RetrogeneDB ID: | retro_mmus_874 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 12:69981296..69982019(+) | ||
| Located in intron of: | ENSMUSG00000021067 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Ppp2r2a | ||
| Ensembl ID: | ENSMUSG00000022052 | ||
| Aliases: | Ppp2r2a, 2410004D02Rik, mKIAA1541 | ||
| Description: | protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), alpha isoform [Source:MGI Symbol;Acc:MGI:1919228] |
Retrocopy-Parental alignment summary:
>retro_mmus_874
CAACACCCCAGTGAGAACAAAATCCAGTCTCATAGCAGAGGAGAATACAATGTTTACAGCACCTTCCAGAGCCATGAGCC
AGAATTTGACTACTTGAAAAGCTTAGAAATAGAAGGGAAGATCAACAAAATTAGGTGGTTACCCCAGAAAAATGCTGCCC
AGTTTTTATTGTCTACCAATGATAAAACAATAAAATTATGGAAAATCAGTGAAAGAGACAAAAGACCAGAAGGCTATAAC
TTGAAAGAGGAAGATGGAAGATATAGAGATCCTACTACAGTCACTACGCTACGGGTGCCAGTATTTAGGCCCATGGATCT
AATGGTGGAAGCCAGTCCACAGAGAATATTTGCCAACACCCACACTTATCACATCAACTCAATTTCTATCAATAGTGATT
ATGAAACCTACTTATCAGCAGATGATTTGTGAATTATCTCTGGCATCTGGAAATTACAGACTGGAGTTTTAATATTGTGG
CTATCAAGCCTGGCAATATGGAAAAGCTCACAGAGGTGCTCACAGCTGCCGAATTTCACCCCAACAGCTGTAACACATTT
GTGTACAGCAGCAGTAAAGGAACCATTCGGTTATGTGACATGAGGGCATCTGCGCTCTGTGACAGGCATTCTAAACTGTT
TGAAGAACGTGAAGATCCCAGCAACAGGTCATTTTTTTTCTGAAATCATCTCCTCTATTTCTGATGTAAAATTCAGCCAT
AGT
ORF - retro_mmus_874 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.18 % |
| Parental protein coverage: | 53.91 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | QQEQENKIQSHSRGEYNVYSTFQSHEPEFDYLKSLEIEEKINKIRWLPQKNAAQFLLSTNDKTIKLWKIS |
| Q...ENKIQSHSRGEYNVYSTFQSHEPEFDYLKSLEIE.KINKIRWLPQKNAAQFLLSTNDKTIKLWKIS | |
| Retrocopy | QHPSENKIQSHSRGEYNVYSTFQSHEPEFDYLKSLEIEGKINKIRWLPQKNAAQFLLSTNDKTIKLWKIS |
| Parental | ERDKRPEGYNLKEEDGRYRDPTTVTTLRVPVFRPMDLMVEASPRRIFANAHTYHINSISINSDYETYLSA |
| ERDKRPEGYNLKEEDGRYRDPTTVTTLRVPVFRPMDLMVEASP.RIFAN.HTYHINSISINSDYETYLSA | |
| Retrocopy | ERDKRPEGYNLKEEDGRYRDPTTVTTLRVPVFRPMDLMVEASPQRIFANTHTYHINSISINSDYETYLSA |
| Parental | DDLRI-NLWHLEITDRSFNIVDIKPANMEELTEVITAAEFHPNSCNTFVYSSSKGTIRLCDMRASALCDR |
| DDL.I..LWHLEITD.SFNIV.IKP.NME.LTEV.TAAEFHPNSCNTFVYSSSKGTIRLCDMRASALCDR | |
| Retrocopy | DDL*I<YLWHLEITDWSFNIVAIKPGNMEKLTEVLTAAEFHPNSCNTFVYSSSKGTIRLCDMRASALCDR |
| Parental | HSKLFEEPEDPSNRS-FFSEIISSISDVKFSHS |
| HSKLFEE.EDPSNRS....EIISSISDVKFSHS | |
| Retrocopy | HSKLFEEREDPSNRS>XXXEIISSISDVKFSHS |
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 .61 RPM | 80 .67 RPM |
| SRP007412_cerebellum | 0 .43 RPM | 52 .37 RPM |
| SRP007412_heart | 0 .53 RPM | 41 .50 RPM |
| SRP007412_kidney | 0 .54 RPM | 35 .46 RPM |
| SRP007412_liver | 0 .36 RPM | 19 .63 RPM |
| SRP007412_testis | 0 .37 RPM | 34 .94 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_874 was not detected
No EST(s) were mapped for retro_mmus_874 retrocopy.
No TSS is located nearby retro_mmus_874 retrocopy 5' end.
retro_mmus_874 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_874 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 | |
|---|---|---|---|
| Equus caballus | ENSECAG00000019205 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000016691 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000022052 | 1 retrocopy |
retro_mmus_874 ,
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