RetrogeneDB ID: | retro_dnov_906 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_11971:6914..7464(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TRAM1 | ||
| Ensembl ID: | ENSDNOG00000009296 | ||
| Aliases: | None | ||
| Description: | translocation associated membrane protein 1 [Source:HGNC Symbol;Acc:20568] |
Retrocopy-Parental alignment summary:
>retro_dnov_906
TTTTTCTATATAATCACTGTTAGCTTACTGATTTCATGCTTTTCCCGAATTCTTCTTCCAGAAACCCAAAAAAGATATTC
CATGTCAGCCTGTCTACACTGGTCTTTCCCTCTTTCCCATTGCAGGAGAGTATCTTTTGAATTTGAATCATCTTGGACTT
GTTCTTTTGATGCTCCATTATTTTGTTGAATTTCTTTTCCATATTTCCTGCCTGCTTTATTTTAGTGATGAAAAATATCA
GAAAGGATTTTCTCTGCGGACAATCCTGTTTGTTTTTAGAAGACTTCTGACTTTAATTTTTTTGGTATTCACTGTTGGCT
TTGGCCTTGTAAGAGCAGAGAATCAGAAGCTGAATTTCAGTACTGGAAACTTCCATGTGCTGGCGGGTAGACTTGCTGTT
CCAGCATCCATTTGCATTATTCTAGTATTCATGACGTGGAAGTTCATTAATTTCCAGCTTCGGAGGTGGAAGGAATATTC
TAGTTTTCAGGCATGAACTGTGAAGAGGAAACCAATAGCTACTAAAGGCAAGTCTTCTAGGAAAGGAACA
ORF - retro_dnov_906 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 77.3 % |
| Parental protein coverage: | 52.44 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | FFYI-SQLAYWFHAFPELYFQKTKKEDIPRQLVYIGLYLFHIAGAYLLNLNHLGLVLLVLHYFVEFLFHI |
| FFYI.S.LAY.FHAFPE..FQK.KK.DIP.Q.VY.GL.LF.IAG.YLLNLNHLGLVLL.LHYFVEFLFHI | |
| Retrocopy | FFYI>SLLAY*FHAFPEFFFQKPKK-DIPCQPVYTGLSLFPIAGEYLLNLNHLGLVLLMLHYFVEFLFHI |
| Parental | SRLFYFSDEKYQ-GFSLWAVLFVLGRLLTLILSVLTVGFGLARAENQKLDFSTGNFNVLAVRIAVLASIC |
| S.L.YFSDEKYQ.GFSL...LFV..RLLTLI..V.TVGFGL.RAENQKL.FSTGNF.VLA.R.AV.ASIC | |
| Retrocopy | SCLLYFSDEKYQKGFSLRTILFVFRRLLTLIFLVFTVGFGLVRAENQKLNFSTGNFHVLAGRLAVPASIC |
| Parental | ITQAFMMWKFINFQLRRWREHSSFQAPTVKKKPTVTKGRSSRKGT |
| I...FM.WKFINFQLRRW.E.SSFQA.TVK.KP..TKG.SSRKGT | |
| Retrocopy | IILVFMTWKFINFQLRRWKEYSSFQA*TVKRKPIATKGKSSRKGT |
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 | 96 .26 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 11 .68 RPM |
| SRP012922_heart | 0 .00 RPM | 13 .92 RPM |
| SRP012922_kidney | 0 .00 RPM | 41 .62 RPM |
| SRP012922_liver | 0 .00 RPM | 76 .47 RPM |
| SRP012922_lung | 0 .00 RPM | 69 .18 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 15 .58 RPM |
| SRP012922_spleen | 0 .00 RPM | 135 .52 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_906 was not experimentally validated.