RetrogeneDB ID: | retro_mmus_1250 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 14:18543807..18545132(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Vps4b | ||
| Ensembl ID: | ENSMUSG00000009907 | ||
| Aliases: | None | ||
| Description: | vacuolar protein sorting 4b (yeast) [Source:MGI Symbol;Acc:MGI:1100499] |
Retrocopy-Parental alignment summary:
>retro_mmus_1250
ATGGCGTCCACGAACACCAACCTCCAGAAAGCAATAGATCTTGCAAGCAAAGCAGCCCAGGAAGACAAAGCTGGGAACTA
TGAGGAAGCTCTTCAACTCTACCAACATGCTGTGCAGTATTTTCTCCATGTTGTTAAATATGAAGCACAAGGTGATAAAG
CCAAGCAAAGTATCGGGACCAAGTGTACAGAATATCTTGATAGAGCAGAAAAACTAAAGGAATATCTGAAGAAAAGAGAG
AAGAAACCACAGAAGCCCGTGAAAGAGGAACAGTCAGGCCCAGATGATGAAAAGGGGAATGACAGTGATGGGGATGCAGA
ATCTGATGATCCTGAAAAAAAGAAACTGCAGAATCAACTTCAAGGTGCCATTGTTATAGAGCGACCAAATGTGAAATGGA
GTGATGTTGCTGGTCTCGAAGGAGCCAAAGAAGCTCTTAAAGAGTCTGTGATTCTGCTTATTAAGTTCCCTCATCTGTTT
ACAGGGAAGAGGACACCTTGGAGAGGAATCCTATTATTTGGACCACCAGGAACAGGAAAATCTTATTTGCCTAAAGCTGT
TGCAACGGAAGCAAACAACTCAACATCTTTCTCAATATCTTCCTCTGACCTTGTGTCTAAGTGGCTGGGGGAAAGGGAAA
AACTGGTTAAGAACTTATTACAGGTTGCCAGAGAGAACAAGCCTTCTATCATCTTCATTGATGAGATTGATTCTCTGTGT
GGTTCCAGAAGTGAGAATGAGAGTGAAGCTGCACAGAGAATTAAGACAGAGTTCCTGGTTCAAATGCAAGGAGTTGGTGT
GGACAATGATGGAATTTTGGTTCTGGGAGCTACAAATATACCCTGGGTTCTGGATTCTGCAATTAGGCGAAGATTTGAGA
AACATATTTATATTCCTTTGCCCGAAGCCCATGCCCGAGCAGCCATGTTTAGACTGCACTTGGGCATCACTCAGAACAGC
CTCACAGAAGCAGAATTCCAAGAACTTGGAAGGAAGACAGATGGCTATTCAGGAGCAGATATAAGTATCATTGTATGGGA
TGCACTTATGCAGCCTGTGAAAAAAGTCAGTCAGCTGCTCACTTCAAAAATGTTCGTGGACCCTCAAGAGCTGATCCTAA
CTGCATTGTAAATGACCTGCTGATCTCCTCTCCAGGAGATCCTGGGGCTATTGAAATGACATGGATGGATGTTCCTGGAG
ATACACTCTTGGAGCCAGTTGTTTCCATATGGGATATGCTGCGGTCCCTGTCCAACACAAAGCTGACAGTCAACGAGCAG
GACTTCTTGAAGCTGAAGAAGTTTACAGAAGATTTTTGCCAGGAA
ORF - retro_mmus_1250 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.24 % |
| Parental protein coverage: | 99.77 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MASTNTNLQKAIDLASKAAQEDKAGNYEEALQLYQHAVQYFLHVVKYEAQGDKAKQSIRAKCTEYLDRAE |
| MASTNTNLQKAIDLASKAAQEDKAGNYEEALQLYQHAVQYFLHVVKYEAQGDKAKQSI..KCTEYLDRAE | |
| Retrocopy | MASTNTNLQKAIDLASKAAQEDKAGNYEEALQLYQHAVQYFLHVVKYEAQGDKAKQSIGTKCTEYLDRAE |
| Parental | KLKEYLKKKEKKPQKPVKEEQSGPVDEKGNDSDGEAESDDPEKKKLQNQLQGAIVIERPNVKWSDVAGLE |
| KLKEYLKK.EKKPQKPVKEEQSGP.DEKGNDSDG.AESDDPEKKKLQNQLQGAIVIERPNVKWSDVAGLE | |
| Retrocopy | KLKEYLKKREKKPQKPVKEEQSGPDDEKGNDSDGDAESDDPEKKKLQNQLQGAIVIERPNVKWSDVAGLE |
| Parental | GAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLVSKWLG |
| GAKEALKE.VIL.IKFPHLFTGKRTPWRGILLFGPPGTGKSYL.KAVATEANNST.FSISSSDLVSKWLG | |
| Retrocopy | GAKEALKESVILLIKFPHLFTGKRTPWRGILLFGPPGTGKSYLPKAVATEANNSTSFSISSSDLVSKWLG |
| Parental | ESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNI |
| E.EKLVKNL.Q.ARENKPSIIFIDEIDSLCGSRSENESEAA.RIKTEFLVQMQGVGVDNDGILVLGATNI | |
| Retrocopy | EREKLVKNLLQVARENKPSIIFIDEIDSLCGSRSENESEAAQRIKTEFLVQMQGVGVDNDGILVLGATNI |
| Parental | PWVLDSAIRRRFEKRIYIPLPEAHARAAMFRLHLGSTQNSLTEADFQELGRKTDGYSGADISIIVRDALM |
| PWVLDSAIRRRFEK.IYIPLPEAHARAAMFRLHLG.TQNSLTEA.FQELGRKTDGYSGADISIIV.DALM | |
| Retrocopy | PWVLDSAIRRRFEKHIYIPLPEAHARAAMFRLHLGITQNSLTEAEFQELGRKTDGYSGADISIIVWDALM |
| Parental | QPVRKV-QSATHFKKVRGPSRADPNCIVNDLLTPCSPGDPGAIEMTWMDVPGDKLLEPVVSMWDMLRSLS |
| QPV.KV.QSA.HFK.VRGPSRADPNCIVNDLL...SPGDPGAIEMTWMDVPGD.LLEPVVS.WDMLRSLS | |
| Retrocopy | QPVKKV<QSAAHFKNVRGPSRADPNCIVNDLLI-SSPGDPGAIEMTWMDVPGDTLLEPVVSIWDMLRSLS |
| Parental | STKPTVNEQDLLKLKKFTEDFGQE |
| .TK.TVNEQD.LKLKKFTEDF.QE | |
| Retrocopy | NTKLTVNEQDFLKLKKFTEDFCQE |
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 .12 RPM | 45 .09 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 35 .82 RPM |
| SRP007412_heart | 0 .06 RPM | 25 .65 RPM |
| SRP007412_kidney | 0 .08 RPM | 57 .33 RPM |
| SRP007412_liver | 0 .11 RPM | 55 .38 RPM |
| SRP007412_testis | 0 .23 RPM | 23 .42 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1250 was not detected
No EST(s) were mapped for retro_mmus_1250 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_33072 | 581 libraries | 268 libraries | 218 libraries | 4 libraries | 1 library |
The graphical summary, for retro_mmus_1250 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_1250 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1250 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mustela putorius furo | ENSMPUG00000016525 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000009907 | 1 retrocopy |
retro_mmus_1250 ,
|
| Mus musculus | ENSMUSG00000031913 | 1 retrocopy |