RetrogeneDB ID: | retro_mmus_1154 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 13:118598056..118598525(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Plscr3 | ||
| Ensembl ID: | ENSMUSG00000019461 | ||
| Aliases: | Plscr3, 2210403O21Rik, 2610037N06Rik, ESTM3, X83310 | ||
| Description: | phospholipid scramblase 3 [Source:MGI Symbol;Acc:MGI:1917560] |
Retrocopy-Parental alignment summary:
>retro_mmus_1154
CTGCTCTGCGGTACCCACTGTCTGCTTTGTGTCCACCTAGCAGTCCCAGAGGATCCGGAATTCCCTGCCTCCACCACCCA
CTCCACTGTGGCTGCAGCTGCAGTTCATGTGGTCTTCAGGACACGGAAGTACATGCTCCACTCGGGACCACTGCCGACCA
TGTGCAACCTACCTGGCCACCCATCCTTCCTAAACTTTCTATCCTAGACTTTGATTACCAAACTGTCCTTTGAGGGGTGG
GGCTTTCCGGAAGTGCGGTTGTGATACAGAGGCCAGTTTTGAAATAAAGACTAAGGATGGTTCTTGAAGAGTGGGCCTCA
TCTGTGAGGGGTTGCTTGGAGGGTAGCTTGGAGAAGCACTCACAGACGCTGATGGCTTTGTCCTACATTTCCCTGTAGAT
CCAGATGTCAGAGTGAAGGCCATGCACCTGGGAGCCACATTCCCTGTTGATTATGTGTTCTTCCAGAAG
ORF - retro_mmus_1154 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 57.23 % |
| Parental protein coverage: | 52.7 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | LCCGARRPFRIRLADPGDRE-VLRLLRPLHCGCSCCPCGLQEMEVQAPPGTTIGHVLQTWHPFLPKFSIL |
| L.CG........LA.P.D.E....L..PLHCGCSC..CGLQ..EV.AP.GTT..HV..TW.P.LPK.SIL | |
| Retrocopy | LLCGTHCLLCVHLAVPEDPE<IPCLHHPLHCGCSCSSCGLQDTEVHAPLGTTADHVQPTWPPILPKLSIL |
| Parental | DADRQPVLRVVGPCWT-CGCGTDTNFEVKTKDESRSVGRISK-QWGGLLREALTDADDFGLQFPVDLDVK |
| D.D.Q.VL..VG.....CGC.T...FE.KTKD.S..VG.I.....GG.L.EALTDAD.F.L.FPVD.DV. | |
| Retrocopy | DFDYQTVL*GVGLSGS<CGCDTEASFEIKTKDGS*RVGLICEGLLGG*LGEALTDADGFVLHFPVDPDVR |
| Parental | VKAVLLGATFLIDYMFFEK |
| VKA..LGATF..DY.FF.K | |
| Retrocopy | VKAMHLGATFPVDYVFFQK |
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 | 10 .49 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 13 .46 RPM |
| SRP007412_heart | 0 .00 RPM | 18 .71 RPM |
| SRP007412_kidney | 0 .06 RPM | 15 .67 RPM |
| SRP007412_liver | 0 .00 RPM | 6 .31 RPM |
| SRP007412_testis | 0 .00 RPM | 2 .42 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1154 was not detected
No EST(s) were mapped for retro_mmus_1154 retrocopy.
No TSS is located nearby retro_mmus_1154 retrocopy 5' end.
retro_mmus_1154 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1154 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 | |
|---|---|---|---|
| Latimeria chalumnae | ENSLACG00000011730 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000019461 | 1 retrocopy |
retro_mmus_1154 ,
|
| Mus musculus | ENSMUSG00000032369 | 1 retrocopy |