RetrogeneDB ID: | retro_mmus_1021 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 13:62813081..62814787(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Me1 | ||
| Ensembl ID: | ENSMUSG00000032418 | ||
| Aliases: | Me1, D9Ertd267e, Mdh-1, Mod-1, Mod1 | ||
| Description: | malic enzyme 1, NADP(+)-dependent, cytosolic [Source:MGI Symbol;Acc:MGI:97043] |
Retrocopy-Parental alignment summary:
>retro_mmus_1021
CCGAGCCCCCCCCGCCGCCGACACACCCACCAGCGCGGCTACCTGCTGACGCGGGACCGCATCTCAACAAGGACTTGGCT
TTTACTCTGGAAGAGAGACAGCAGTTGAACATTCATGGATTGTTGCCGCCCTGCATCATCAGCCAGGAACTCCAGGTCCT
TAGAATAATTAAGAATTTCGAGCGACTGAACTCTGACTTCGACAGGTATCTCCTGTTAATGGACCTGCAAGACAGAAATG
AGAAGCTCTTCTACAGCGTGCTCATGTCTGATGTTGAAAAGTTCATGCCTATTGTTTACACCCCCACCGTGGGCCTCGCA
TGCCAGCAGTACAGTTTGGCATTCCGGAAGCCAAGAGGCCTCTTTATTAGTATCCATGACAAAGGGCACATTGCTTCAGT
TCTTAATGCATGGCCAGAGGATGTCCTCAAGGCTATTGTGGTAACTGATGGAGAGCGCATCCTTGGCTTGGGAGACCTTG
GCTGTAATGGAATGGGCATCCCTATGGGTAAACTGGCCTTGTACACGGCATGTGGAGGGGTGAACCCACAACAGTGTCTA
CCCATCACTTTGGACGTGGGAACAGAAAATGAGTTACTTAAGGATCCACTGTACATCGGGCTGCGGCACCGGCGAGTCAG
AGGCCCTGAGTACGACGCCTTCCTGGATGAGTTCATGGAGGCAGCGTCTTCCAAATACTGCATGAATTGCCTTATTCAGT
TTGAAGATTTTGCCAATCGGAATGCATTTCGTCTCCTGAACAAGTATTGAAACAAGTGTTGCACATTTAACGATGATATT
CAAGGAACAGCGTCTGTTGCGGTTGCGGGTCTCCTTGCAGCTCTTCGAATTACCAAGAACAAGCTCTCTGATCAGACAGT
GCTGTTCCAGGGAGCTGGAGAGGCTGCCTTGGGGATTGCTCACTTGGTTGTTATGGCCATGGAGAAAGAAGGTTTATCAA
AGGAGAATGCTAGAAAGAAGACATGGTTGGTTGACTCAAAAGGACTAATAGTTAAGGGTCGTGCTTCTCTCACAGAAGAG
AAAGAGGTGTTTGCCCATGAACATGAAGAAATGAAGAATCTGGAAGCCATTGTTCAAAAGATAAAACCAACTGCTCTCAT
AGGAGTTGCTGCAATTGGTGGTGCTTTCACTGAACAAATTCTCAAGGATATGGCTGCCTTCAACGAGCGGCCCATCATCT
TTGCTTTGAGCAATCCGACCAGCAAAGCGGAGTGCTCTGCAGAGCAGTGCTACAAGGTGACCAAGGGACGTGCAATCTTT
GCCAGCGGCAGTCCTTTTGATCCAGTCACTCTCCCAGATGGACGGACTCTGTTTCCTGGCCAAGGCAACAATTCCTACGT
GTTCCCTGGAGTTGCTCTTGGGGTGGTGGCCTGCGGACTGAGACACATCGATGATAAGGTCTTCCTCACCACTGCTGAGG
TCATATCTCAGCAAGTGTCAGATAAACACCTGCAAGAAGGCCGGCTCTATCCTCCTTTGAATACCATTCGAGACGATTCG
TTGAAAATTGCAGTAAAGATTGTGCAAGATGCATACAAAGAAAAGATGGCCACTGTTTATCCTGAACCCCAAAACAAAGA
AGAAGTTGTCTCCTCCCAGATGTACAGCACTAATTATGACCAGATCCTACCTGATTGTTATCCGTGGCCTGCAGAAGTCC
AGAAATTACAGACCAAAGTCAACCAG
ORF - retro_mmus_1021 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.55 % |
| Parental protein coverage: | 99.65 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | PRAPRRRHTHQRGYLLTRD-PHLNKDLAFTLEERQQLNIHGLLPPCIISQELQVLRIIKNFERLNSDFDR |
| P..PRRRHTHQRGYLLTRD.PHLNKDLAFTLEERQQLNIHGLLPPCIISQELQVLRIIKNFERLNSDFDR | |
| Retrocopy | PSPPRRRHTHQRGYLLTRD<PHLNKDLAFTLEERQQLNIHGLLPPCIISQELQVLRIIKNFERLNSDFDR |
