RetrogeneDB ID: | retro_rnor_2358 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 6:48421265..48422005(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Fbxw2 | ||
| Ensembl ID: | ENSRNOG00000018687 | ||
| Aliases: | None | ||
| Description: | F-box/WD repeat-containing protein 2 [Source:UniProtKB/Swiss-Prot;Acc:B2RZ17] |
Retrocopy-Parental alignment summary:
>retro_rnor_2358
GTGACAGGCTCCTTTGATAGCACTATGGCCTGCTGGGAATGGAGTTCCGGAGCCAGGACCCAGCACTTCCGGGGTCATAT
GGGTGCGGTGTTCAGTGCGGACTACAGTGATGAACTGGATATTTTGGTAAGTGGTTCTGCAGACTTCGTTATGAAAGTAT
GGGCTTTGACTGATGGGACATACCTGAACACACTCCTTGGGCATACTGAATGAGTTACCAAGGTGGTCTTGCAGAAGTGC
CAAGTCAAGTCTCCTTGCACAGCCGTGGAGACTACATCCTCATAAGTGCAGACAAATATGAGATTGAGATTTGGCCAATT
GGGAGAGAAGTCAACTGTAAGTGCTTAACGGGACTGTCTATCTCCAAGGATAGAAGTATCTGCTTACAGTCAAGACTTCA
CTTTGATGGAAAATACATTGTATGTAGTTCAGCCCTGGGTTTGTATCAGTGGGACTTTGCTAGTTATGATATTCTCGGGG
TCATCAAGACACCCAAGGTAGCAAACTTGGCCTTCCTTGGCTTTGGAGATGTCTTCACTCTACTTCGCCACTGCCTATAC
ATCATGGACTTGAGGACAGGGAGCTCATTAACCACTGGCCACTGCCAGAGGACAGAAAATCAGAGAAGCTCCAGCTTCCT
GGCAGGAGAAGCATCCTGGCTGAATGGACTGGATGAACGCAATGACATGGGCTTGGTGTTTGCCACCAGCATGCTTGACC
ACAGTGTTCACCTGGTCTTA
ORF - retro_rnor_2358 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.88 % |
| Parental protein coverage: | 55.07 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | VTGSFDNTVACWEWSSGARTQHFRGHTGAVFSVDYSDELDILVSGSADFAVKVWALSAGTCLNTLTGHTE |
| VTGSFD.T.ACWEWSSGARTQHFRGH.GAVFS.DYSDELDILVSGSADF..KVWAL..GT.LNTL.GHTE | |
| Retrocopy | VTGSFDSTMACWEWSSGARTQHFRGHMGAVFSADYSDELDILVSGSADFVMKVWALTDGTYLNTLLGHTE |
| Parental | WVTKVVLQQCKVKS-LLHSPGDYILLSADKYEIKIWPIGREINCKCLKTLSVSEDRSICLQPRLHFDGKY |
| .VTKVVLQ.C.VKS..LHS.GDYIL.SADKYEI.IWPIGRE.NCKCL..LS.S.DRSICLQ.RLHFDGKY | |
| Retrocopy | *VTKVVLQKCQVKS<SLHSRGDYILISADKYEIEIWPIGREVNCKCLTGLSISKDRSICLQSRLHFDGKY |
| Parental | IVCSSALGLYQWDFASYDILRVIKTPEVANLALLGFGDVFALLFDNHYLYIMDLRTESLISRWPLPEYRK |
| IVCSSALGLYQWDFASYDIL.VIKTP.VANLA.LGFGDVF.LL...H.LYIMDLRT.S............ | |
| Retrocopy | IVCSSALGLYQWDFASYDILGVIKTPKVANLAFLGFGDVFTLL--RHCLYIMDLRTGSSLTTGHC-QRTE |
| Parental | SKRGSSFLAGEASWLNGLDGHNDTGLVFATSMPDHSIHLVL |
| ..R.SSFLAGEASWLNGLD..ND.GLVFATSM.DHS.HLVL | |
| Retrocopy | NQRSSSFLAGEASWLNGLDERNDMGLVFATSMLDHSVHLVL |
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 |
|---|---|---|
| SRP017611_brain | 0 .00 RPM | 63 .70 RPM |
| SRP017611_kidney | 0 .00 RPM | 31 .82 RPM |
| SRP017611_liver | 0 .00 RPM | 34 .49 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2358 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2358 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_2358 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Rattus norvegicus | ENSRNOG00000016280 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000018687 | 1 retrocopy |
retro_rnor_2358 ,
|
| Tarsius syrichta | ENSTSYG00000008021 | 1 retrocopy |