RetrogeneDB ID: | retro_dnov_1908 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_36216:4899..5492(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HPRT1 | ||
| Ensembl ID: | ENSDNOG00000008495 | ||
| Aliases: | None | ||
| Description: | hypoxanthine phosphoribosyltransferase 1 [Source:HGNC Symbol;Acc:5157] |
Retrocopy-Parental alignment summary:
>retro_dnov_1908
AATTTATTTTGCATATCTAATCATTATGCTGAAGATTTGAATGGGTACTTATTACTCGGGGACTGATTATGGACAGAACC
AGCCAGTTTGTTCAAGATGTGATGAAGGAGATGGAAGACCATGGCATTGCAGCCCTCTGTGTGCTTAAGGGGGATGCATT
CTTTGACCTCTTACTGGATTACATCAAAGTACTGAACAGAAATAGAGATAGATGCATTCCTATGACTGTAGATTTTAGCA
GACTACAGAGCTACTGTAATGACCCATCAACAGGAGACATAAAAGTAATTGGTGGAGATAGTCTCTCAACTTTAACCGGA
AAGAATGTCATGATTGTTGAAGATATAATTAGCTCTGGCAAAACAATGCAACCCTTGCTTTCCTTGGTCAAGCAGTATAA
TCCGAAGATGGTCAAGTTTGCAAGGTTACTGGTGAAAAGGGCCCCTCAAAGTGTTGGATTAAGACCAGACTTTCTTGGAT
TTGAAATTCCAGACAAGTTTGTTGTAGGATATATCCTTGACTAGAATGAATACTTCAGGGATTTGAATCCTATTTGTATC
ATTAGCAAAACTGGAAAAGCAAAATACCAAGCC
ORF - retro_dnov_1908 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.5 % |
| Parental protein coverage: | 95.22 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | NLFCIPNHYAEDL-ERVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRN |
| NLFCI.NHYAEDL.E.V.I..GLIMDRT.....DVMKEM..H.I.ALCVLKG...FF..LLDYIK.LNRN | |
| Retrocopy | NLFCISNHYAEDL<EWVLITRGLIMDRTSQFVQDVMKEMEDHGIAALCVLKGD-AFFDLLLDYIKVLNRN |
| Parental | SDRSIPMTVDFIRLKSYCNDQSTGDIKVIGGDDLSTLTGKXXXXXXDIIDTGKTMQTLLSLVKQYNPKMV |
| .DR.IPMTVDF.RL.SYCND.STGDIKVIGGD.LSTLTGK......DII..GKTMQ.LLSLVKQYNPKMV | |
| Retrocopy | RDRCIPMTVDFSRLQSYCNDPSTGDIKVIGGDSLSTLTGKNVMIVEDIISSGKTMQPLLSLVKQYNPKMV |
| Parental | KVASLLVKRTPRSVGYRPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAKYKA |
| K.A.LLVKR.P.SVG.RPDF.GFEIPDKFVVGY.LD.NEYFRDLN..C.IS.TGKAKY.A | |
| Retrocopy | KFARLLVKRAPQSVGLRPDFLGFEIPDKFVVGYILD*NEYFRDLNPICIISKTGKAKYQA |
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 | 9 .14 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 24 .06 RPM |
| SRP012922_heart | 0 .00 RPM | 12 .99 RPM |
| SRP012922_kidney | 0 .00 RPM | 6 .02 RPM |
| SRP012922_liver | 0 .00 RPM | 15 .17 RPM |
| SRP012922_lung | 0 .00 RPM | 26 .73 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 8 .83 RPM |
| SRP012922_spleen | 0 .00 RPM | 34 .45 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_1908 was not experimentally validated.