RetrogeneDB ID: | retro_dnov_128 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | GeneScaffold_1939:630411..630915(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | JOSD1 | ||
| Ensembl ID: | ENSDNOG00000016015 | ||
| Aliases: | None | ||
| Description: | Josephin domain containing 1 [Source:HGNC Symbol;Acc:28953] |
Retrocopy-Parental alignment summary:
>retro_dnov_128
GTGAATTGTGTGTCATGGAAAGGAGACAAGGCCAAGTCTGAATCATTGGAGCTGCCCCAGGCCGCACCCCCTCAGATCTA
TCAAGAGAAACAGGGCAGGGAGCTTTCCCCCGCCCTCCATGCCCTCAATAACGTCTTCCAGGACAGCCACGCCTTCACCC
AGGAAGCTCTGCAAGAGATTTTTCAGAAGTTGTCTTCAAAGACCATGGTGACACCCCACGAGAAGAGCGTGTTGGGAAAT
GAGAACTGCTATAGGAACATCATCATGGCAGCACTTCAGACCGAAGGCTGTGAAGCTGTTTGGTGGACAAGGCAGGGACG
TCAGTGTATTGCTCTCTCTAATGTCTTGGCTTTATTGTGAATCTGCTCTCCAGCCTGTGCTGGAGTCCACTGAAGTTGCT
TCTCAAAGGTAGCACTGGATCTGCATTGAGAGAGCAGAGGTGCCTACCACAACCCAGACTCCAAACTCAAGATGCCTGAG
TGGATTGGAGGCCGGAGCGACCTC
ORF - retro_dnov_128 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.16 % |
| Parental protein coverage: | 82.74 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | IRCMPWKGEKTKFESLELP-AVPPWIYHEEQCRQLY-ALHALNNIFP----FTQEML-DIFQRLSPNTMV |
| ..C..WKG.K.K.ESLELP.A.PP.IY.E.Q.R.L..ALHALNN.F.....FTQE.L..IFQ.LS..TMV | |
| Retrocopy | VNCVSWKGDKAKSESLELPQAAPPQIYQEKQGRELSPALHALNNVFQDSHAFTQEALQEIFQKLSSKTMV |
| Parental | TPHKKSMLGNGNYDVNVIMAALQTKGYEAVWWDKRRDVSVIALTNV-MGFIMNLPSSLCWGPLKLPLK-R |
| TPH.KS.LGN.N...N.IMAALQT.G.EAVWW..R.....IAL.NV..GFI.NL.SSLCW.PLKL.LK.R | |
| Retrocopy | TPHEKSVLGNENCYRNIIMAALQTEGCEAVWW-TRQGRQCIALSNV<LGFIVNLLSSLCWSPLKLLLK<R |
| Parental | QHWICVR-EVGGAYYNLDSKLKMPEWIGGESEL |
| .HWIC...E..GAY.N.DSKLKMPEWIGG.S.L | |
| Retrocopy | *HWICIE<ESRGAYHNPDSKLKMPEWIGGRSDL |
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 | 4 .86 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 3 .57 RPM |
| SRP012922_heart | 0 .00 RPM | 1 .86 RPM |
| SRP012922_kidney | 0 .00 RPM | 1 .10 RPM |
| SRP012922_liver | 0 .00 RPM | 5 .73 RPM |
| SRP012922_lung | 0 .00 RPM | 5 .35 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 3 .12 RPM |
| SRP012922_spleen | 0 .00 RPM | 5 .84 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_128 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 4 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000016015 | 1 retrocopy |
retro_dnov_128 ,
|
| Macropus eugenii | ENSMEUG00000002899 | 2 retrocopies | |
| Sarcophilus harrisii | ENSSHAG00000015931 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000024999 | 1 retrocopy |