RetrogeneDB ID: | retro_mmus_2387 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 4:112537060..112537660(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000083599 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Dnttip1 | ||
| Ensembl ID: | ENSMUSG00000017299 | ||
| Aliases: | None | ||
| Description: | deoxynucleotidyltransferase, terminal, interacting protein 1 [Source:MGI Symbol;Acc:MGI:1923483] |
Retrocopy-Parental alignment summary:
>retro_mmus_2387
ATGGGGGTGACTGGTGACACCAAGCAGCCACAGAGCCCTGGAGGGGCAGAGCTAGGTGGCCTGGAGCTGGGCGACGTGGG
CGTGGCGGGCCAGCCAGTTCTCAGGAACCCTTGGAACATAATGATAAAACACTGTCAGGTGCAGCGAAGGGGCCGCCGAT
CTCAGATGATCACAAGTTTCACAATCCCAGCCATCTCTATGGATCTCCTCTGTGCTGTCCTGCAGCCTAGCATCAATGAG
GAGATCCAGAGTGTCTTCAACAAGTACATGAAGTTCTTCCAGAAGGCAGTGCTGAATGTGTGAGACAATGTTGGGGAAGA
AGTGGACGCAGAGCAGTTGATTCAGGAGGCCTGCCACAGCTGCCTGGAGCAGGTAAAGCTGCTCTTTTCTGATGGAGAGA
AAGTGATACCCACATTGGCCCATGAGCTTCCAGGGATCAAGCAGGGCCAGCAAGCAGCAGAGGAGTCCCACCGAGGAAGC
CCCATTCCCAAAAAGAGGAAAGGTCGGCCTCCTGGACATGTCCTGTCGAATGACCACATAGCTGCTGCCATGGTATGGAA
ACCAAAATCCTGTGAACCAATTCGCCGAGAAGGCCCCAAG
ORF - retro_mmus_2387 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.5 % |
| Parental protein coverage: | 94.79 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MGATGDTEQPRGPGGAERGGLELGDAGAAGQPVLTNPWNIMIKHRQVQRRGRRSQMTTSFTDPAISMDLL |
| MG.TGDT.QP..PGGAE.GGLELGD.G.AGQPVL.NPWNIMIKH.QVQRRGRRSQM.TSFT.PAISMDLL | |
| Retrocopy | MGVTGDTKQPQSPGGAELGGLELGDVGVAGQPVLRNPWNIMIKHCQVQRRGRRSQMITSFTIPAISMDLL |
| Parental | RAVLQPSINEEIQGVFNKYMKFFQKAALNVRDNVGEEVDAEQLIQEACRSCLEQAKLLFSDGEKVIPRLA |
| .AVLQPSINEEIQ.VFNKYMKFFQKA.LNV.DNVGEEVDAEQLIQEAC.SCLEQ.KLLFSDGEKVIP.LA | |
| Retrocopy | CAVLQPSINEEIQSVFNKYMKFFQKAVLNV*DNVGEEVDAEQLIQEACHSCLEQVKLLFSDGEKVIPTLA |
| Parental | HELPGIKRGRQAEEESHRGSPIPKKRKGRPPGHVLSNDRAAAGMVWKQKSCEPIRREGPK |
| HELPGIK.G.QA.EESHRGSPIPKKRKGRPPGHVLSND..AA.MVWK.KSCEPIRREGPK | |
| Retrocopy | HELPGIKQGQQAAEESHRGSPIPKKRKGRPPGHVLSNDHIAAAMVWKPKSCEPIRREGPK |
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 | 11 .84 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 12 .72 RPM |
| SRP007412_heart | 0 .00 RPM | 11 .05 RPM |
| SRP007412_kidney | 0 .00 RPM | 10 .18 RPM |
| SRP007412_liver | 0 .00 RPM | 6 .66 RPM |
| SRP007412_testis | 0 .05 RPM | 22 .78 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2387 was not detected
No EST(s) were mapped for retro_mmus_2387 retrocopy.
No TSS is located nearby retro_mmus_2387 retrocopy 5' end.
retro_mmus_2387 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2387 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000017299 | 1 retrocopy |
retro_mmus_2387 ,
|
| Pteropus vampyrus | ENSPVAG00000000368 | 1 retrocopy | |
| Sarcophilus harrisii | ENSSHAG00000002289 | 1 retrocopy |