RetrogeneDB ID: | retro_mmus_2044 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 2:69799153..69799612(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000081857 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rbm3 | ||
| Ensembl ID: | ENSMUSG00000031167 | ||
| Aliases: | Rbm3, 2600016C11Rik | ||
| Description: | RNA binding motif protein 3 [Source:MGI Symbol;Acc:MGI:1099460] |
Retrocopy-Parental alignment summary:
>retro_mmus_2044
ATGTCGTCTGAAGAAGGGAAGCTCTTCGTGGGAGGGCTCAACTTCAACACCCATGAACAGGCACTTGAAAACTACTTTAG
CAGCTTTGGGCCTATCTCTGAGGTGGTTGTTGTCAAGGACCGGGAGACTCAAAGATCCTGGGGTTTTGGCTTCATCACCT
TCACAAACCCAGAGCATGCCTCAGATGCGATGAGAGCCATGAATGGAGAGTCCCTGGATGGGCGCCAAATCCGAGTTGAT
CATGCAGGAAAGTCTGCCAGGGGATCCAGAGGGGGTGCCTTTGGTGGGCGTGGTCACAGTTACTCTAGAGGTGGTAGAGA
CCAGGGATATGGAAGTGGAAGATATGACAGTCAACCTGGAGAATATGGATATGGGTATGGGTGGTCTAGAGACTACAGTG
GCAGCCAGGGTGGCTATGACTGCTACTCAGGAGGAAATTACAGAGACAATTATGACAAC
ORF - retro_mmus_2044 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.46 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSSEEGKLFVGGLNFNTDEQALEDHFSSFGPISEVVVVKDRETQRSRGFGFITFTNPEHASDAMRAMNGE |
| MSSEEGKLFVGGLNFNT.EQALE..FSSFGPISEVVVVKDRETQRS.GFGFITFTNPEHASDAMRAMNGE | |
| Retrocopy | MSSEEGKLFVGGLNFNTHEQALENYFSSFGPISEVVVVKDRETQRSWGFGFITFTNPEHASDAMRAMNGE |
| Parental | SLDGRQIRVDHAGKSARGSRGGAFGGRGRSYSRGGGDQGYGSGRYDSRPGGYGYGYGRSRDYSGSQGGYD |
| SLDGRQIRVDHAGKSARGSRGGAFGGRG.SYSRGG.DQGYGSGRYDS.PG.YGYGYG.SRDYSGSQGGYD | |
| Retrocopy | SLDGRQIRVDHAGKSARGSRGGAFGGRGHSYSRGGRDQGYGSGRYDSQPGEYGYGYGWSRDYSGSQGGYD |
| Parental | RYSGGNYRDNYDN |
| .YSGGNYRDNYDN | |
| Retrocopy | CYSGGNYRDNYDN |
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 | 32 .10 RPM |
| SRP007412_cerebellum | 0 .13 RPM | 46 .16 RPM |
| SRP007412_heart | 0 .00 RPM | 27 .61 RPM |
| SRP007412_kidney | 0 .06 RPM | 33 .07 RPM |
| SRP007412_liver | 0 .00 RPM | 21 .33 RPM |
| SRP007412_testis | 0 .05 RPM | 8 .60 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2044 was not detected
No EST(s) were mapped for retro_mmus_2044 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_88460 | 395 libraries | 495 libraries | 179 libraries | 1 library | 2 libraries |
The graphical summary, for retro_mmus_2044 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_2044 was not experimentally validated.