RetrogeneDB ID: | retro_mmus_693 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 11:16439161..16439915(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000083925 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Pygo2 | ||
| Ensembl ID: | ENSMUSG00000047824 | ||
| Aliases: | Pygo2, 1190004M21Rik, mpygo2 | ||
| Description: | pygopus 2 [Source:MGI Symbol;Acc:MGI:1916161] |
Retrocopy-Parental alignment summary:
>retro_mmus_693
GCCCCACTGCCCCGACCGCCCAGCACTGGGAGGATGCAGGGCAAAGCTATTCTGCAAATGAAGAGGCCTGAAAAGAAGCG
AAGAAATTCCAATACTCAGGGTCCTGCATGCACACATCTGATGGAGTTAGCCCCACTGTTGACCCAACCCCCATGGTGGA
TCATCTGGTCATTTCTAACCCCTTTGATGATTTCGGAGTCCCTAAGGTGGGGGACGCAGGCCCTCCATTCCTTGCCAGTC
CTGTGCCCCTTGGAGGCTTTGGTGAATAGGGGGGCACAGCAGGCCCGGTATCCCCAGGCCATAGCACTAGAGGACTATCC
CAGCCACTTTGTCGGCAGTCCCTTCCTTTTCCTCCCAACTCTATGGGTCCAGCTTTTAATATGCCTCCTCAGGGCCCTGG
CTATCCACCCCTGGGAACACATAAACTTTTCCAGTCAACCCTTCAACCAGTCTCTGAGCCAAAACTTTAGCCCACCTGGT
AGACAGGTAATTCGAGGCCCAGTTGGGGGATTTGATCCCTTGGTCTGACCCACCATGGTCGCCTCCTAGAGGGGAGCTGG
GTCCTCTTCCTCTCCACCAATGCCTTACCCAACCAGGAGCACCTTTTGTTCATTCTCTTCATAGACCTGGTCAGGGACTC
CCCAGCCTGCCTCCCAACACGAGTCCCTTCCCTGGTCCAGACCCTGGTTTTCCTGACCCTGGTGGTGAGGATGGTGAAAG
GCCCTTGAATCCACCTGCCCCCACTGCTTTTCCC
ORF - retro_mmus_693 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 70.16 % |
| Parental protein coverage: | 62.47 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | APPPAPPSTGRKQGKAGLQMKSPE-KKRRKSNTQGPAYSHLTEFAPP--PTPMVDHLVASNPFEDDFGAP |
| AP.P.PPSTGR.QGKA.LQMK.PE.K...K....G..........P...PTPMVDHLV.SNPF.DDFG.P | |
| Retrocopy | APLPRPPSTGRMQGKAILQMKRPE<KEAKKFQYSGSCMHTSDGVSPTVDPTPMVDHLVISNPF-DDFGVP |
| Parental | KVGGAGPPFLGSPVPFGGFRVQGGMAGQVPPGYGTGGGGGPQPLRRQPPPFPPNPMGPAFNMPPQGPGYP |
| KVG.AGPPFL.SPVP.GGF...GG.AG.V.PG..T.G....QPL.RQ..PFPPN.MGPAFNMPPQGPGYP | |
| Retrocopy | KVGDAGPPFLASPVPLGGFGE*GGTAGPVSPGHSTRGLS--QPLCRQSLPFPPNSMGPAFNMPPQGPGYP |
| Parental | PPG-NMNFPSQPFNQSLGQNFSPPGGQVMPGPVGGFG-PMISPTMGQPPRGELGPPPLPQRFTQPGAPFG |
| P.G...NF.SQPFNQSL.QNFSPPG.QV..GPVGGF..P...P....PPRGELGP.PL.Q..TQPGAPF. | |
| Retrocopy | PLG>HINFSSQPFNQSLSQNFSPPGRQVIRGPVGGFD>PWSDPPWS-PPRGELGPLPLHQCLTQPGAPFV |
| Parental | PSLQRPGQGLPSLPPNTSPFPGPDPGFPGPGGEDGGKPLNPPAPTAFP |
| .SL.RPGQGLPSLPPNTSPFPGPDPGFP.PGGEDG..PLNPPAPTAFP | |
| Retrocopy | HSLHRPGQGLPSLPPNTSPFPGPDPGFPDPGGEDGERPLNPPAPTAFP |
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 | 36 .80 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 28 .35 RPM |
| SRP007412_heart | 0 .00 RPM | 16 .69 RPM |
| SRP007412_kidney | 0 .00 RPM | 22 .68 RPM |
| SRP007412_liver | 0 .00 RPM | 15 .65 RPM |
| SRP007412_testis | 0 .14 RPM | 21 .63 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_693 was not detected
No EST(s) were mapped for retro_mmus_693 retrocopy.
No TSS is located nearby retro_mmus_693 retrocopy 5' end.
retro_mmus_693 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_693 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 | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000047824 | 1 retrocopy |
retro_mmus_693 ,
|
| Ictidomys tridecemlineatus | ENSSTOG00000000053 | 1 retrocopy |