RetrogeneDB ID: | retro_rnor_2880 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | X:151809464..151810797(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSRNOG00000048610 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Ppp3cb | ||
| Ensembl ID: | ENSRNOG00000007757 | ||
| Aliases: | Ppp3cb, Calna2 | ||
| Description: | serine/threonine-protein phosphatase 2B catalytic subunit beta isoform [Source:RefSeq peptide;Acc:NP_058738] |
Retrocopy-Parental alignment summary:
>retro_rnor_2880
CCTCCTCTGCCCCCACCGCCCCCTCTCGGGGCCGACCTCGTGGTCAAAGCTGTTCCTTTTCCCCCAACTCACCGGATGAA
ATCTAAAGAAGTGTTTGATATGGATGGGATACCCAGGGTTGATGTTCTGAAGAACCATCTGGTAAAAGAAGGCCGGGTAG
ATGAAGAAATTGCACCAAGAATTATCAATGAGGGTGCTGCCATACTTTGGTGGGAGAAAACCATGATAGAAGTAGAAGCT
CCAATTACAGTGTGTGGTGACATCCATGGCCAATTTTTTGATCTGATGAAACTTTTTGAAGTAGGAGGATCACCTGCTAA
TTCACGATACCTTTTTCTTGGTGATTATGTGGACAGAGGTTATTTTAGTATAGAGTGTGTCTTGTATTTATGGGTCTTGA
AGATCCTATACCCAAGCACATTATTCCTTCTGAGAGGCAACCATGAATGCAGACACCTCACTGAGTATTTTACCTGTAAG
CAGGAATGTAAAATTAAATATTCAGAAAGGGTCTATGAAGCTTGTATGGAGGCTTTTGACAGCTTGTCCCTTGCTGCACT
TCTAAACCAACAATTTCTTTGTGTTCATGGTGGACTTTCACCAGAGATATACACACACTGGATGATATTAGGAGATTAGA
TAGATTTAAAGAGCCACTTGCATTTGGACCAATGTGTGACTTGCTATGGTCTGATCCTTCTGAAGACTTTGGAAATGAAA
AATCACAAGAACATTTTATTCATAATATGGTTCGATGATGTTCTTATTTTTATAACTATCGAGCAGTGTATGAATTTTTA
CAAAACAATAATTTGTTATTGATTATAAGAGCTCATGAAGCTCAAGATGCAGGCTATAGAATGTACAGAAAAAGTCAAAC
TACAAGGTTTCCTTCATTAATAACATTTTTTTCGGCACCTAATTACTTAGATGTCTACAATAATAAAGCTGCTGTACTAA
AGTATGAGAACAATGTGATGAACATCTGGCAGTTTAACTGTTCTCCACATCCTTACTGGTTGTGCAATTTTATGGATGTC
TTTAAATGGTCTTTACCATTTGTTAGAGAAAATGTCACAGAAATGTTGGTAAATGTTCTGAGTATTTGCTCTGATGATGA
ACTAATGACAGAAGGTGAAGACCAGTTTGATGTAGGTTCAGCTGCAGCCCGGAAAGAAATCATAAGAAACACCGAGCAAT
TGGCAAGATGGCAAGAGTCTTCTCTGTTCTCAGGGAGGAGAGTGAAAGCGTGCTGACACTCAAGGGCCTGACTCTCACAG
GGATGTTGCCTAGTGGAGTGTTGGCTGAAGGATGGTACACCTTGCACAGTGCA
ORF - retro_rnor_2880 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.22 % |
| Parental protein coverage: | 84.82 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | PPPPPPPPPGPDRVVTAVPFPPTHRLTSEEVFDMDGIPRVDVLKNHLVKEGRVDEEIALRIINEGAAILR |
| PP.PPPPP.G.D.VV.AVPFPPTHR..S.EVFDMDGIPRVDVLKNHLVKEGRVDEEIA.RIINEGAAIL. | |
| Retrocopy | PPLPPPPPLGADLVVKAVPFPPTHRMKSKEVFDMDGIPRVDVLKNHLVKEGRVDEEIAPRIINEGAAILW |
| Parental | REKTMIEVEAPITVCGDIHGQFFDLMKLFEVGGSPANTRYLFLGDYVDRGYFSIECVLYLWVLKILYPST |
| .EKTMIEVEAPITVCGDIHGQFFDLMKLFEVGGSPAN.RYLFLGDYVDRGYFSIECVLYLWVLKILYPST | |
| Retrocopy | WEKTMIEVEAPITVCGDIHGQFFDLMKLFEVGGSPANSRYLFLGDYVDRGYFSIECVLYLWVLKILYPST |
| Parental | LFLLRGNHECRHLTEYFTFKQECKIKYSERVYEACMEAFDSL-PLAALLNQQF-LCVHGGLSPEIHTLDD |
| LFLLRGNHECRHLTEYFT.KQECKIKYSERVYEACMEAFDSL.PL.......F.LC........IHTLDD | |
| Retrocopy | LFLLRGNHECRHLTEYFTCKQECKIKYSERVYEACMEAFDSL>PLLHF*TNNF>LCSWWTFTRDIHTLDD |
| Parental | IRRLDRFKEPPAFGPMCDLLWSDPSEDFGNEKSQEHFSHNTVRGCSYFYNYPAVCEFLQNNNLLSIIRAH |
| IRRLDRFKEP.AFGPMCDLLWSDPSEDFGNEKSQEHF.HN.VR.CSYFYNY.AV.EFLQNNNLL.IIRAH | |
| Retrocopy | IRRLDRFKEPLAFGPMCDLLWSDPSEDFGNEKSQEHFIHNMVR*CSYFYNYRAVYEFLQNNNLLLIIRAH |
| Parental | EAQDAGYRMYRKSQTTGFPSLITIFSAPNYLDVYNNKAAVLKYENNVMNIRQFNCSPHPYWLPNFMDVFT |
| EAQDAGYRMYRKSQTT.FPSLIT.FSAPNYLDVYNNKAAVLKYENNVMNI.QFNCSPHPYWL.NFMDVF. | |
| Retrocopy | EAQDAGYRMYRKSQTTRFPSLITFFSAPNYLDVYNNKAAVLKYENNVMNIWQFNCSPHPYWLCNFMDVFK |
| Parental | WSLPFVGEKVTEMLVNVLSICSDDELMTEGEDQFDVKVGSAAARKEII-RNKIRAIGKMARVFSVLREES |
| WSLPFV.E.VTEMLVNVLSICSDDELMTEGEDQFDV.....AA....I...K.RAIGKMARVFSVLREES | |
| Retrocopy | WSLPFVRENVTEMLVNVLSICSDDELMTEGEDQFDV---GSAAARKEI<HKKHRAIGKMARVFSVLREES |
| Parental | ESVLTLKGLTPTGMLPSGVLAGGRQTLQSA |
| ESVLTLKGLT.TGMLPSGVLA.G..TL.SA | |
| Retrocopy | ESVLTLKGLTLTGMLPSGVLAEGWYTLHSA |
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 |
|---|---|---|
| SRP017611_brain | 1 .01 RPM | 306 .64 RPM |
| SRP017611_kidney | 0 .07 RPM | 34 .61 RPM |
| SRP017611_liver | 0 .00 RPM | 16 .41 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2880 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2880 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_2880 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 | |
|---|---|---|---|
| Rattus norvegicus | ENSRNOG00000007757 | 1 retrocopy |
retro_rnor_2880 ,
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