RetrogeneDB ID: | retro_mmus_3325 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 9:31434045..31434707(-) | ||
| Located in intron of: | ENSMUSG00000041737 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Snrpb2 | ||
| Ensembl ID: | ENSMUSG00000008333 | ||
| Aliases: | None | ||
| Description: | U2 small nuclear ribonucleoprotein B [Source:MGI Symbol;Acc:MGI:104805] |
Retrocopy-Parental alignment summary:
>retro_mmus_3325
ATGGATATCAGACCAAATCACACGATTTATATCAACAATATGAATGACAAAATGAAAAAAGAAGAATTGAAGAGATCCCT
GTATGCCCTGTTTTCTCAGTTTGGACACGTGGTAGATATTGTGGCTTTAAAGACCATGAAGATGAGGGCACAGGCTTTTG
TTATATTTAAGGAACTGTGTTCATCACAAATGCTTTGAGACAGTTACAAGGATTTCCATTTTATGGTAAACCAATGAAAA
TTCAGTACGCAAAAACAGTTTCTGATATAATATCTAAAATGCGTGGTACTTTCGCTGACAAGGAAAAGAAGAAAGCTAAA
ACCATGGACCAGGCTGCAGCGGCTGCAAACAAGAAGCCTGGTTAGGGAACACCCAAGTCAGCTAATACCCAAGGAACTGC
AGCGCCAAACCCTCAGGTCCCTGATTATCCTCCAAACTATAGCCTGTTCCTTAATAACTTACCAGAGGAGACAAATGAGA
TGGTGTTATCCATGCTGTTCAAACAGTGCCCTGGATTCAAGGAGGTTCGCTTGGTACCAGGGAGACATGACATTGTGTTT
GTAGAATTTGAGAATGATGGGCAGGCTGGAGCTGCCAGAGATGCTCTGCAGGGGTTTAAGATGACACTGTCCCATGCCAT
GAAGATCACCTATGCTAAGAAG
ORF - retro_mmus_3325 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.71 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MDIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGSS-TNALRQL |
| MDIRPNHTIYINNMNDK.KKEELKRSLYALFSQFGHVVDIVALKTMKMR.QAFVIFKEL.SS.TNALRQL | |
| Retrocopy | MDIRPNHTIYINNMNDKMKKEELKRSLYALFSQFGHVVDIVALKTMKMRAQAFVIFKELCSS<TNALRQL |
| Parental | QGFPFYGKPMRIQYAKTDSDIISKMRGTFADKEKKKEKKKAKTMEQAAAAANKKPGQGTPNAANTQGTAA |
| QGFPFYGKPM.IQYAKT.SDIISKMRGTFAD....KEKKKAKTM.QAAAAANKKPG.GTP..ANTQGTAA | |
| Retrocopy | QGFPFYGKPMKIQYAKTVSDIISKMRGTFAD----KEKKKAKTMDQAAAAANKKPG*GTPKSANTQGTAA |
| Parental | PNPQVPDYPPNYILFLNNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFVEFENDGQAGAARDALQG |
| PNPQVPDYPPNY.LFLNNLPEETNEM.LSMLF.Q.PGFKEVRLVPGRHDI.FVEFENDGQAGAARDALQG | |
| Retrocopy | PNPQVPDYPPNYSLFLNNLPEETNEMVLSMLFKQCPGFKEVRLVPGRHDIVFVEFENDGQAGAARDALQG |
| Parental | FKITPSHAMKITYAKK |
| FK.T.SHAMKITYAKK | |
| Retrocopy | FKMTLSHAMKITYAKK |
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 | 17 .22 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 11 .98 RPM |
| SRP007412_heart | 0 .00 RPM | 9 .43 RPM |
| SRP007412_kidney | 0 .27 RPM | 12 .92 RPM |
| SRP007412_liver | 0 .00 RPM | 8 .33 RPM |
| SRP007412_testis | 0 .00 RPM | 18 .71 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3325 was not detected
No EST(s) were mapped for retro_mmus_3325 retrocopy.
| TSS No. | TSS Name | TSS expression level (Expr) in TPM range: | ||||
|---|---|---|---|---|---|---|
| no expression | 0 < Expr ≤ 1 | 1 < Expr ≤ 5 | 5 < Expr ≤ 10 | Expr > 10 | ||
| TSS #1 | TSS_149194 | 404 libraries | 475 libraries | 190 libraries | 3 libraries | 0 libraries |
The graphical summary, for retro_mmus_3325 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)
retro_mmus_3325 was not experimentally validated.