RetrogeneDB ID: | retro_mmus_570 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 10:71162927..71163374(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Txnl4b | ||
| Ensembl ID: | ENSMUSG00000031723 | ||
| Aliases: | Txnl4b, AI595343, D530025J19Rik, DLP, Dim2 | ||
| Description: | thioredoxin-like 4B [Source:MGI Symbol;Acc:MGI:2443724] |
Retrocopy-Parental alignment summary:
>retro_mmus_570
ATGAGCTTCCTCTTGCCCAAACTGACCAGCAAGAAAGAAGTAGAGCAGGCGATCGAAAGCACTGTGGAGAAGGTGTTGGC
TCTCAGGTTTGGGAGGGGTGAGGACCCCATCTGTCTGCAGCTGGATGATATTCTCTCAAAGACTTCAGCCGACCTGAGTA
AAATGGCTGCTATTTAGCTGGTGGATGTGGACCACATGCCGGTTTACACACAGTATTTTGACATCAGTTACATTCCCTCT
ACCGTATTTTTCTTCAATGGGCAGCACATGAAGGTGGATTATGGGTCTCCGGATCACACTAAATTCGTAGGAAGCTTCAA
AACCAAACAAGACTTCATAGATTTGATTGAAGTCATCTACCAGGGAGCGATGAGGGGGAAACTTATTGTCCAGAGTCCTG
TTGATCCCAAGAATGTGCCCAAATATGACCTCCTCTATCAAGACATT
ORF - retro_mmus_570 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.29 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSFLLPKLTSKKEVDQAIKSTAEKVLVLRFGRDEDPVCLQLDDILSKTSADLSKMAAIYLVDVDHTPVYT |
| MSFLLPKLTSKKEV.QAI.ST.EKVL.LRFGR.EDP.CLQLDDILSKTSADLSKMAAI.LVDVDH.PVYT | |
| Retrocopy | MSFLLPKLTSKKEVEQAIESTVEKVLALRFGRGEDPICLQLDDILSKTSADLSKMAAI*LVDVDHMPVYT |
| Parental | QYFDISYIPSTVFFFNGQHMKVDYGSPDHTKFVGSFKTKQDFIDLIEVIYRGAMRGKLIVQSPIDPKNVP |
| QYFDISYIPSTVFFFNGQHMKVDYGSPDHTKFVGSFKTKQDFIDLIEVIY.GAMRGKLIVQSP.DPKNVP | |
| Retrocopy | QYFDISYIPSTVFFFNGQHMKVDYGSPDHTKFVGSFKTKQDFIDLIEVIYQGAMRGKLIVQSPVDPKNVP |
| Parental | KYDLLYQDI |
| KYDLLYQDI | |
| Retrocopy | KYDLLYQDI |
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 | 13 .57 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 8 .21 RPM |
| SRP007412_heart | 0 .03 RPM | 3 .80 RPM |
| SRP007412_kidney | 0 .02 RPM | 7 .20 RPM |
| SRP007412_liver | 0 .03 RPM | 9 .18 RPM |
| SRP007412_testis | 0 .00 RPM | 64 .08 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_570 was not detected
No EST(s) were mapped for retro_mmus_570 retrocopy.
No TSS is located nearby retro_mmus_570 retrocopy 5' end.
retro_mmus_570 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_570 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 | |
|---|---|---|---|
| Felis catus | ENSFCAG00000005830 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000031723 | 1 retrocopy |
retro_mmus_570 ,
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