RetrogeneDB ID: | retro_mmus_1334 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 15:23489890..23490498(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rpl13a | ||
| Ensembl ID: | ENSMUSG00000074129 | ||
| Aliases: | Rpl13a, 1810026N22Rik, Tstap198-7, tum-antigen | ||
| Description: | ribosomal protein L13A [Source:MGI Symbol;Acc:MGI:1351455] |
Retrocopy-Parental alignment summary:
>retro_mmus_1334
ATGGCAGAGGGGCAGGTTCTGGTATTGGGTGGCCGAGGCCATCTTCGTGGTCTCCTGGCGCCCATTGTGGCCAAGCAGGT
ACTTCTGGGCAGGAAAGTGGTGGTCGTACACTGTGAAGGCATCAACATTTCTGGAAACTTCTACAGAAACAAGTTAAAGT
ATCTGGCCTTTCTCCAGAAGCAGATGAATACCAACCCCTCCCGAGGCCCCTACCACTTCAGAGCCCCCAGCCGCATTTTC
TGGCGCACTGTGCAAGGCATGCTGCCCATAAGACGGAGAGAGTCCAGGCTGCCCTGGAACGCCTCGAGGTGTTGGATGGG
ATCCCTCCACCCTATGACAAGAAAAAGCAGATGGTGGTCCCTGCCGCCCTCAAGGTTGTGTGGCTGAAGCCTACCAGAAA
GTTTGCTTACCTGGGGCGTCTGGCTCATGAGGTCAGGTGGAAGTACAAGGCAGTGACAGCCACTCTGGAGGAGAAACGGA
AGGAGAAGGCCAAGGTGCACTGTCTGAAGAAGAAGCAGATCTTGAGGTCACGGAAACAGGCAGAAAAGAATGTGGAGAAG
AAAATCTGCAAGTTCACAGAGGTCCTTAAGACCAATGGACTCCTGGTA
ORF - retro_mmus_1334 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.2 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MAEGQVLVLDGRGHLLGRLAAIVAKQVLLGRKVVVVRCEGINISGNFYRNKLKYLAFLRKRMNTNPSRGP |
| MAEGQVLVL.GRGHL.G.LA.IVAKQVLLGRKVVVV.CEGINISGNFYRNKLKYLAFL.K.MNTNPSRGP | |
| Retrocopy | MAEGQVLVLGGRGHLRGLLAPIVAKQVLLGRKVVVVHCEGINISGNFYRNKLKYLAFLQKQMNTNPSRGP |
| Parental | YHFRAPSRIFWRTVRGMLP-HKTKRGQAALERLKVLDGIPPPYDKKKRMVVPAALKVVRLKPTRKFAYLG |
| YHFRAPSRIFWRTV.GMLP.HKT.R.QAALERL.VLDGIPPPYDKKK.MVVPAALKVV.LKPTRKFAYLG | |
| Retrocopy | YHFRAPSRIFWRTVQGMLP<HKTERVQAALERLEVLDGIPPPYDKKKQMVVPAALKVVWLKPTRKFAYLG |
| Parental | RLAHEVGWKYQAVTATLEEKRKEKAKMHYRKKKQILRLRKQAEKNVEKKICKFTEVLKTNGLLV |
| RLAHEV.WKY.AVTATLEEKRKEKAK.H..KKKQILR.RKQAEKNVEKKICKFTEVLKTNGLLV | |
| Retrocopy | RLAHEVRWKYKAVTATLEEKRKEKAKVHCLKKKQILRSRKQAEKNVEKKICKFTEVLKTNGLLV |
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 | 173 .82 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 165 .87 RPM |
| SRP007412_heart | 0 .00 RPM | 193 .19 RPM |
| SRP007412_kidney | 0 .06 RPM | 234 .92 RPM |
| SRP007412_liver | 0 .03 RPM | 237 .86 RPM |
| SRP007412_testis | 0 .00 RPM | 139 .37 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1334 was not detected
No EST(s) were mapped for retro_mmus_1334 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_39325 | 182 libraries | 392 libraries | 439 libraries | 50 libraries | 9 libraries |
The graphical summary, for retro_mmus_1334 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_1334 was not experimentally validated.