| Parental | YLLLMDLQDRNEKLFYSVLMSDVEKFMPIVYTPTVGLACQQYSLAFRKPRGLFISIHDKGHIASVLNAWP |
| YLLLMDLQDRNEKLFYSVLMSDVEKFMPIVYTPTVGLACQQYSLAFRKPRGLFISIHDKGHIASVLNAWP | |
| Retrocopy | YLLLMDLQDRNEKLFYSVLMSDVEKFMPIVYTPTVGLACQQYSLAFRKPRGLFISIHDKGHIASVLNAWP |
| Parental | EDVVKAIVVTDGERILGLGDLGCNGMGIPVGKLALYTACGGVNPQQCLPITLDVGTENEELLKDPLYIGL |
| EDV.KAIVVTDGERILGLGDLGCNGMGIP.GKLALYTACGGVNPQQCLPITLDVGTENE.LLKDPLYIGL | |
| Retrocopy | EDVLKAIVVTDGERILGLGDLGCNGMGIPMGKLALYTACGGVNPQQCLPITLDVGTENE-LLKDPLYIGL |
| Parental | RHRRVRGPEYDAFLDEFMEAASSKYGMNCLIQFEDFANRNAFRLLNKYRNKYCTFNDDIQGTASVAVAGL |
| RHRRVRGPEYDAFLDEFMEAASSKY.MNCLIQFEDFANRNAFRLLNKY.NK.CTFNDDIQGTASVAVAGL | |
| Retrocopy | RHRRVRGPEYDAFLDEFMEAASSKYCMNCLIQFEDFANRNAFRLLNKY*NKCCTFNDDIQGTASVAVAGL |
| Parental | LAALRITKNKLSDQTVLFQGAGEAALGIAHLVVMAMEKEGLSKENARKKIWLVDSKGLIVKGRASLTEEK |
| LAALRITKNKLSDQTVLFQGAGEAALGIAHLVVMAMEKEGLSKENARKK.WLVDSKGLIVKGRASLTEEK | |
| Retrocopy | LAALRITKNKLSDQTVLFQGAGEAALGIAHLVVMAMEKEGLSKENARKKTWLVDSKGLIVKGRASLTEEK |
| Parental | EVFAHEHEEMKNLEAIVQKIKPTALIGVAAIGGAFTEQILKDMAAFNERPIIFALSNPTSKAECSAEQCY |
| EVFAHEHEEMKNLEAIVQKIKPTALIGVAAIGGAFTEQILKDMAAFNERPIIFALSNPTSKAECSAEQCY | |
| Retrocopy | EVFAHEHEEMKNLEAIVQKIKPTALIGVAAIGGAFTEQILKDMAAFNERPIIFALSNPTSKAECSAEQCY |
| Parental | KVTKGRAIFASGSPFDPVTLPDGRTLFPGQGNNSYVFPGVALGVVACGLRHIDDKVFLTTAEVISQQVSD |
| KVTKGRAIFASGSPFDPVTLPDGRTLFPGQGNNSYVFPGVALGVVACGLRHIDDKVFLTTAEVISQQVSD | |
| Retrocopy | KVTKGRAIFASGSPFDPVTLPDGRTLFPGQGNNSYVFPGVALGVVACGLRHIDDKVFLTTAEVISQQVSD |
| Parental | KHLQEGRLYPPLNTIRGVSLKIAVKIVQDAYKEKMATVYPEPQNKEEFVSSQMYSTNYDQILPDCYPWPA |
| KHLQEGRLYPPLNTIR..SLKIAVKIVQDAYKEKMATVYPEPQNKEE.VSSQMYSTNYDQILPDCYPWPA | |
| Retrocopy | KHLQEGRLYPPLNTIRDDSLKIAVKIVQDAYKEKMATVYPEPQNKEEVVSSQMYSTNYDQILPDCYPWPA |
| Parental | EVQKIQTKVNQ |
| EVQK.QTKVNQ | |
| Retrocopy | EVQKLQTKVNQ |
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 .44 RPM | 27 .61 RPM |
| SRP007412_cerebellum | 0 .69 RPM | 24 .79 RPM |
| SRP007412_heart | 0 .28 RPM | 64 .60 RPM |
| SRP007412_kidney | 3 .58 RPM | 163 .10 RPM |
| SRP007412_liver | 2 .10 RPM | 84 .63 RPM |
| SRP007412_testis | 4 .39 RPM | 135 .71 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1021 was not detected
No EST(s) were mapped for retro_mmus_1021 retrocopy.
No TSS is located nearby retro_mmus_1021 retrocopy 5' end.
retro_mmus_1021 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1021 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000009064 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000032418 | 1 retrocopy |
retro_mmus_1021 ,
|