RetrogeneDB ID: | retro_cpor_1397 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_8:27154482..27155015(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CAPSL | ||
| Ensembl ID: | ENSCPOG00000007724 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_1397
AAGATGGCAATTCAGGTCAAGAAAAAGCTCACCACCACCACCACTGAGCCCATTAAAAGACTCTAACCCCAATGCCTGCT
CAGGGGCTCTGCAGGCTCCAAAGGATTTGGCAGAGTGTTTCAAATTATGGATGATGACAACAACAGAACCCTTGCTTTCA
AAGATGTCTGAAAGGGTTAAATGATTATACAGTGGTTATGGAAAAAGGAAGAGGCAGAAGAGCTTTTCTGCAGGTCTGAT
AAAGATGGAAATGGAATGAGAGACTTCACTGAATTTCTTCTCACATTAAGACCTCCAATGTATAGATCCAGAAGAGAGCT
AATGATGTGAGCTTTTAGAAAGTTAGACAAGACTGGAGATGGTGTAATAACAATTAAAGACCTGAGTGGAGTGTATAATG
CAAAAACACCATCCAAAGTAACCAAAGTGGAGAATGGGCAGAAGAGCACATCTTCAGGAAATTTCTAGATAATTTTGACT
CACTCTAGGACAAAGACAGATTGGTGAGCCCCGAGGAGTTCACAAACTACTAC
ORF - retro_cpor_1397 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 74.03 % |
| Parental protein coverage: | 84.62 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | EMAIQAKKKLTTTT-DPIERLRLQCLARGSAGIKGLSRVFRIMDDNNNRTLDFKEF-LKGLNDYAVVMEK |
| .MAIQ.KKKLTTTT..PI.RL..QCL.RGSAG.KG..RVF.IMDD.NNRTL.FK...LKGLNDY.VVMEK | |
| Retrocopy | KMAIQVKKKLTTTTTEPIKRL*PQCLLRGSAGSKGFGRVFQIMDDDNNRTLAFKDV<LKGLNDYTVVMEK |
| Parental | -EEAEELFRRFDKDGSGTIDFNEFLLTLRPPMSRARKEVILRAFRKLDKTGDGVITIEDLRGVYNA-KHH |
| .EEAEELF.R.DKDG.G..DF.EFLLTLRPPM.R.R.E....AFRKLDKTGDGVITI.DL.GVYNA.KHH | |
| Retrocopy | >EEAEELFCRSDKDGNGMRDFTEFLLTLRPPMYRSRRELMM*AFRKLDKTGDGVITIKDLSGVYNA>KHH |
| Parental | PK-YQNGEWTEEQVFRKFLDNFDSPYEKDGLVTPEEFMNYY |
| PK..Q.GEW.EE..FRKFLDNFDS...KD.LV.PEEF.NYY | |
| Retrocopy | PK>NQSGEWAEEHIFRKFLDNFDSL*DKDRLVSPEEFTNYY |
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 | 0 .81 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP017611_liver | 0 .04 RPM | 0 .00 RPM |
| SRP040447_lung | 0 .00 RPM | 3 .96 RPM |
| SRP040447_skeletal_muscle | 0 .05 RPM | 0 .01 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1397 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1397 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 | ENSCPOG00000007724 | 1 retrocopy |
retro_cpor_1397 ,
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