RetrogeneDB ID: | retro_cfam_1714 | ||
Retrocopylocation | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 4:80126496..80127066(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
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_1714
GTCTTTGAGTGGATCAATCGTGTGCTCCAGGTCTAGTACTCTACAAGAAATCTGGAAAACTTTTATTCTTGGGTTTGGAC
AATGCAGGAAAAACCACTCTTCTACACATATTCAATGATGACCAACTGGGTCAACATATTTCAACATTAGATCTGACATC
AGAAGAGCTGATGATCGCCAGAAATGACTTTTACAACTTTTGACCTTGGTGGGCAGAGGAGCAAGCAAGTTGGGTTTGGA
AAAATTACCTCCCAGCAATTAATGATATTGTCTTTCTGGCAGATTCTGTAGATCATCCTCCACTCATGGAAACCAGATTT
GAGCTAAATGCTTTAATGACCAATGAAACAACATCTAATGTGCCAATCCTTATCTTGGGCAACAAAAACAACAAAACTGA
TGCAGTCAGGGAAGACAACTCCAAGAGATATTTGGGTTTTAGGGATAGACCACGGGAAAGGGGAATGTGACCCTGCAGGA
GCTGAATGCCCTCCCCATGGAAATGTCACATGCAGTGTGCTCAAGAGACAAGGCTATCACAAGGACTTCTGCTGGCTTTC
CCAGGATATT
GTCTTTGAGTGGATCAATCGTGTGCTCCAGGTCTAGTACTCTACAAGAAATCTGGAAAACTTTTATTCTTGGGTTTGGAC
AATGCAGGAAAAACCACTCTTCTACACATATTCAATGATGACCAACTGGGTCAACATATTTCAACATTAGATCTGACATC
AGAAGAGCTGATGATCGCCAGAAATGACTTTTACAACTTTTGACCTTGGTGGGCAGAGGAGCAAGCAAGTTGGGTTTGGA
AAAATTACCTCCCAGCAATTAATGATATTGTCTTTCTGGCAGATTCTGTAGATCATCCTCCACTCATGGAAACCAGATTT
GAGCTAAATGCTTTAATGACCAATGAAACAACATCTAATGTGCCAATCCTTATCTTGGGCAACAAAAACAACAAAACTGA
TGCAGTCAGGGAAGACAACTCCAAGAGATATTTGGGTTTTAGGGATAGACCACGGGAAAGGGGAATGTGACCCTGCAGGA
GCTGAATGCCCTCCCCATGGAAATGTCACATGCAGTGTGCTCAAGAGACAAGGCTATCACAAGGACTTCTGCTGGCTTTC
CCAGGATATT
ORF - retro_cfam_1714 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 65.98 % |
| Parental protein coverage: | 95.96 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | IYNGFSSVLQF-LGLYKKSGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTF-D |
| .......VLQ..L.LYKKSGKL.FLGLDNAGKTTLLH...DD.LGQH..TL..TSEEL.IA...F..F.. | |
| Retrocopy | VFEWINRVLQV<LVLYKKSGKLLFLGLDNAGKTTLLHIFNDDQLGQHISTLDLTSEELMIARNDFYNF*P |
| Parental | LGGHEQARRVWKNYLPAINGIVFLVDCADHPRLMESKVELNALMTDETISNVPILILGNKIDRTDAISEE |
| ....EQA..VWKNYLPAIN.IVFL.D..DHP.LME...ELNALMT.ET.SNVPILILGNK...TDA..E. | |
| Retrocopy | WWAEEQASWVWKNYLPAINDIVFLADSVDHPPLMETRFELNALMTNETTSNVPILILGNKNNKTDAVRED |
| Parental | -KLREIFGLYGQTTGKGNVTLKELNARPMEV-FMCSVLKRQGYGEGFRWLSQYI |
| ..L.EIFG..G.TTGKGNVTL.ELNA.PME....CSVLKRQGY...F.WLSQ.I | |
| Retrocopy | <QLQEIFGF*G*TTGKGNVTLQELNALPMEM<VTCSVLKRQGYHKDFCWLSQDI |
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_1714 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1714 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1714 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,
|