RetrogeneDB ID: | retro_mmus_3555 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:159588604..159589024(+) | ||
| Located in intron of: | ENSMUSG00000044150 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000083906 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Tmem126a | ||
| Ensembl ID: | ENSMUSG00000030615 | ||
| Aliases: | Tmem126a, 1810020E01Rik | ||
| Description: | transmembrane protein 126A [Source:MGI Symbol;Acc:MGI:1913521] |
Retrocopy-Parental alignment summary:
>retro_mmus_3555
CGAATCTTGAATGTGACACACGCTCGATTAGCTTCTACCTTACCAATGGCTATGATCCCATTTTTGACAGCAAACCTGTT
CTACCAAAGTCTTGTAAGTTTACCTTTGAGTACAGGTGATTTGAACTGTGAAACCTATACCACAACACAGGGTGCACTAG
TTGGTTTGGTTATGGGTGGTCTGTACCCTATCCTTCTGGCTGTACCCATCAATAGGGGCCTTGATGCCAGGTATGAATCA
AGTCCCCTACCACAGAGGGGAAACATCTTCAATTACTGGATTACAGTTTCTAAGTCTGTTTTTAGAAAAATGTTATTTCC
TACTTTACTTCAGACTGTGTTTGCATCCTATGTTGGGTCTAGACAATATAAACTCTTCATAAAGGCCTTTCAGTTACCTG
AACCTGACTTAGAAATTCAT
ORF - retro_mmus_3555 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.0 % |
| Parental protein coverage: | 71.43 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | RILNVTQARLASSLPMAVIPFLTANLSYQSLVSLPLSTGDLNCETCTTTRGALVGLVMGGLYPILLAIPV |
| RILNVT.ARLAS.LPMA.IPFLTANL.YQSLVSLPLSTGDLNCET.TTT.GALVGLVMGGLYPILLA.P. | |
| Retrocopy | RILNVTHARLASTLPMAMIPFLTANLFYQSLVSLPLSTGDLNCETYTTTQGALVGLVMGGLYPILLAVPI |
| Parental | NGGLAARYESSPLPQRGNIFNYWITVSKPVFRKMLFPTLLQTVFASYLGSRQYKLLIKALQLPEPDLEIH |
| N.GL.ARYESSPLPQRGNIFNYWITVSK.VFRKMLFPTLLQTVFASY.GSRQYKL.IKA.QLPEPDLEIH | |
| Retrocopy | NRGLDARYESSPLPQRGNIFNYWITVSKSVFRKMLFPTLLQTVFASYVGSRQYKLFIKAFQLPEPDLEIH |
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 .54 RPM | 12 .13 RPM |
| SRP007412_cerebellum | 0 .30 RPM | 9 .21 RPM |
| SRP007412_heart | 0 .22 RPM | 22 .44 RPM |
| SRP007412_kidney | 0 .10 RPM | 15 .36 RPM |
| SRP007412_liver | 0 .00 RPM | 10 .49 RPM |
| SRP007412_testis | 0 .05 RPM | 3 .89 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3555 was not detected
No EST(s) were mapped for retro_mmus_3555 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_156087 | 447 libraries | 225 libraries | 374 libraries | 25 libraries | 1 library |
The graphical summary, for retro_mmus_3555 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_3555 was not experimentally validated.