RetrogeneDB ID: | retro_mmus_347 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 1:98457767..98459159(+) | ||
| Located in intron of: | ENSMUSG00000026336 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000089791 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Stk38l | ||
| Ensembl ID: | ENSMUSG00000001630 | ||
| Aliases: | Stk38l, 4930473A22Rik, B230328I19, Ndr2, Ndr54 | ||
| Description: | serine/threonine kinase 38 like [Source:MGI Symbol;Acc:MGI:1922250] |
Retrocopy-Parental alignment summary:
>retro_mmus_347
ATGGCAATGACGGCAGGGGCAACAACTACCTTTCCTATGAGCAACCATACCCGGGAAAGAGTAACTGTGGCCAAGCTCAC
ACTGGAGAATTTTTACAGCAACCTAATTTTACAGCATGAAGAGAGAGAAACCAGGCAGAAGAAGTTAGAAGTGGCTATGG
AAGAAGAAGGATTGGCAGATGAGGAGAAAAAGTTACGTCGATCGCAGCATGCTCATAAAGAAACAGAGTTCTTACGCCTT
AAGAGGACCAGACTTGGCCTGGATGACTTTGAGTCTCTGAAGGTTATAGGAAGAGGAGCTTTCGGAGAGGTGCGGCTGGT
CCAGAAGAAAGACACGGGGCACATCTATGCCATGAAGATCCTGAGGAAAGCTGACATGCTTGAGAAAGAGCAGGTGGCTC
ATATCCAAGCAGAAAGGGACATTTTGGTGGAAGCAGATGGAGCCTGGGTGGTGAAGATGTTCTACAGTTTTCAGGACAAA
CGGAATCTCTATCTCATCATGGAATTTCTTCCTGGAGGTGACATGATGACATTGCTGATGAAGAAGGACACCTTAACAGA
AGAAGAGACACAGTTCTACATCTCAGAGACTGTCTTGGCGATAGATGCAATTCACCAGCTGGGCTTCATCCACTGGGACA
TCAAACCAGACAACCTTTTACTAGATGCCAAGGGACATGTAAAATTATCTGATTTTGGTTTGTGCACGGGGTTAAAGAAA
GCTCACAGGACTGAATTGTACAGAAACCTCACACATAACCCGCCAAGCGACTTCTCATTTCAGAACATGAATTCAAAGTG
GACAGCAGAGACATGGAAGAAGAACAGGAGACAGCTGGCTTACTCCACAGTTGGAACAGCAGACTACATTGCTCCAGAAG
TATTCATGCAGACTGGCTCTAACAAATTGTGTGACTGGTGGTCCTTGGGAGTGATTATGTACGAGATGCTAATAGGCTTT
CCACCTTTCTGCTCCGAAACACCACAAGAAACGTACAGAAAAGTTATGAGCTGGAAGGAGACGCTGGCATTTCCTCCGGA
AGTGCCCGTCTCTGAGAAAGCCAAGGACTTGATTCTCAGATTTTGTACTGATTCTGAAAACAGAATTGGGAATGGTGGTG
TGGAAGAAATCAGAGGTCATCCGTTCTTTGAGGGTGTAGACTGGGGGCACATAAGGGAAAGACCAGCAGCTATTCCTATA
GAAATCCGGAGTATAGATGACACCTCAAACTTTGATGACTTCCCCGAGTCTGATATCTTACAGCCAGTGCTGAATACCAC
AGAGCCCGACTACAAATCCAAAGACTGGGTTTTTCTCAATTACACCTACAAAAGGTTTGAAGGGCTGATCCAGAGAGGCT
CCATTCCTACATACATGAAAGCTGGGAAGTTA
ORF - retro_mmus_347 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.41 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAMTAGATTTFPMSNHTRERVTVAKLTLENFYSNLILQHEERETRQKKLEVAMEEEGLADEEKKLRRSQH |
| MAMTAGATTTFPMSNHTRERVTVAKLTLENFYSNLILQHEERETRQKKLEVAMEEEGLADEEKKLRRSQH | |
| Retrocopy | MAMTAGATTTFPMSNHTRERVTVAKLTLENFYSNLILQHEERETRQKKLEVAMEEEGLADEEKKLRRSQH |
