RetrogeneDB ID: | retro_mmus_1258 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 14:27551371..27552140(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Snapc2 | ||
| Ensembl ID: | ENSMUSG00000011837 | ||
| Aliases: | Snapc2, 0610007H10Rik, AU015675 | ||
| Description: | small nuclear RNA activating complex, polypeptide 2 [Source:MGI Symbol;Acc:MGI:1914861] |
Retrocopy-Parental alignment summary:
>retro_mmus_1258
CAGGCTCGGCGGGGCCAGCTGGAGCCAGACGCCGCGGAGCTGACCCAGGAGTAAGGCCACAGTGAGGCTGAGATCTGTCG
CTTTATCCAGAAGCTCAAAGGACCGGGTGGTTCAAGAGGCCATTCAGAAGATGCAGCCAGGTGGCAGAGAGGGGCCAAGA
CATCAAGAAATACAGCTCCCAGCCCCGGTAGAGGTATGGATGGATCTTGCTGAGAAACTAACAGGCCCACTGGAGGAAGC
CCTGACTGCAGCTTTCTCCCAGGTGCTCACCATTGCTGCAGGAGAACCCCTCAGCCTCCTGCACTCCAGGCCGAGCAAGC
CCACAAAGACCCGTGGAAAGGCACTGGTGTTCTTGAGCAACCAAGATGGGCAGAAGGATGCTGCGTCTGAAGGTTCTGGG
CCTGTCCCTATGACTGCTACTGACACCACTCGTGAGGCTTCTGTCTCTGATCCTAAGGCCTCTGGAGTCAACCCTGAGAC
CTCTGGTCTTGCCTCAGAGGTTACTGTCCCTGACCCTGATGCCCCAACCAAGTCCCTGGCTGGATCCTCCACAGAGAGAG
GCTTTGCCGTGGACTTTGAGAAGATCTACAAATACCCTTCCTTCTCCTCCAGAGGTGGCCATGGCCCTGAGCTCTCAGCA
GCTGAGTCAGCTGGGGTCCTTAACCTGCTCATGGCACTTCCAGAGGAACTGTCCCACCTGCCTTGCACAGCTCTGCTGGA
ACATATGACCAAAACATATGCTCAACTGATGGCTCCCCAGACCTCTCTC
ORF - retro_mmus_1258 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.7 % |
| Parental protein coverage: | 71.59 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | QARRGQPEPDAAELAQELRGRSEAEICRFIQQLKG-RVVREAIQKMQPGGREGPRHQGTPLPAPVEVWMD |
| QARRGQ.EPDAAEL.QE..G.SEAEICRFIQ.LKG.RVV.EAIQKMQPGGREGPRHQ...LPAPVEVWMD | |
| Retrocopy | QARRGQLEPDAAELTQE*-GHSEAEICRFIQKLKG>RVVQEAIQKMQPGGREGPRHQEIQLPAPVEVWMD |
| Parental | LAEKLTGPMEEALTAAFSQVLTIAAAEPLSLLHSRPGKPTKARGKALVFLSNQDGQKDPASEGSGPVPMT |
| LAEKLTGP.EEALTAAFSQVLTIAA.EPLSLLHSRP.KPTK.RGKALVFLSNQDGQKD.ASEGSGPVPMT | |
| Retrocopy | LAEKLTGPLEEALTAAFSQVLTIAAGEPLSLLHSRPSKPTKTRGKALVFLSNQDGQKDAASEGSGPVPMT |
| Parental | AADPTREASVSDPKASGANPETSGLASEVTVPDPDAPTKSLAGSSTERDLAVDFEKIYKYLSFSSRGGHG |
| A.D.TREASVSDPKASG.NPETSGLASEVTVPDPDAPTKSLAGSSTER..AVDFEKIYKY.SFSSRGGHG | |
| Retrocopy | ATDTTREASVSDPKASGVNPETSGLASEVTVPDPDAPTKSLAGSSTERGFAVDFEKIYKYPSFSSRGGHG |
| Parental | PELSAAESAVVLNLLMALPEELSHLPCTALLEHMTKTYAQLMAPQTAL |
| PELSAAESA.VLNLLMALPEELSHLPCTALLEHMTKTYAQLMAPQT.L | |
| Retrocopy | PELSAAESAGVLNLLMALPEELSHLPCTALLEHMTKTYAQLMAPQTSL |
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 |
|---|---|---|
| SRP007412_brain | 0 .00 RPM | 14 .98 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 10 .29 RPM |
| SRP007412_heart | 0 .00 RPM | 10 .24 RPM |
| SRP007412_kidney | 0 .02 RPM | 9 .84 RPM |
| SRP007412_liver | 0 .00 RPM | 5 .43 RPM |
| SRP007412_testis | 0 .00 RPM | 6 .82 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1258 was not detected
No EST(s) were mapped for retro_mmus_1258 retrocopy.
No TSS is located nearby retro_mmus_1258 retrocopy 5' end.
retro_mmus_1258 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1258 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000011837 | 1 retrocopy |
retro_mmus_1258 ,
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