RetrogeneDB ID: | retro_mmus_580 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 10:82585425..82586680(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000094683 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Ap3m1 | ||
| Ensembl ID: | ENSMUSG00000021824 | ||
| Aliases: | None | ||
| Description: | adaptor-related protein complex 3, mu 1 subunit [Source:MGI Symbol;Acc:MGI:1929212] |
Retrocopy-Parental alignment summary:
>retro_mmus_580
ATGATCCACAGTCTATTTCTCATAAACTGCTCTGGCGACATTTTTCTAGAAAAACACTGGAAGAGCGTTGTAAGCCAGTC
AGTGTGTGACTATTTCTTTGAAGCTCAGGAGAAAGCTGCTGATGTTGAAAATGTCCCACCTATCATTTCAACACCTCACC
ACTACCTCATTAGTATCTACCGGGATAAGCTCTTCTTTGTGTCTGTGATACAGACCGAAGTGCCACCTCTCTTTGTAATT
GAATTTCTGCATCGAGTTGCTGACACTTTTCAGGACTACTTTGGTGAGTGTTCAGAGGCTGCAATTAAGGATAATGTGGT
CATAGTATATGAGCTCTTGGAAGAAATGTTAGACAATGGATTCCCACTGACTACTGAATCTAACATTTTGAAAGAACTGA
TTAAACCACCAACAATTCTACGTTCTGTCGTCAATTCTATTACAGGCAGTAGTAATGTTGGGGATACACTCCCCACTGGG
CAGCTATCCAACATCCCATGGCGTCGAGCAGGAGTAAAGTACACAAACAATGAAGCCTATTTTGATGTAGTTGAAGAGAT
AGATGCAATTATAGATAAATCAGGATCTACAGTCTTTGCAGAAATTCAAGGGGTCATTGATGCTTGCATTAAGCTGTCTG
GAATGCCTGATCTCTCCCTCTCTTTCATGAACCCAAGGCTCCTAGATGACGTCAGCTTCCACCCATGCATCCGATTCAAA
CGCTGGGAGTCTGAAAGAGTTTTGTCATTCATTCCTCCAGATGGAAATTTCCGACTCATATCGTATCGTGTCAGCTCACA
AAATCTAGTGGCAATACCAGTGTATGTGAAACACAGTATCAGCTTTAAGGAAAACAGCTCTTGTGGCCGGTTTGATATAA
CAATTGGACCGAAACAGAATATGGGAAAAACAATTGAAGGAATCACAGTGACTGTTCACATGCCCAAAGTTGTGCTGAAT
ATGAACCTGACACCAACGCAAGGCAGCTATACATTTGATCCAGTGACCAAGGTACTAGCATGGGATGTGGGCAAAATTAC
TCCACAAAAGCTCCCAAGTCTTAAAGGACTAGTAAATTTACAGTCAGGAGCACCCAAGCCAGAAGAGAACCCAAACCTCA
ACATACAGTTCAAGATCCAGCAGCTTGCTATTTCAGGCTTAAAAGTGAACCCGCTTGGACATGTATGGTGAGAAGTATAA
GCCATTTAAAGAAGTCAAATATGTCACAAAGGCTGGGAAGTTCCAAGTGAGGACA
ORF - retro_mmus_580 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.05 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MIHSLFLINCSGDIFLEKHWKSVVSQSVCDYFFEAQEKAADVENVPPVISTPHHYLISIYRDKLFFVSVI |
| MIHSLFLINCSGDIFLEKHWKSVVSQSVCDYFFEAQEKAADVENVPP.ISTPHHYLISIYRDKLFFVSVI | |
| Retrocopy | MIHSLFLINCSGDIFLEKHWKSVVSQSVCDYFFEAQEKAADVENVPPIISTPHHYLISIYRDKLFFVSVI |
| Parental | QTEVPPLFVIEFLHRVADTFQDYFGECSEAAIKDNVVIVYELLEEMLDNGFPLATESNILKELIKPPTIL |
| QTEVPPLFVIEFLHRVADTFQDYFGECSEAAIKDNVVIVYELLEEMLDNGFPL.TESNILKELIKPPTIL | |
| Retrocopy | QTEVPPLFVIEFLHRVADTFQDYFGECSEAAIKDNVVIVYELLEEMLDNGFPLTTESNILKELIKPPTIL |
| Parental | RSVVNSITGSSNVGDTLPTGQLSNIPWRRAGVKYTNNEAYFDVVEEIDAIIDKSGSTVFAEIQGVIDACI |
| RSVVNSITGSSNVGDTLPTGQLSNIPWRRAGVKYTNNEAYFDVVEEIDAIIDKSGSTVFAEIQGVIDACI | |
| Retrocopy | RSVVNSITGSSNVGDTLPTGQLSNIPWRRAGVKYTNNEAYFDVVEEIDAIIDKSGSTVFAEIQGVIDACI |
| Parental | KLSGMPDLSLSFMNPRLLDDVSFHPCIRFKRWESERVLSFIPPDGNFRLISYRVSSQNLVAIPVYVKHSI |
| KLSGMPDLSLSFMNPRLLDDVSFHPCIRFKRWESERVLSFIPPDGNFRLISYRVSSQNLVAIPVYVKHSI | |
| Retrocopy | KLSGMPDLSLSFMNPRLLDDVSFHPCIRFKRWESERVLSFIPPDGNFRLISYRVSSQNLVAIPVYVKHSI |
| Parental | SFKENSSCGRFDITIGPKQNMGKTIEGITVTVHMPKVVLNMNLTPTQGSYTFDPVTKVLAWDVGKITPQK |
| SFKENSSCGRFDITIGPKQNMGKTIEGITVTVHMPKVVLNMNLTPTQGSYTFDPVTKVLAWDVGKITPQK | |
| Retrocopy | SFKENSSCGRFDITIGPKQNMGKTIEGITVTVHMPKVVLNMNLTPTQGSYTFDPVTKVLAWDVGKITPQK |
| Parental | LPSLKGLVNLQSGAPKPEENPNLNIQFKIQQLAISGLKVN-RLDMYGEKYKPFKGVKYVTKAGKFQVRT |
| LPSLKGLVNLQSGAPKPEENPNLNIQFKIQQLAISGLKVN.RLDMYGEKYKPFK.VKYVTKAGKFQVRT | |
| Retrocopy | LPSLKGLVNLQSGAPKPEENPNLNIQFKIQQLAISGLKVN>RLDMYGEKYKPFKEVKYVTKAGKFQVRT |
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 | 32 .80 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 29 .01 RPM |
| SRP007412_heart | 0 .03 RPM | 16 .81 RPM |
| SRP007412_kidney | 0 .06 RPM | 22 .56 RPM |
| SRP007412_liver | 0 .22 RPM | 99 .29 RPM |
| SRP007412_testis | 0 .18 RPM | 14 .77 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_580 was not detected
No EST(s) were mapped for retro_mmus_580 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_6508 | 108 libraries | 102 libraries | 748 libraries | 102 libraries | 12 libraries |
The graphical summary, for retro_mmus_580 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_580 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_580 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000004510 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000000660 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000021824 | 1 retrocopy |
retro_mmus_580 ,
|
| Mus musculus | ENSMUSG00000022841 | 2 retrocopies | |
| Ictidomys tridecemlineatus | ENSSTOG00000012881 | 1 retrocopy |