RetrogeneDB ID: | retro_mmus_1937 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 2:77291330..77292437(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000081611 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Prpsap2 | ||
| Ensembl ID: | ENSMUSG00000020528 | ||
| Aliases: | Prpsap2, A230054F23Rik | ||
| Description: | phosphoribosyl pyrophosphate synthetase-associated protein 2 [Source:MGI Symbol;Acc:MGI:2384838] |
Retrocopy-Parental alignment summary:
>retro_mmus_1937
ATGTTTTGTGTGGCGCCTCCTGAATTAGAAACCAAGATGAACATAACCAAAGGAGGCCTCCTGTTGTTTTCAGCAAATTC
CAATTCATCATGTATGGAGCTTTCAAAGAAAATTGCTGAGCGGCTGGGGGTGGAGATGGGCAAAGTGCAGGTTTACCAGG
AACCTAACAGAGAAACAAGAGTTCAAATACAGGAGTCTGTGAGAGGAAAAGATGTATTTATCATCCAAACCATCTCAAAG
GACGTGAACACCACCATCATGGAGCTGCTGATCATGGTATATGCATGTAAGACCTCATGTGCCAAGAGCATCATCGGAGT
GATCCCCTACTTTCCTTAAAGCAAGCAATGCAAAATGAGAAAAAGGGGCTCCATTGTCTCAAAATTGCTGGCTTCTATGA
TGTGCAAAGCTGGTCTGACTCATCTCATCACTATGGATTTACACCAGAAGGAAATCCAGGGCTTCTTCAATATTCCAGTA
GATAATTTAAGAGCCTCCCCATTCCTGTTACAATATATTCAAGAAGAGATCCCAGATTATAGGAATGCAGTCATCGTGGC
CAAGTCTCCAGCCTCAGCCAAGAGGGCACAATCTTTTGCAGAGCGTCTACATCTGGGAATCGCAGTGATCCATGGAGAAG
CACAGGATGCTGAGTCTGACTTGGTGGATGGCCGGCACTCCCCACCAATGGTCAGGAGTGTAGCTGCCATCCACCCCAGC
CTGGAGATCCCTATGCTGATTCCTAAAGAGAAGCCCCTAATCACAGTTGTTGGTGATGTTGGAGGAAGAATCGCCATCAT
TGTGGATGACATTATTGATGATGTGGATAGCTTTCTTGCTGCAGCAGAGACCCTGAAGGAAAGAGGTGCATACAAGATCT
TTGTGATGGCCACTCACAGCTTGTTATCCTCTGATGCTCCCCGGCTGATTGAAGAGTCTGCCATTGATGAGGTGGTGGTC
ACTAACACGATCCCACACGAGATCCAGAAGCTGCAGTGCCCCAATATCAAGACTGTGGACATCAGCATGATCCTATCAGA
AGCCATCCGCCGAATTCACAGCGGGGAGTCCATGTCCTACCTTTTCAGAAACATAGGCTTAGATGAC
ORF - retro_mmus_1937 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.1 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MFCVAPPELETKMNITKGGLVLFSANSNSSCMELSKKIAERLGVEMGKVQVYQEPNRETRVQIQESVRGK |
| MFCVAPPELETKMNITKGGL.LFSANSNSSCMELSKKIAERLGVEMGKVQVYQEPNRETRVQIQESVRGK | |
| Retrocopy | MFCVAPPELETKMNITKGGLLLFSANSNSSCMELSKKIAERLGVEMGKVQVYQEPNRETRVQIQESVRGK |
| Parental | DVFIIQTISKDVNTTIMELLIMVYACKTSCAKSIIGVIPYFPYSKQCKMRKRGSIVSKLLASMMCKAGLT |
| DVFIIQTISKDVNTTIMELLIMVYACKTSCAKSIIGVIPYFP.SKQCKMRKRGSIVSKLLASMMCKAGLT | |
| Retrocopy | DVFIIQTISKDVNTTIMELLIMVYACKTSCAKSIIGVIPYFP*SKQCKMRKRGSIVSKLLASMMCKAGLT |
| Parental | HLITMDLHQKEIQGFFNIPVDNLRASPFLLQYIQEEIPDYRNAVIVAKSPASAKRAQSFAERLRLGIAVI |
| HLITMDLHQKEIQGFFNIPVDNLRASPFLLQYIQEEIPDYRNAVIVAKSPASAKRAQSFAERL.LGIAVI | |
| Retrocopy | HLITMDLHQKEIQGFFNIPVDNLRASPFLLQYIQEEIPDYRNAVIVAKSPASAKRAQSFAERLHLGIAVI |
| Parental | HGEAQDAESDLVDGRHSPPMVRSVAAIHPSLEIPMLIPKEKPPITVVGDVGGRIAIIVDDIIDDVDSFLA |
| HGEAQDAESDLVDGRHSPPMVRSVAAIHPSLEIPMLIPKEKP.ITVVGDVGGRIAIIVDDIIDDVDSFLA | |
| Retrocopy | HGEAQDAESDLVDGRHSPPMVRSVAAIHPSLEIPMLIPKEKPLITVVGDVGGRIAIIVDDIIDDVDSFLA |
| Parental | AAETLKERGAYKIFVMATHGLLSSDAPRLIEESAIDEVVVTNTIPHEIQKLQCPKIKTVDISMILSEAIR |
| AAETLKERGAYKIFVMATH.LLSSDAPRLIEESAIDEVVVTNTIPHEIQKLQCP.IKTVDISMILSEAIR | |
| Retrocopy | AAETLKERGAYKIFVMATHSLLSSDAPRLIEESAIDEVVVTNTIPHEIQKLQCPNIKTVDISMILSEAIR |
| Parental | RIHNGESMSYLFRNIGLDD |
| RIH.GESMSYLFRNIGLDD | |
| Retrocopy | RIHSGESMSYLFRNIGLDD |
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 .12 RPM | 14 .88 RPM |
| SRP007412_cerebellum | 0 .09 RPM | 11 .51 RPM |
| SRP007412_heart | 0 .03 RPM | 3 .05 RPM |
| SRP007412_kidney | 0 .08 RPM | 8 .99 RPM |
| SRP007412_liver | 0 .05 RPM | 4 .26 RPM |
| SRP007412_testis | 0 .00 RPM | 9 .15 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1937 was not detected
No EST(s) were mapped for retro_mmus_1937 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_89237 | 545 libraries | 325 libraries | 194 libraries | 8 libraries | 0 libraries |
The graphical summary, for retro_mmus_1937 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_1937 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1937 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000020528 | 2 retrocopies |
retro_mmus_1937 , retro_mmus_3515,
|
| Mus musculus | ENSMUSG00000031432 | 2 retrocopies |