RetrogeneDB ID: | retro_mmus_2396 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 4:129899092..129899899(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000070729 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Srsf5 | ||
| Ensembl ID: | ENSMUSG00000021134 | ||
| Aliases: | Srsf5, Sfrs5 | ||
| Description: | serine/arginine-rich splicing factor 5 [Source:MGI Symbol;Acc:MGI:98287] |
Retrocopy-Parental alignment summary:
>retro_mmus_2396
ATGAGTGGCTGTCGAGTGTTCATTGGGAGACTAAATCCAGCAGCGAGGGTGAAAGATGTGGAAAGATTCTTCAAGGGTTA
CGGACGGATCCGAGATATTGACTTGAAAACAGGTTTTGGTTTTGTGGAATTTGAGGACCCAAGGGATGCAGATGATGCTG
TTTATGAACTTGATGGGAAGGAACTTTGCAGTGAAAGGGTGACGATTGAACATGCTCGGGCTCGATCTCGAGGTGGAAGA
GGTAGAGGACGATACTCCGACCGTTTTAGCAGTCGCAGACCTCGAAATGATAGACGAAATGCTCCACCTGTAAGAACAGA
AAATCGACTTATAGTTGAGAATTTATCCTCAAGAGTCAGCTGGCAGGATCTCAAAGATTTCATGAGACAAGCTGGGGAAG
TAACCTTTGCGGATGCACATCGACCTAAACTAAATGAAGGGGTAGTTGAGTTTGCCTCTTATGGTGACTTAAAGAATGCT
ATTGAGAAACTTTCTGGAAAGGAAATTAACGGGAGAAAAATCAAATTAATTGTAGGCAGCAAAAGGCACAGGTCAAGAAG
CAGGTCACGATCTCGGACCAGGAGTTCCTCTAGGTCCCGTAGCCGATCCCGTTCACGCAGGAGCAAGTCTTACAGCCGAT
CAAGGAGCAGGAGCCGGAGCCAGAGCAAGTCCCGTTCTGGTAGTAGGTCTCCTGTGCCTGAGAAGAGCCAGAAACGTGGT
TCTTCGAGTAGATCTAAATCTCCAGCATCTGTGGATCGCCAGAGGTCCCGATCCCGGTCCAGGTCCAGATCAGTTGACAG
TGGCAAT
ORF - retro_mmus_2396 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.51 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSGCRVFIGRLNPAAREKDVERFFKGYGRIRDIDLKRGFGFVEFEDPRDADDAVYELDGKELCSERVTIE |
| MSGCRVFIGRLNPAAR.KDVERFFKGYGRIRDIDLK.GFGFVEFEDPRDADDAVYELDGKELCSERVTIE | |
| Retrocopy | MSGCRVFIGRLNPAARVKDVERFFKGYGRIRDIDLKTGFGFVEFEDPRDADDAVYELDGKELCSERVTIE |
| Parental | HARARSRGGRGRGRYSDRFSSRRPRNDRRNAPPVRTENRLIVENLSSRVSWQDLKDFMRQAGEVTFADAH |
| HARARSRGGRGRGRYSDRFSSRRPRNDRRNAPPVRTENRLIVENLSSRVSWQDLKDFMRQAGEVTFADAH | |
| Retrocopy | HARARSRGGRGRGRYSDRFSSRRPRNDRRNAPPVRTENRLIVENLSSRVSWQDLKDFMRQAGEVTFADAH |
| Parental | RPKLNEGVVEFASYGDLKNAIEKLSGKEINGRKIKLIEGSKRHRSRSRSRSRTRSSSRSRSRSRSRRSKS |
| RPKLNEGVVEFASYGDLKNAIEKLSGKEINGRKIKLI.GSKRHRSRSRSRSRTRSSSRSRSRSRSRRSKS | |
| Retrocopy | RPKLNEGVVEFASYGDLKNAIEKLSGKEINGRKIKLIVGSKRHRSRSRSRSRTRSSSRSRSRSRSRRSKS |
| Parental | YSRSRSRSRSRSKSRSGSRSPVPEKSQKRGSSSRSKSPASVDRQRSRSRSRSRSVDSGN |
| YSRSRSRSRS.SKSRSGSRSPVPEKSQKRGSSSRSKSPASVDRQRSRSRSRSRSVDSGN | |
| Retrocopy | YSRSRSRSRSQSKSRSGSRSPVPEKSQKRGSSSRSKSPASVDRQRSRSRSRSRSVDSGN |
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 .49 RPM | 187 .91 RPM |
| SRP007412_cerebellum | 0 .69 RPM | 258 .44 RPM |
| SRP007412_heart | 0 .56 RPM | 169 .91 RPM |
| SRP007412_kidney | 1 .15 RPM | 219 .93 RPM |
| SRP007412_liver | 0 .55 RPM | 161 .31 RPM |
| SRP007412_testis | 0 .69 RPM | 176 .69 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2396 was not detected
No EST(s) were mapped for retro_mmus_2396 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_100852 | 260 libraries | 492 libraries | 315 libraries | 1 library | 4 libraries |
The graphical summary, for retro_mmus_2396 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_2396 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2396 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 7 parental genes, and 16 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Macropus eugenii | ENSMEUG00000001521 | 2 retrocopies | |
| Monodelphis domestica | ENSMODG00000011362 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000021134 | 1 retrocopy |
retro_mmus_2396 ,
|
| Mus musculus | ENSMUSG00000024097 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000071172 | 9 retrocopies | |
| Rattus norvegicus | ENSRNOG00000005513 | 1 retrocopy | |
| Tupaia belangeri | ENSTBEG00000001972 | 1 retrocopy |