RetrogeneDB ID: | retro_mmus_2033 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 2:57425157..57425697(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000084338 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Chmp6 | ||
| Ensembl ID: | ENSMUSG00000025371 | ||
| Aliases: | Chmp6, 2400004G01Rik | ||
| Description: | charged multivesicular body protein 6 [Source:MGI Symbol;Acc:MGI:3583942] |
Retrocopy-Parental alignment summary:
>retro_mmus_2033
GAATAGGACAGAGTCATCCTGCAACTGAAGCAACAGAGGGACAAGCTGAGGCAGGACCAGAAGAGGGCCAGGCAACAGCT
AAAGAGGAAGTAGGCTCTGGCCAGGCAGCTGCTGCGGGATAGCAGGAAAGAATGGGCCAAGCTGCTGCCCCAAAAGAGGT
ACTGAGAGCAACTGCTTGATAGGACAGAAAACCAGATCAGCAGCCTGGAAGCCATGGTTCAGAGCATCAAGTTCACGCAG
ATCGAGATGAAGGTGATGGAGGAGCTTCAGGTGGGGGACGAATGTCTAAATAAGATGCACCAGGTGATGTCCAAAGAGGA
GGTGGAGAGGATCCTGGAGGAGACCCAAGAGGCAGTGGAGTACCAGGGGCAAACTGATGAGCTGCTGGCAGAAAGCTTCA
CCCAGGAGGACGAGGATGCCATCCTGGGAGAGCTGAAAACAATCACTCTGGAACAAATCGAGTTACAAGAGGTTCCTTCG
GAGCCCCTCCCTGATGTTAACCCAAAAGCCCCTGCCAAGGCCAGATGCAGGGCTGGTGAC
ORF - retro_mmus_2033 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.66 % |
| Parental protein coverage: | 90.5 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | EQDRAILQLKQQRDKLRQYQKRVTQQLERERALARQLLRDGRKERAKLLLKKKRYREQLLDRTENQISSL |
| E.DR.ILQLKQQRDKLRQ.QKR..QQL.R..ALARQLLRD.RKE.AKLL...KRY.EQLLDRTENQISSL | |
| Retrocopy | E*DRVILQLKQQRDKLRQDQKRARQQLKRK*ALARQLLRDSRKEWAKLL-PQKRY*EQLLDRTENQISSL |
| Parental | EAMVQSIEFTQIEMKVMEGLQVGNECLNKMHQVMSIEEVERILDETQEAVEYQRQIDELLAGNFTQEDED |
| EAMVQSI.FTQIEMKVME.LQVG.ECLNKMHQVMS.EEVERIL.ETQEAVEYQ.Q.DELLA..FTQEDED | |
| Retrocopy | EAMVQSIKFTQIEMKVMEELQVGDECLNKMHQVMSKEEVERILEETQEAVEYQGQTDELLAESFTQEDED |
| Parental | AILEELNAITQEQMELPEVPSEPLPDRNPEAPAKARSRQAE |
| AIL.EL..IT.EQ.EL.EVPSEPLPD.NP.APAKAR.R... | |
| Retrocopy | AILGELKTITLEQIELQEVPSEPLPDVNPKAPAKARCRAGD |
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 | 17 .01 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 15 .28 RPM |
| SRP007412_heart | 0 .00 RPM | 20 .45 RPM |
| SRP007412_kidney | 0 .02 RPM | 32 .49 RPM |
| SRP007412_liver | 0 .00 RPM | 13 .33 RPM |
| SRP007412_testis | 0 .00 RPM | 43 .86 RPM |
RNA Polymerase II activity may be related with retro_mmus_2033 in 1 libraries
| ENCODE library ID | Target | ChIP-Seq Peak coordinates |
|---|---|---|
| ENCFF001YIJ | POLR2A | 2:57424562..57425938 |
No EST(s) were mapped for retro_mmus_2033 retrocopy.
No TSS is located nearby retro_mmus_2033 retrocopy 5' end.
retro_mmus_2033 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2033 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 | |
|---|---|---|---|
| Macropus eugenii | ENSMEUG00000003320 | 2 retrocopies | |
| Mus musculus | ENSMUSG00000025371 | 1 retrocopy |
retro_mmus_2033 ,
|
| Rattus norvegicus | ENSRNOG00000004014 | 1 retrocopy |