| Parental | ARKETEFLRLKRTRLGLDDFESLKVIGRGAFGEVRLVQKKDTGHIYAMKILRKADMLEKEQVAHIRAERD |
| A.KETEFLRLKRTRLGLDDFESLKVIGRGAFGEVRLVQKKDTGHIYAMKILRKADMLEKEQVAHI.AERD | |
| Retrocopy | AHKETEFLRLKRTRLGLDDFESLKVIGRGAFGEVRLVQKKDTGHIYAMKILRKADMLEKEQVAHIQAERD |
| Parental | ILVEADGAWVVKMFYSFQDKRNLYLIMEFLPGGDMMTLLMKKDTLTEEETQFYISETVLAIDAIHQLGFI |
| ILVEADGAWVVKMFYSFQDKRNLYLIMEFLPGGDMMTLLMKKDTLTEEETQFYISETVLAIDAIHQLGFI | |
| Retrocopy | ILVEADGAWVVKMFYSFQDKRNLYLIMEFLPGGDMMTLLMKKDTLTEEETQFYISETVLAIDAIHQLGFI |
| Parental | HRDVKPDNLLLDAKGHVKLSDFGLCTGLKKAHRTEFYRNLTHNPPSDFSFQNMNSKRKAETWKKNRRQLA |
| H.D.KPDNLLLDAKGHVKLSDFGLCTGLKKAHRTE.YRNLTHNPPSDFSFQNMNSK..AETWKKNRRQLA | |
| Retrocopy | HWDIKPDNLLLDAKGHVKLSDFGLCTGLKKAHRTELYRNLTHNPPSDFSFQNMNSKWTAETWKKNRRQLA |
| Parental | YSTVGTPDYIAPEVFMQTGYNKLCDWWSLGVIMYEMLIGFPPFCSETPQETYRKVMSWKETLAFPPEVPV |
| YSTVGT.DYIAPEVFMQTG.NKLCDWWSLGVIMYEMLIGFPPFCSETPQETYRKVMSWKETLAFPPEVPV | |
| Retrocopy | YSTVGTADYIAPEVFMQTGSNKLCDWWSLGVIMYEMLIGFPPFCSETPQETYRKVMSWKETLAFPPEVPV |
| Parental | SEKAKDLILRFCTDSENRIGNGGVEEIKGHPFFEGVDWGHIRERPAAIPIEIRSIDDTSNFDDFPESDIL |
| SEKAKDLILRFCTDSENRIGNGGVEEI.GHPFFEGVDWGHIRERPAAIPIEIRSIDDTSNFDDFPESDIL | |
| Retrocopy | SEKAKDLILRFCTDSENRIGNGGVEEIRGHPFFEGVDWGHIRERPAAIPIEIRSIDDTSNFDDFPESDIL |
| Parental | QPVPNTTEPDYKSKDWVFLNYTYKRFEGLTQRGSIPTYMKAGKL |
| QPV.NTTEPDYKSKDWVFLNYTYKRFEGL.QRGSIPTYMKAGKL | |
| Retrocopy | QPVLNTTEPDYKSKDWVFLNYTYKRFEGLIQRGSIPTYMKAGKL |
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 .12 RPM | 25 .30 RPM |
| SRP007412_cerebellum | 0 .13 RPM | 21 .97 RPM |
| SRP007412_heart | 0 .03 RPM | 16 .78 RPM |
| SRP007412_kidney | 0 .37 RPM | 17 .98 RPM |
| SRP007412_liver | 0 .08 RPM | 16 .28 RPM |
| SRP007412_testis | 0 .69 RPM | 8 .51 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_347 was not detected
No EST(s) were mapped for retro_mmus_347 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_67957 | 284 libraries | 427 libraries | 336 libraries | 21 libraries | 4 libraries |
The graphical summary, for retro_mmus_347 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_347 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_347 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000025573 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000016636 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000001630 | 2 retrocopies |
retro_mmus_3100, retro_mmus_347 ,
|