RetrogeneDB ID: | retro_mmus_2107 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 2:150499468..150500821(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000083325 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Btbd1 | ||
| Ensembl ID: | ENSMUSG00000025103 | ||
| Aliases: | Btbd1, 1190005H08Rik | ||
| Description: | BTB (POZ) domain containing 1 [Source:MGI Symbol;Acc:MGI:1933765] |
Retrocopy-Parental alignment summary:
>retro_mmus_2107
TCTGCTCTCTGGCCGCTGCTGCTCCTGCAGCTCGAGCTACTGTACAACTGGCAGGCCACCAAGGCGTCGCTCAAGGAGCG
CTTCGCCTTCTTCTTCAACTCCGAGCTGCTGAGCGATGTGCGTTTCGTGCTGGGCAAGGGCCGAGGTGCGGCGGCCGCCG
GGGGCCCGCAGCGCATCCCGGACCACCGCTTCGTGCTGGCGGCTGGCATTGCGGTCTTCGACGCCATGTTCAACGGCGGC
ATGGCCACGACGTCGGCCGAGATCGAGCTGCCGGACGTGGAGCCCGCCGCCTTCCTGGCGCTGCTGAGATTTTTGTATTC
AGACGAAGTTCAAATTGGTCCAGAAACCGTTATGACCACTCTTTATACTGCTAAGAAATATGCAGTCCCTGCCTTGGAAG
CACATTGCGTAGAATTTCTCACCAAACATCTTAGGGCAGATAATGCCTTTATGTTGCTTATTCAGGCGCGGTTGTTTGAT
GAGCCCCAGCTGGCTAGTCTTTGTCTGGACACCATAGACAAGAGCACAGTGGATGCAATCAGTGCGGAGGGGTTTACTGA
TATTGACATAGATACACTCTGTGCAGTTCTAGAAAGAGACACACTGAGTATCCGAGAAAGTCGACTTTTTGGAGCTATTG
TACGTTGGGCAGAAGCAGAGTGTCAGAGACAACAACTGGCTGTGACATTTGGAAACAAACAGAAAGTTCTAGGAAAAGCA
CTTTCCTTAATCCGCTTCCCACTGATGACAATTGAGGAGTTTGCAGCAGGTCCTGCTCAATCTGGAATTTTGTCAGACCG
TGAAGTGGTAAACCTCTTTCTTCATTTTACTGTCAATCCTAAACCCCGAGTAGAGTACATTGATCGGCCACGATGCTGCC
TCAGAGGAAAGGAGTGCTGCATCAACGGATTCCAGCAAGTAGAGAGCCGCTGGGGTTACAGTGGGACAAGCGATCGCATC
AGGTTCACAGTTAACAGAAGAATCTCTGTAGTTGGATTTGGTTTGTATGGATCTATTCACGGGCCCACAGATTATCAAGT
GAATATACAGATCATTGAATATGAGAAAAAACAAACCTTGGGACAGAATGATACTGGATTTAGTTGTGATAGGACTGCTA
ACACATTCAGGGTCATGTTCAAAGAACCTATAGAGATCCTGCTCAATGTCTGCTACACAGCATGCGCAACACTCAAGGGC
CCAGATTCTCACTATGGCACAAAAGGACTGAAGAAAGTAGTGCATGAGACCCCTGCTGCAAGCAAGACTGTTTTCCTATT
TTTCAGTTCCCCTGGCAATAACAATGGCACATCAATAGAAGATGGACAAATAACAGAAATAATATTTTATACA
ORF - retro_mmus_2107 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.34 % |
| Parental protein coverage: | 92.42 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | SALGPLLPLQREPLYNWQATKASLKERFAFLFNSELLSDVRFVLGKGRGAAAAGGPQRIPAHRFVLAAGS |
| SAL.PLL.LQ.E.LYNWQATKASLKERFAF.FNSELLSDVRFVLGKGRGAAAAGGPQRIP.HRFVLAAG. | |
