RetrogeneDB ID: | retro_dnov_206 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | GeneScaffold_2604:274149..274629(-) | ||
| Located in intron of: | ENSDNOG00000017715 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | VAPB | ||
| Ensembl ID: | ENSDNOG00000012711 | ||
| Aliases: | None | ||
| Description: | VAMP (vesicle-associated membrane protein)-associated protein B and C [Source:HGNC Symbol;Acc:12649] |
Retrocopy-Parental alignment summary:
>retro_dnov_206
GAAAGTAAACACAAGTTTATGGTTCAGTCTATGTTTGTTCCAACTGACACTTCTGATATGGAAGCAATATGGAAGGAGGC
AAAACCGGAAGATCTTATGGATTCAAAAACTTAGATGTGCGTTCGAATTGCCAGCAGAAAATGATAAACCACATGATGTA
GAAATAAATAAAATTATAACCACATTTGCATCAAAGACAGAAACACCAACAATGTCTAAATCTCTGAGTTTTTCTTTGGA
TGACACTGAAGTTAAAGTGATGGAAGAATGTAAGAGGCTGCAAGGTGAAGTTCAGAGGCTACGGGAGGAGAACAAACAAT
TCAAGGAAGAAGATGGACCTCAGGTGAGGAAGACAGTGCAGAGCAACAGCCCGCGTCTGCGTGGGCCACAGCCAGGAAGG
AAGAAGGTCTCAGCACCCGGCTACTTGCTCTAGAGGTCTTGTTCTTTATTGTTGGTATAATTATAGGGAAATCTGCCTTG
ORF - retro_dnov_206 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.73 % |
| Parental protein coverage: | 66.8 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | EKSHKFMVQSMFAPTDTSDMEAVWKEAKPEDLMDSK-LRCVFELPAENDKPHDVEINKIITTSASKTETP |
| E..HKFMVQSMF.PTDTSDMEA.WKEAKPEDLMDSK.LRC.FELPAENDKPHDVEINKIITT.ASKTETP | |
| Retrocopy | ESKHKFMVQSMFVPTDTSDMEAIWKEAKPEDLMDSK>LRCAFELPAENDKPHDVEINKIITTFASKTETP |
| Parental | TMSKSLSSSLDDTEVKKVMEECKRLQGEVQRLREENKQFKEEDGLRMRKTVQSNS-PVSALATAGKEEGL |
| TMSKSLS.SLDDTEV.KVMEECKRLQGEVQRLREENKQFKEEDG...RKTVQSNS.P.SA.ATA.KEEGL | |
| Retrocopy | TMSKSLSFSLDDTEV-KVMEECKRLQGEVQRLREENKQFKEEDGPQVRKTVQSNS<PASAWATARKEEGL |
| Parental | RTRLLALVVLFFIVGVIIGKIAL |
| .TRLLAL.VLFFIVG.IIGK.AL | |
| Retrocopy | STRLLALEVLFFIVGIIIGKSAL |
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 .19 RPM | 38 .70 RPM |
| SRP012922_cerebellum | 0 .27 RPM | 28 .32 RPM |
| SRP012922_heart | 0 .00 RPM | 20 .19 RPM |
| SRP012922_kidney | 0 .00 RPM | 24 .92 RPM |
| SRP012922_liver | 0 .15 RPM | 19 .51 RPM |
| SRP012922_lung | 0 .46 RPM | 23 .83 RPM |
| SRP012922_quadricep_muscle | 0 .17 RPM | 27 .52 RPM |
| SRP012922_spleen | 0 .00 RPM | 23 .01 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_206 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 5 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000017424 | 1 retrocopy | |
| Dasypus novemcinctus | ENSDNOG00000012711 | 1 retrocopy |
retro_dnov_206 ,
|
| Macropus eugenii | ENSMEUG00000009788 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000016549 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000009351 | 1 retrocopy |