RetrogeneDB ID: | retro_cpor_1017 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_4:35562044..35562816(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PPP2R3C | ||
| Ensembl ID: | ENSCPOG00000004781 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_1017
GAAAAAAATAGTGAACAAGAATTAAAAGTTGAAGAAATGAATTTTTTACCAAATACTACTCAGAATGGAAAGGAGGTAAA
AAGAATGAATTTTATAAGACAACTGCCCAGTTTTATTATGGACTGCCAGCAGAAGATGAAGCTTTATTACAGAAATTGAG
ATTAATCCAGAGCAATGTTTCTACAAAAGAAAAATAGGGAACTCTTAGATAATGAAAGTTACAGAACTTGTGGTTTTTGC
AACAAAACCACACTCCACCTGTGATTGGAGAAGAAGCGATGATCAATTATGAAAATTTTGTGAAGGTTGGTGAAAAGGCT
GGACTAAATGGCAAGCAATTTTTCACTTCAAAAGTCCTTGATAAACTCCTTCATACAGATTCATATGGAAGAATTTCCAT
CATGCAGTTCTTTAAGTATGTCATGTGAAAAGATTTGCTTCATCAGACAAGAATAGGACTCAGTTTATATGATGTTGTTG
GACAAGGATACCTTTGGGAATCTGATTTAGAAAACTACATATTGGAACTCATCCCTACTTTGCCACAGTTAAATGTGCTT
GAAAAATCATTTTATTTCTTCCATGTTTGTACAGCAGTTAGAAGTTCTTTTTGGACTCTCTAAGAAGAGGGAAGATGAAA
ATTCAAGATATTTTAGCATGCATGTTCCTGGATGATTTACTGGAGCTAAGGGCTGAGGAATTGCCCAAGGAGACAAATTG
GTTTTCTGTTCCTTCTGTCCTAAGAGTTTATGGCCAGTATTTGAATCTTAAT
ORF - retro_cpor_1017 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 76.47 % |
| Parental protein coverage: | 58.94 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | KKKSEQELKDEEM-DLFTKYYSEWKGGRKNTNEFYKMIPRFYYRLPAEDEVLLQKLREESRAV-FLQRK- |
| .K.SEQELK.EEM...FTKYYSEWKGG.KN..EFYK....FYY.LPAEDE.LLQKLR.....V.F..RK. | |
| Retrocopy | EKNSEQELKVEEM<EFFTKYYSEWKGGKKN--EFYKTTAQFYYGLPAEDEALLQKLRLIQSNV<FYKRK< |
| Parental | SRELLDNE-ELQNLWFLLDKHQTPPMIGEEAMINYENFLKVGEKAGPKCKQFFTAKVFAKLLHTDSYGRI |
| .RELLDNE..LQNLWFL...H.TPP.IGEEAMINYENF.KVGEKAG...KQFFT.KV..KLLHTDSYGRI | |
| Retrocopy | NRELLDNE<KLQNLWFLQQNH-TPPVIGEEAMINYENFVKVGEKAGLNGKQFFTSKVLDKLLHTDSYGRI |
| Parental | SIMQFFNYVMRKVWLHQTRIGLSLYDVAGQGYLRESDLENYILELIPTLPQLDGLEKSFYSFYVCTAVR- |
| SIMQFF.YVM.K..LHQTRIGLSLYDV.GQGYL.ESDLENYILELIPTLPQL..LEKSFY.F.VCTAVR. | |
| Retrocopy | SIMQFFKYVM*KDLLHQTRIGLSLYDVVGQGYLWESDLENYILELIPTLPQLNVLEKSFYFFHVCTAVR< |
| Parental | KFFFFLDPLRTGKIKIQDILACSFLDDLLELRDEELSKESQETNWFSAPSALRVYGQYLNLD |
| KF..FLD.LR.GK.KIQDILAC.FLDDLLELR.EEL.KE...TNWFS.PS.LRVYGQYLNL. | |
| Retrocopy | KF--FLDSLRRGKMKIQDILACMFLDDLLELRAEELPKE---TNWFSVPSVLRVYGQYLNLN |
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 | 16 .97 RPM |
| SRP017611_kidney | 0 .00 RPM | 19 .16 RPM |
| SRP017611_liver | 0 .00 RPM | 11 .49 RPM |
| SRP040447_lung | 0 .00 RPM | 16 .44 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 13 .70 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1017 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1017 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 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000004781 | 1 retrocopy |
retro_cpor_1017 ,
|
| Oryctolagus cuniculus | ENSOCUG00000005768 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000008489 | 1 retrocopy |