| Retrocopy | SALWPLLLLQLELLYNWQATKASLKERFAFFFNSELLSDVRFVLGKGRGAAAAGGPQRIPDHRFVLAAGI |
| Parental | AVFDAMFNGGMATTSAEIELPDVEPAAFLALLRFLYSDEVQIGPETVMTTLYTAKKYAVPALEAHCVEFL |
| AVFDAMFNGGMATTSAEIELPDVEPAAFLALLRFLYSDEVQIGPETVMTTLYTAKKYAVPALEAHCVEFL | |
| Retrocopy | AVFDAMFNGGMATTSAEIELPDVEPAAFLALLRFLYSDEVQIGPETVMTTLYTAKKYAVPALEAHCVEFL |
| Parental | TKHLRADNAFMLLTQARLFDEPQLASLCLDTIDKSTVDAISAEGFTDIDIDTLCAVLERDTLSIRESRLF |
| TKHLRADNAFMLL.QARLFDEPQLASLCLDTIDKSTVDAISAEGFTDIDIDTLCAVLERDTLSIRESRLF | |
| Retrocopy | TKHLRADNAFMLLIQARLFDEPQLASLCLDTIDKSTVDAISAEGFTDIDIDTLCAVLERDTLSIRESRLF |
| Parental | GAIVRWAEAECQRQQLAVTFGNKQKVLGKALSLIRFPLMTIEEFAAGPAQSGILSDREVVNLFLHFTVNP |
| GAIVRWAEAECQRQQLAVTFGNKQKVLGKALSLIRFPLMTIEEFAAGPAQSGILSDREVVNLFLHFTVNP | |
| Retrocopy | GAIVRWAEAECQRQQLAVTFGNKQKVLGKALSLIRFPLMTIEEFAAGPAQSGILSDREVVNLFLHFTVNP |
| Parental | KPRVEYIDRPRCCLRGKECCINRFQQVESRWGYSGTSDRIRFTVNRRISVVGFGLYGSIHGPTDYQVNIQ |
| KPRVEYIDRPRCCLRGKECCIN.FQQVESRWGYSGTSDRIRFTVNRRISVVGFGLYGSIHGPTDYQVNIQ | |
| Retrocopy | KPRVEYIDRPRCCLRGKECCINGFQQVESRWGYSGTSDRIRFTVNRRISVVGFGLYGSIHGPTDYQVNIQ |
| Parental | IIEYEKKQTLGQNDTGFSCDGTANTFRVMFKEPIEILPNVCYTACATLKGPDSHYGTKGLKKVVHETPAA |
| IIEYEKKQTLGQNDTGFSCD.TANTFRVMFKEPIEIL.NVCYTACATLKGPDSHYGTKGLKKVVHETPAA | |
| Retrocopy | IIEYEKKQTLGQNDTGFSCDRTANTFRVMFKEPIEILLNVCYTACATLKGPDSHYGTKGLKKVVHETPAA |
| Parental | SKTVFLFFSSPGNNNGTSIEDGQIPEIIFYT |
| SKTVFLFFSSPGNNNGTSIEDGQI.EIIFYT | |
| Retrocopy | SKTVFLFFSSPGNNNGTSIEDGQITEIIFYT |
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 .07 RPM | 61 .09 RPM |
| SRP007412_cerebellum | 0 .09 RPM | 40 .90 RPM |
| SRP007412_heart | 0 .34 RPM | 63 .60 RPM |
| SRP007412_kidney | 0 .37 RPM | 50 .92 RPM |
| SRP007412_liver | 0 .03 RPM | 19 .47 RPM |
| SRP007412_testis | 0 .82 RPM | 178 .79 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2107 was not detected
No EST(s) were mapped for retro_mmus_2107 retrocopy.
No TSS is located nearby retro_mmus_2107 retrocopy 5' end.
retro_mmus_2107 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2107 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000025103 | 1 retrocopy |
retro_mmus_2107 ,
|