RetrogeneDB ID: | retro_cpor_329 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_128:3278413..3279531(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PPP3CC | ||
| Ensembl ID: | ENSCPOG00000001113 | ||
| Aliases: | None | ||
| Description: | Serine/threonine-protein phosphatase [Source:UniProtKB/TrEMBL;Acc:H0UVH2] |
Retrocopy-Parental alignment summary:
>retro_cpor_329
CGTGGACAGTATAGAGTGTGTGTTGTTTTCATGGAGTTGAAAGAATATCCTAAAACATTGTTTCAGCTTTGAGGAAATCA
TGAACGCAGGCATCTTACTGAATACTTCACCTTCAAATATGAATGTCTAGTCAAATATTCGGAATGGGTGTATGAGGCAT
GTATGGACATATTCGCTATCTTTTCCTTACTGCCCTCTTAACCCAGCAGCTTCTCTGTGTCCATGGAGAAATGTCACCAG
AAATCACTTGTTTAGATGATATTAGGAAATTAGACAGGTTTACTGAACCTCCGGCCTTTGGGGCAGCGGGTGACCTGCTT
TGGTCTGATCCCTTGGAGCATTCCGGCAGTGCAAAGACCATGGGAAACTATGCCCACGGTACTGTCCGAGGGGGCTCTTA
CTTTTTCAGTTGCCCTGCAGTTTGTGAGTCTTTACAGAACAATTTATCATCAAAAATCAGAGCCCATGAAGCTCAAGACG
CTGGGCATCAAATGTACAGGAAGAGCGAGACCACCGGCTTTCCATCACTTATTACAATTTTCTCTGCCCCTAATTACCTA
GATGTCTATAACAATAAAGCTGCAGTGTTGAAAACTGACACCGATGTCATAAATATCAGGCAGTTTAACTGTTCTCCACA
CTCCTGTTGGCTTCCAAACTTTATGCATGTTTTCACCTGGTCTTTGCCTTTTGTTGGGGAAAAAGTCACAGAGATGCTGG
TTAACATTCTGAATATATTCTCTGATAATAAACTGATGTCTGACAATGAAACAGAAGGAGGCACTGTGGTTCGAAAAGAG
ATGATCAAGAATAAAATCAGAGCCGGTGGGAAGACGGCCTGGGTCTTTTCGGTTCTTCACGAAGAGAGTGAGAGTGTGCT
GACCGTCAAGGGCCTCACACCCACAGGCACACTCCCCCAGAGCATCCCGTTGGGAGGAAAGCAGACGGTTGAGACTGCCA
CAGGAGAAGCAGTAGAGGCCCAGGAAGCCACCCAACAGTTTTCACTGCAGCACAAAATTCGGAGTTTTGGAAAAGCCTGA
GGACTGGATCGAATTAATGAGTGAATGGCACCTCAAAAAGACAGTGGACATGATGGGCCAGTGAAACTGGTGTGACCC
ORF - retro_cpor_329 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 77.57 % |
| Parental protein coverage: | 75.15 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | RGYFSIECVLFLWSLKIIHPKTLFLLRGNHECRHLTEYFTFKQECNLIKYSERVYEACMDTFDC-LPLAA |
| RG.....CV.F...LK...PKTLF.L.GNHE.RHLTEYFTFK.EC.L.KYSE.VYEACMD.F...L.L.A | |
| Retrocopy | RGQYRV-CVVFM-ELKE-YPKTLFQL*GNHERRHLTEYFTFKYEC-LVKYSEWVYEACMDIFAI<LFLTA |
| Parental | LLNQQFLCVHGGMSPEITCLDDIRKLDRFTEPPAFGPVCDLLWSDPSEDYGSEKTLENYTHNTVRGCSYF |
| LL.QQ.LCVHG.MSPEITCLDDIRKLDRFTEPPAFG...DLLWSDP.E..GS.KT..NY.H.TVRG.SYF | |
| Retrocopy | LLTQQLLCVHGEMSPEITCLDDIRKLDRFTEPPAFGAAGDLLWSDPLEHSGSAKTMGNYAHGTVRGGSYF |
| Parental | FSYPAVCEFLQNNNLLSIIRAHEAQDAGYRMYRKSQTTGFPSLITIFSAPNYLDVYNNKAAVLKYENNVM |
| FS.PAVCE.LQNN.L.S.IRAHEAQDAG..MYRKS.TTGFPSLITIFSAPNYLDVYNNKAAVLK....V. | |
| Retrocopy | FSCPAVCESLQNN-LSSKIRAHEAQDAGHQMYRKSETTGFPSLITIFSAPNYLDVYNNKAAVLKTDTDVI |
| Parental | NIRQFNCSPHPYWLPNFMDVFTWSLPFVGEKVTEMLVNILNICSDDELMSDDETEGGTTVRKEIIKNKIR |
| NIRQFNCSPH..WLPNFM.VFTWSLPFVGEKVTEMLVNILNI.SD..LMSD.ETEGGT.VRKE.IKNKIR | |
| Retrocopy | NIRQFNCSPHSCWLPNFMHVFTWSLPFVGEKVTEMLVNILNIFSDNKLMSDNETEGGTVVRKEMIKNKIR |
| Parental | AIGKMARVFSVLREESESVLTLKGLTPTGTLPLGVLSGGKQTIETATVEAVEAQEAIRGFSLQHKIRSFE |
| A.GK.A.VFSVL.EESESVLT.KGLTPTGTLP.....GGKQT.ETAT.EAVEAQEA...FSLQHKIRSF. | |
| Retrocopy | AGGKTAWVFSVLHEESESVLTVKGLTPTGTLPQSIPLGGKQTVETATGEAVEAQEATQQFSLQHKIRSFG |
| Parental | EARGLDRINERMPPRKDSGHDGPAKLVTP |
| .A.GLDRINE.M.P.KDSGHDGP.KLV.P | |
| Retrocopy | KA*GLDRINE*MAPQKDSGHDGPVKLV*P |
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 | 0 .00 RPM | 14 .90 RPM |
| SRP017611_kidney | 0 .10 RPM | 11 .31 RPM |
| SRP017611_liver | 0 .04 RPM | 4 .18 RPM |
| SRP040447_lung | 0 .00 RPM | 14 .53 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 34 .95 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_329 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_329 was not experimentally validated.
Retrocopy orthology:
Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000001113 | 1 retrocopy |
retro_cpor_329 ,
|