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:
| 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 |
(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 | ENSMLUG00000015087 | 1 retrocopy |