RetrogeneDB ID: | retro_mmus_23 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 11:94741975..94742689(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000020870 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Cdc34 | ||
| Ensembl ID: | ENSMUSG00000020307 | ||
| Aliases: | Cdc34, AI327276, UBE2R1 | ||
| Description: | cell division cycle 34 [Source:MGI Symbol;Acc:MGI:102657] |
Retrocopy-Parental alignment summary:
>retro_mmus_23
ATGGCCGGACCGCTGGTGCCCAGCTCACAGAAGGTGCTGCTACTGGAACTGAAGGGGCTGCAGGAGGAGCCGGTGGAGGG
CTTCCGGGTGACGCTGGTGGACGAGGGTGACCTGTACAACTGGGAGGTGGCCATCTTCGGGCCCCCCAACACCTACTATG
AGGGTGGCTACTTCAAGGCTCACCTCAAGTTCCCCATCGACTACCCGTATTCCCCACCAACCTTCTGGTTCCTCACCAAG
ATGTGGCACCCAAACATCCATGAGACAGGGTTCGTGTGCATCTCCATTCTCCATCCCCCAGATGACAACCCACAGGGTGG
GGAGCTGCCCTCAGAGCGGTGGAACCCCACACAGAATGTCAGAACCATCCTCCTGAGTGTAATCTCGCTGCTGAATGAGC
CCAACACCTCCTCTCCTGCCAACGTGGACGCCTCGGTGATGTACAGAAAATGGAAGGAGAGCAAGGGGAAGGACCACGAG
TACACGGACATCATCCGGAAGCAGGTCCTGGGGACCAAGGTGGACGCAGAGCGCGATGGCGTGAAGGTGCCCACTACGCT
GGCCGAGTACTGCGTGAAGACCAAGGCGCCGGCGCCGGATGAGGGCTCGGACCTCTTCGACTACTACGTGGACGGCGAAG
TGGAGGAGGCCGACAGCTGCTTTGGGGATGAAGAGGATGACTTTGGCCCGAAGAGTCCTGACCCACGTCCCTGA
ORF - retro_mmus_23 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.07 % |
| Parental protein coverage: | 98.3 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MARPLVPSSQKALLLELKGLQEEPVEGFRVTLVDEGDLYNWEVAIFGPPNTYYEGGYFKARLKFPIDYPY |
| MA.PLVPSSQK.LLLELKGLQEEPVEGFRVTLVDEGDLYNWEVAIFGPPNTYYEGGYFKA.LKFPIDYPY | |
| Retrocopy | MAGPLVPSSQKVLLLELKGLQEEPVEGFRVTLVDEGDLYNWEVAIFGPPNTYYEGGYFKAHLKFPIDYPY |
| Parental | SPPAFRFLTKMWHPNIYETGDVCISILHPPVDDPQSGELPSERWNPTQNVRTILLSVISLLNEPNTFSPA |
| SPP.F.FLTKMWHPNI.ETG.VCISILHPP.D.PQ.GELPSERWNPTQNVRTILLSVISLLNEPNT.SPA | |
| Retrocopy | SPPTFWFLTKMWHPNIHETGFVCISILHPPDDNPQGGELPSERWNPTQNVRTILLSVISLLNEPNTSSPA |
| Parental | NVDASVMYRKWKESKGKDREYTDIIRKQVLGTKVDAERDGVKVPTTLAEYCVKTKAPAPDEGSDLFYDDY |
| NVDASVMYRKWKESKGKD.EYTDIIRKQVLGTKVDAERDGVKVPTTLAEYCVKTKAPAPDEGSDLF..DY | |
| Retrocopy | NVDASVMYRKWKESKGKDHEYTDIIRKQVLGTKVDAERDGVKVPTTLAEYCVKTKAPAPDEGSDLF--DY |
| Parental | YEDGEVEEADSCFGDEEDDSG |
| Y.DGEVEEADSCFGDEEDD.G | |
| Retrocopy | YVDGEVEEADSCFGDEEDDFG |
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 .21 RPM | 21 .38 RPM |
| SRP007412_cerebellum | 0 .30 RPM | 21 .06 RPM |
| SRP007412_heart | 0 .03 RPM | 75 .43 RPM |
| SRP007412_kidney | 0 .69 RPM | 41 .31 RPM |
| SRP007412_liver | 0 .46 RPM | 38 .61 RPM |
| SRP007412_testis | 6 .04 RPM | 224 .40 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_23 was not detected
No EST(s) were mapped for retro_mmus_23 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_19063 | 554 libraries | 434 libraries | 84 libraries | 0 libraries | 0 libraries |
The graphical summary, for retro_mmus_23 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_23 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_23 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 8 parental genes, and 9 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000023874 | 1 retrocopy | |
| Macropus eugenii | ENSMEUG00000000812 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000020307 | 1 retrocopy |
retro_mmus_23 ,
|
| Ochotona princeps | ENSOPRG00000001017 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000010153 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000008348 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000023255 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000000391 | 2 retrocopies |