLSC..DMDWKV.
RetrocopyIRITNSPVLPSLIQLLGRNFFLFIILGTMEKM*NSIVVFFVFYLWSTIK<IFRYPVYMLSCL>DMDWKVP
ParentalTW-LRYTVWIPLYPLGCLSEAVSVIQSI
T..L.Y.V.IP.YP.GC...AVSVIQSI
RetrocopyTG<LPYRVRIPIYPVGCSAQAVSVIQSI

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

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
Dasypus novemcinctus was not studied using ChIP-Seq data.
Dasypus novemcinctus was not studied using EST data.
Dasypus novemcinctus was not studied using FANTOM5 data.
retro_dnov_352 was not experimentally validated.

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.

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 ENSMLUG000000150871 retrocopy



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