RetrogeneDB ID: | retro_mmus_1798 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 18:84659379..84659844(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000092056 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Npm1 | ||
| Ensembl ID: | ENSMUSG00000057113 | ||
| Aliases: | Npm1, B23, NO38, Npm | ||
| Description: | nucleophosmin 1 [Source:MGI Symbol;Acc:MGI:106184] |
Retrocopy-Parental alignment summary:
>retro_mmus_1798
ATGGAAGACTCGATGGACATGAGTCCTCTTAGGCCTCAGAACTACCTTTTCGGCTGTGAACTAAAGGCTGACAAAGACTA
TCACTTTAAAGTGGATAATGATGACAATGAGCACCAGTTGTCATTAAGAACGGTCAGTTTAGGAGCAGGGGCAAAAGATG
AATTACACATCACAGAGGCAGAAGCAATGAACGATGAAGGCAGTCCAATTAAAGTCACACTGGAAACTTTGAAAATGTCT
GTACAACCAACAGTTTCCCTTGGGGGCTTCGAAATTACACTACCTGTGGTCTTATGGTTGAAGAGTGGTTCAGGGCCTGT
GCACATTAGGGGACAGTACCTAATAGCTGTAGAGGAAGATGCAGAGTCTGAAGATGAAGAAGGGGAGGACGAAAAACTCT
TAGGCATGTCTGGAAAGTGATCTGCTCCTGGAGGTGGTAACAAGGATCCACAGAAAAAAGTAAAA
ORF - retro_mmus_1798 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.17 % |
| Parental protein coverage: | 55.09 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MEDSMDMDMSPLRPQNYLFGCELKADKDYHFKVDNDENEHQLSLRTVSLGAGAKDELHIVEAEAMNYEGS |
| MEDS..MDMSPLRPQNYLFGCELKADKDYHFKVDND.NEHQLSLRTVSLGAGAKDELHI.EAEAMN.EGS | |
| Retrocopy | MEDS--MDMSPLRPQNYLFGCELKADKDYHFKVDNDDNEHQLSLRTVSLGAGAKDELHITEAEAMNDEGS |
| Parental | PIKVTLATLKMSVQPTVSLGGFEITPPVVLRLKCGSGPVHISGQHLVAVEEDAESEDEDEEDVKLLGMSG |
| PIKVTL.TLKMSVQPTVSLGGFEIT.PVVL.LK.GSGPVHI.GQ.L.AVEEDAESEDE..ED.KLLGMSG | |
| Retrocopy | PIKVTLETLKMSVQPTVSLGGFEITLPVVLWLKSGSGPVHIRGQYLIAVEEDAESEDEEGEDEKLLGMSG |
| Parental | KRSAPGGGNKVPQKKVK |
| K.SAPGGGNK.PQKKVK | |
| Retrocopy | K*SAPGGGNKDPQKKVK |
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 | 73 .57 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 80 .20 RPM |
| SRP007412_heart | 0 .00 RPM | 66 .87 RPM |
| SRP007412_kidney | 0 .00 RPM | 103 .18 RPM |
| SRP007412_liver | 0 .03 RPM | 81 .95 RPM |
| SRP007412_testis | 0 .00 RPM | 144 .40 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1798 was not detected
No EST(s) were mapped for retro_mmus_1798 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_61853 | 678 libraries | 351 libraries | 43 libraries | 0 libraries | 0 libraries |
The graphical summary, for retro_mmus_1798 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_1798 was not experimentally validated.