RetrogeneDB ID: | retro_mmus_2578 | ||
Retrocopylocation | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 5:72409485..72409954(+) | ||
| Located in intron of: | ENSMUSG00000005220 | ||
Retrocopyinformation | Ensembl ID: | ENSMUSG00000093644 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | Syce2 | ||
| Ensembl ID: | ENSMUSG00000003824 | ||
| Aliases: | Syce2, 1700013H19Rik, AA407907, Cesc1 | ||
| Description: | synaptonemal complex central element protein 2 [Source:MGI Symbol;Acc:MGI:1919096] |
Retrocopy-Parental alignment summary:
>retro_mmus_2578
AAAAGGGCCAGGACTCCAGAGGTTGTGGAGAGCAGAAAGCATCAACAGAAAGAGAACCGCGAGGAGACAGCTAGCTCAGT
GGCGCCCAGTACCAACTGCTAGCTGCCAGGACTGGTATCTCTGGTCTCCTGCATCGAAATCCTGAAGAAGAAAGCCCAGG
AACTGATTGATAATATCAGTGAATGGAGACAAAAGGATCATGTACTTATGACCAACTTCAGAGACAGCCTGAAGATGAAG
GTTTGAGCTCTGACAGAGGAGTTGGGGAAGATGTACCAGATGTACAGCCTCCACAGCAAAATATCATTCAGGAAAGACTA
CAAGAATTTACCCAGAAAATGGCAAAAATCAGCCATCTAGAAATGGAACTCAAACAGGCTGCCAAACTATAGAAACCGTG
TACAAGGACCTATGCGTCCAGTCTGAGGCTCCCACTTCCAAAGAACAGAATTACAAGGATGATGAATGC
AAAAGGGCCAGGACTCCAGAGGTTGTGGAGAGCAGAAAGCATCAACAGAAAGAGAACCGCGAGGAGACAGCTAGCTCAGT
GGCGCCCAGTACCAACTGCTAGCTGCCAGGACTGGTATCTCTGGTCTCCTGCATCGAAATCCTGAAGAAGAAAGCCCAGG
AACTGATTGATAATATCAGTGAATGGAGACAAAAGGATCATGTACTTATGACCAACTTCAGAGACAGCCTGAAGATGAAG
GTTTGAGCTCTGACAGAGGAGTTGGGGAAGATGTACCAGATGTACAGCCTCCACAGCAAAATATCATTCAGGAAAGACTA
CAAGAATTTACCCAGAAAATGGCAAAAATCAGCCATCTAGAAATGGAACTCAAACAGGCTGCCAAACTATAGAAACCGTG
TACAAGGACCTATGCGTCCAGTCTGAGGCTCCCACTTCCAAAGAACAGAATTACAAGGATGATGAATGC
ORF - retro_mmus_2578 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 65.22 % |
| Parental protein coverage: | 89.27 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | KDQEPPAIVESGEHRQSENHEETPGSVAPSASCQLPGPFSSLDSSIETLKKKAQELIENINESRQKDHAL |
| K....P..VES..H.Q.EN.EET..SVAPS..C.LPG...SL.S.IE.LKKKAQELI.NI.E.RQKDH.L | |
| Retrocopy | KRARTPEVVESRKHQQKENREETASSVAPSTNC*LPG-LVSLVSCIEILKKKAQELIDNISEWRQKDHVL |
| Parental | MTNFRDSLKMKVSDLTEKLEERMYQVYSHHSKI-IQERLQEFTQKMAK-INHLEMELKQV-CQTVETVYK |
| MTNFRDSLKMKV..LTE.L...MYQ.YS.HSKI...........K..K.I.HLEMELKQ..CQT.ETVYK | |
| Retrocopy | MTNFRDSLKMKV*ALTEEL-GKMYQMYSLHSKISFRKDYKNLPRKWQK<ISHLEMELKQA<CQTIETVYK |
| Parental | DLCVQSEVPTCEEQNYKDGEC |
| DLCVQSE.PT..EQNYKD.EC | |
| Retrocopy | DLCVQSEAPTSKEQNYKDDEC |
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 | 1 .99 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 2 .48 RPM |
| SRP007412_heart | 0 .00 RPM | 0 .56 RPM |
| SRP007412_kidney | 0 .04 RPM | 3 .35 RPM |
| SRP007412_liver | 0 .00 RPM | 3 .71 RPM |
| SRP007412_testis | 0 .00 RPM | 158 .39 RPM |
RNA Polymerase II actvity near the 5' end of retro_mmus_2578 was not detected
No EST(s) were mapped for retro_mmus_2578 retrocopy.
No TSS is located nearby retro_mmus_2578 retrocopy 5' end.
retro_mmus_2578 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2578 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000003824 | 1 retrocopy |
retro_mmus_2578 ,
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