RetrogeneDB ID: | retro_mmus_50 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 13:3803753..3804203(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000063130 | |
| Aliases: | Calml3, 2310068O22Rik, AI326174 | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Calm1 | ||
| Ensembl ID: | ENSMUSG00000001175 | ||
| Aliases: | Calm1, AI256814, AI327027, AI461935, AL024000, CaM, Calm | ||
| Description: | calmodulin 1 [Source:MGI Symbol;Acc:MGI:88251] |
Retrocopy-Parental alignment summary:
>retro_mmus_50
ATGGCCGACCAGCTGACTGAGGAGCAAATCGCCGAGTTCAAAGAGGCTTTCTCTCTGTTTGACAAGGATGGGGATGGCAG
TATCACCACCCAAGAATTGGGCACTGTCATGCGGTCCCTGGGTCAGAACCCCACAGAGGCTGAGCTTCAAGGCATGGTGA
ATGAAATTGACAAAGATGGAAACGGCACCGTGGACTTCCCCGAGTTCCTGACAATGATGTCCAGGAAGATGAAAGACACT
GACAGCGAGGAGGAGATCCGAGAGGCCTTCCGAGTGTTCGACAAGGATGGCAATGGCTTCGTCAGTGCAGCCGAGCTGAG
GCACGTGATGACCAAGCTGGGGGAGAAGCTGAGCGATGAGGAAGTGGACGAAATGATACAGGCGGCAGATACAGATGGTG
ATGGGCAAGTGAACTATGAGGAGTTTGTCCACATGCTGGTGTCCAAATGA
ORF - retro_mmus_50 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.25 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFL |
| MADQLTEEQIAEFKEAFSLFDKDGDG.ITT.ELGTVMRSLGQNPTEAELQ.M.NE.D.DGNGT.DFPEFL | |
| Retrocopy | MADQLTEEQIAEFKEAFSLFDKDGDGSITTQELGTVMRSLGQNPTEAELQGMVNEIDKDGNGTVDFPEFL |
| Parental | TMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE |
| TMM.RKMKDTDSEEEIREAFRVFDKDGNG..SAAELRHVMT.LGEKL.DEEVDEMI..AD.DGDGQVNYE | |
| Retrocopy | TMMSRKMKDTDSEEEIREAFRVFDKDGNGFVSAAELRHVMTKLGEKLSDEEVDEMIQAADTDGDGQVNYE |
| Parental | EFVQMMTAK |
| EFV.M...K | |
| Retrocopy | EFVHMLVSK |
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 | 1862 .86 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 1219 .10 RPM |
| SRP007412_heart | 0 .00 RPM | 173 .24 RPM |
| SRP007412_kidney | 1 .21 RPM | 178 .48 RPM |
| SRP007412_liver | 0 .00 RPM | 175 .35 RPM |
| SRP007412_testis | 1 .65 RPM | 478 .02 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_50 was not detected
No EST(s) were mapped for retro_mmus_50 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_28770 | 896 libraries | 92 libraries | 53 libraries | 10 libraries | 21 libraries |
| TSS #2 | TSS_28771 | 808 libraries | 128 libraries | 64 libraries | 34 libraries | 38 libraries |
The graphical summary, for retro_mmus_50 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_50 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_50 has 6 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_59 |
| Pan troglodytes | retro_ptro_83 |
| Gorilla gorilla | retro_ggor_187 |
| Pongo abelii | retro_pabe_45 |
| Rattus norvegicus | retro_rnor_318 |
| Equus caballus | retro_ecab_59 |