RetrogeneDB ID: | retro_cfam_284 | ||
Retrocopylocation | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 1:115620894..115621477(+) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | ENSCAFG00000006155 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | TYSND1 | ||
| Ensembl ID: | ENSCAFG00000014026 | ||
| Aliases: | None | ||
| Description: | trypsin domain containing 1 [Source:HGNC Symbol;Acc:28531] |
Retrocopy-Parental alignment summary:
>retro_cfam_284
ATGCCTTTCATCTTTGAGTGGATATACAATGGCTTCAGCGGTGTGCTCCAGTTCCTAGGACTCTACAAGAAATCTGGAAA
ACTTGTATTTTTAGGTTTGGACAATGCAGGCAAAACCACTCTTCTACACATGTCCAAAGATGACCGACTGGGCCAAAATG
TTCCGACATTACATCTGACATCAGAAGAGCTGACAATTGCTGGAATGACTTTTACAACTTTTGAGCTTGGTGGGCCGGGC
AAGCGCGCCGGGTTTGGAAAAATTACCTCCCAGCAATTAATGGGATTGTCTTTCTGGTGGACTGTGTAGATCATCCTCAC
CTCGTGGTATCCAAAGTTGAGCTAAATGCTCTAATGACTGATGAGACAATATCCAATGTGCCAATCCTGATCTTGGGTAA
CAAGATAGACGCAATCAGTGAAGAAAAACTCTGGGAGATATTTGGGCTTTATGGACAGACCACAGAAAAGGTAAACATGA
CCCTGAAGGAGCTGAATGCGTGCCCCATGGAAGTGTTCGTATGCAGTGTGCTCAAGAGGCAAGGCTAGAGTGAGGGCTTC
CAGGGCTTTCCCAGTATATTGAC
ATGCCTTTCATCTTTGAGTGGATATACAATGGCTTCAGCGGTGTGCTCCAGTTCCTAGGACTCTACAAGAAATCTGGAAA
ACTTGTATTTTTAGGTTTGGACAATGCAGGCAAAACCACTCTTCTACACATGTCCAAAGATGACCGACTGGGCCAAAATG
TTCCGACATTACATCTGACATCAGAAGAGCTGACAATTGCTGGAATGACTTTTACAACTTTTGAGCTTGGTGGGCCGGGC
AAGCGCGCCGGGTTTGGAAAAATTACCTCCCAGCAATTAATGGGATTGTCTTTCTGGTGGACTGTGTAGATCATCCTCAC
CTCGTGGTATCCAAAGTTGAGCTAAATGCTCTAATGACTGATGAGACAATATCCAATGTGCCAATCCTGATCTTGGGTAA
CAAGATAGACGCAATCAGTGAAGAAAAACTCTGGGAGATATTTGGGCTTTATGGACAGACCACAGAAAAGGTAAACATGA
CCCTGAAGGAGCTGAATGCGTGCCCCATGGAAGTGTTCGTATGCAGTGTGCTCAAGAGGCAAGGCTAGAGTGAGGGCTTC
CAGGGCTTTCCCAGTATATTGAC
ORF - retro_cfam_284 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.5 % |
| Parental protein coverage: | 100. % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MSFIFEWIYNGFSSVLQFLGLYKKSGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMT |
| M.FIFEWIYNGFS.VLQFLGLYKKSGKLVFLGLDNAGKTTLLHM.KDDRLGQ.VPTLH.TSEELTIAGMT | |
| Retrocopy | MPFIFEWIYNGFSGVLQFLGLYKKSGKLVFLGLDNAGKTTLLHMSKDDRLGQNVPTLHLTSEELTIAGMT |
| Parental | FTTFDLGG-HEQARRVWKNYLPAINGIVFLVDCADHPRLMESKVELNALMTDETISNVPILILGNKIDRT |
| FTTF.LGG...QARRVWKNYLPAINGIVFLVDC.DHP.L..SKVELNALMTDETISNVPILILGNKID.. | |
| Retrocopy | FTTFELGG<AGQARRVWKNYLPAINGIVFLVDCVDHPHLVVSKVELNALMTDETISNVPILILGNKID-- |
| Parental | DAISEEKLREIFGLYGQTTGKGNVTLKELNARPMEVFMCSVLKRQGYGEGFR-WLSQYID |
| .AISEEKL.EIFGLYGQTT.K.N.TLKELNA.PMEVF.CSVLKRQG..EGF...LSQYID | |
| Retrocopy | -AISEEKLWEIFGLYGQTTEKVNMTLKELNACPMEVFVCSVLKRQG*SEGFQ<GLSQYID |
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 |
|---|---|---|
| SRP012049_cerebellum | 0 .00 RPM | 34 .48 RPM |
| SRP017611_brain | 0 .00 RPM | 29 .06 RPM |
| SRP017611_kidney | 0 .00 RPM | 38 .04 RPM |
| SRP017611_liver | 0 .00 RPM | 46 .70 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_284 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_284 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_284 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000014026 | 2 retrocopies |
retro_cfam_1714, retro_cfam_284 ,
|