RetrogeneDB ID: | retro_mmus_3098 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 8:4087657..4088572(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000074482 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Aida | ||
| Ensembl ID: | ENSMUSG00000042901 | ||
| Aliases: | Aida, 2610208M17Rik, BC004835 | ||
| Description: | axin interactor, dorsalization associated [Source:MGI Symbol;Acc:MGI:1919737] |
Retrocopy-Parental alignment summary:
>retro_mmus_3098
ATGTCGGAGGTGACCTGGAGTCTGCTGCAGCGCTGGGGCGCCAGTCTTAGGAGAGGCGCCGACTTCGACTCTTGGGGCCA
GCTGTTGGAGGCGATAGACGAGTATCAGATATTAGCAAGACACTTACAGAAGGAGGCCCAAGCTCAACACAATAATTCTG
AATTTACAGAAGAACAAAAGAAAACCATAGGCAAAATTGCGACATGTTTGGAATTGCGAAGTGCAGCATTACAGGCCACA
CAGTCCCAAGAAGAGTTTAAACTGGAGGACCTGAAGAAGCTAGAACCAATCCTGAAGAATATTCTTACATATAATAAAGA
ATTCCCATTTGATGTTCAGCCTATTCCATTAAGACGTATTTTAGCACCTGGTGAAGAAGAGAATTTGGAATTTGAAGAAG
ATGAAGAAGGTGGTGCTGGAGCAGGACCTCCTGATTCTTTCTCTGCTAGAGTTCCTGGTACTTTATTGCCACGGTTGCCA
TCGGAACCAGGGATGACGTTACTCACCATCAGGATTGAGAAAATTGGTTTGAAAGATGCGGGGCAGTGCATCGATCCCTA
CATCACAGTCAGCGTGAAAGATTTGAATGGCATAGATTTAACTCCCGTACAAGACACTCCTGTGGCTTCAAGAAAAGAAG
ATACTTACGTTCACTTTAATGTGGACATTGAGCTCCAGAAACACGTTGAAAAGTTAACCAAAGGTGCGGCCATTTTCTTT
GAATTCAAACATTACAAGCCTAAAAAGAGGTTTACCAGCACTAAGTGTTTTGCCTTCATGGAGATGGATGAAATTAAACC
TGGGCCAATCGTAATAGAACTATACAAGAAACCCACTGACTTTAAAAGAAAGAAATTGCAATTGTTGACCAAGAAACCAC
TTTATCTTCATCTACATCAAAGTTTGCACAAAGAA
ORF - retro_mmus_3098 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.69 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSEVTRSLLQRWGASLRRGADFDSWGQLVEAIDEYQILARHLQKEAQAQHNNSEFTEEQKKTIGKIATCL |
| MSEVT.SLLQRWGASLRRGADFDSWGQL.EAIDEYQILARHLQKEAQAQHNNSEFTEEQKKTIGKIATCL | |
| Retrocopy | MSEVTWSLLQRWGASLRRGADFDSWGQLLEAIDEYQILARHLQKEAQAQHNNSEFTEEQKKTIGKIATCL |
| Parental | ELRSAALQSTQSQEEFKLEDLKKLEPILKNILTYNKEFPFDVQPIPLRRILAPGEEENLEFEEDEEGGAG |
| ELRSAALQ.TQSQEEFKLEDLKKLEPILKNILTYNKEFPFDVQPIPLRRILAPGEEENLEFEEDEEGGAG | |
| Retrocopy | ELRSAALQATQSQEEFKLEDLKKLEPILKNILTYNKEFPFDVQPIPLRRILAPGEEENLEFEEDEEGGAG |
| Parental | AGPPDSFSARVPGTLLPRLPSEPGMTLLTIRIEKIGLKDAGQCIDPYITVSVKDLNGIDLTPVQDTPVAS |
| AGPPDSFSARVPGTLLPRLPSEPGMTLLTIRIEKIGLKDAGQCIDPYITVSVKDLNGIDLTPVQDTPVAS | |
| Retrocopy | AGPPDSFSARVPGTLLPRLPSEPGMTLLTIRIEKIGLKDAGQCIDPYITVSVKDLNGIDLTPVQDTPVAS |
| Parental | RKEDTYVHFNVDIELQKHVERLTKGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPTD |
| RKEDTYVHFNVDIELQKHVE.LTKGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPTD | |
| Retrocopy | RKEDTYVHFNVDIELQKHVEKLTKGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPTD |
| Parental | FKRKKLQLLTKKPLYLHLHQSLHKE |
| FKRKKLQLLTKKPLYLHLHQSLHKE | |
| Retrocopy | FKRKKLQLLTKKPLYLHLHQSLHKE |
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 .33 RPM | 28 .71 RPM |
| SRP007412_cerebellum | 0 .26 RPM | 21 .58 RPM |
| SRP007412_heart | 0 .06 RPM | 15 .47 RPM |
| SRP007412_kidney | 0 .54 RPM | 17 .17 RPM |
| SRP007412_liver | 0 .05 RPM | 6 .12 RPM |
| SRP007412_testis | 0 .23 RPM | 13 .45 RPM |
RNA Polymerase II activity may be related with retro_mmus_3098 in 3 libraries
| ENCODE library ID | Target | ChIP-Seq Peak coordinates |
|---|---|---|
| ENCFF001XVA | POLR2A | 8:4087221..4087765 |
| ENCFF001YIJ | POLR2A | 8:4087125..4087853 |
| ENCFF001YKA | POLR2A | 8:4087057..4087784 |
No EST(s) were mapped for retro_mmus_3098 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_141963 | 266 libraries | 480 libraries | 319 libraries | 5 libraries | 2 libraries |
| TSS #2 | TSS_141965 | 471 libraries | 520 libraries | 80 libraries | 1 library | 0 libraries |
| TSS #3 | TSS_141966 | 10 libraries | 0 libraries | 41 libraries | 121 libraries | 900 libraries |
| TSS #4 | TSS_141967 | 73 libraries | 103 libraries | 651 libraries | 178 libraries | 67 libraries |
| TSS #5 | TSS_141968 | 403 libraries | 462 libraries | 199 libraries | 7 libraries | 1 library |
| TSS #6 | TSS_141969 | 602 libraries | 423 libraries | 46 libraries | 0 libraries | 1 library |
The graphical summary, for retro_mmus_3098 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_3098 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3098 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 8 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000004774 | 3 retrocopies | |
| Mus musculus | ENSMUSG00000042901 | 3 retrocopies |
retro_mmus_1939, retro_mmus_3098 , retro_mmus_763,
|
| Oryctolagus cuniculus | ENSOCUG00000017030 | 1 retrocopy | |
| Pteropus vampyrus | ENSPVAG00000010662 | 1 retrocopy |