RetrogeneDB ID: | retro_cpor_1533 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_95:1287918..1288775(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCPOG00000023395 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_1533
AAGGTTATCTTTGGCTCATTTTAATCTACACTGACTGTAAATGGATAATTTTCTTTGCTCTATCAGGTGGCCCCAAAGGA
CACATATTTGGTCATTGGAAAGGTGTCCTTGATGCTTCATTTCTACTGGACGTGGGTGGGGCTGCTCATTACAGAAGGCC
ATAAGGGTCTTCAGTTTCTCTCAGATGTGAGAACTGAGATTAATAAGAACCGAATTTGGATAGCCTTTGTAAAATGATCT
CAACTATGACTGTGTCATATCTCTCAGGCATACAGAATCATAGTATCCTGCCTGCAGATACATCTTCAGTCAATGTAGTG
GTTATTTACTATGACAGTGATAATCCAAGTGATGTGAGATACATATAGTGCAACATTTAGAGTCATGGAAAATCTGGATA
ACAAACTCACAATGGCAAGCTGACATGGATGGATGAAATTTCATACATGATCCATTCCATGTTCTTACTTTTTCACACCA
GCATGAAGAGATTTTAAATTTTAAAACTTTTGTACAAAAGCTACCACATTTAAATACTCTGAAGACAATTTTTTGTTATG
TATCAATACAAGTATTTCTGTTGCTCCTTCTCTGAATCTGACTGTGCACTGGAGAACTGTACACCTAATGCCTCTCTGGC
TTGGCTGCCTCCAAATAGTTTTGACACAACCATGAGTGATAGAAGCTACAATATACACAATGATGTGTATGCTGTGGCCT
ATACCTTCCAGGTGATGCTTTCTGAAGAAGTACAAAGCCCTTAAATGAGAAATAGACAAGATGATGTTTCCCCCTCGCAG
GTAATACGTGTTCTTTTGGATGGCATGCAGTGTCACCAATGTGCCTCAGTCCAATTG
ORF - retro_cpor_1533 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 62.12 % |
| Parental protein coverage: | 56.23 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | QVYYGLFDPTLSESGQYPLLHQVAQKDTFLALAMVSLMLHFHWTWVGLLTTEGHKGLQFLSDVRTEMDRN |
| .V..G.F..TL...G...LL.QVA.KDT.L....VSLMLHF.WTWVGLL.TEGHKGLQFLSDVRTE...N | |
| Retrocopy | KVIFGSF*STLTVNG*FSLLYQVAPKDTYLVIGKVSLMLHFYWTWVGLLITEGHKGLQFLSDVRTEINKN |
| Parental | RVCVAFVK-IVASSTVLYFSAMQKHDILTADTSSVNVVVIYYDTNSIHDVSY-HIVQNLMTWKIWVTNSQ |
| R...AFVK......TV.Y.S..Q.H.IL.ADTSSVNVVVIYYD.....DV.Y.HIVQ.L..WKIW.TNSQ | |
| Retrocopy | RIWIAFVK<MISTMTVSYLSGIQNHSILPADTSSVNVVVIYYDSDNPSDVRY<HIVQHLESWKIWITNSQ |
| Parental | WQADLDGRNFILDSFHGVLVFSHHYEEISGFKNYVQE-ATPFKYPDDTYLF-MYWYKNFHCSFSESDCTL |
| WQAD.DG.NFI.D.FH.VL.FSH..EEI..FK..VQ..AT.FKY..D..L..MY.YK.F.CSFSESDC.L | |
| Retrocopy | WQADMDG*NFIHDPFH-VLTFSHQHEEILNFKTFVQK<ATTFKYSEDNFLL<MYQYKYFCCSFSESDCAL |
| Parental | ENCTPNASLAWLPPNHFDTAMNDRSYNIYNGVYAVAHALHAMLFAEEQGPSMRNRQMKMFSPWQQLNPFL |
| ENCTPNASLAWLPPN.FDT.M.DRSYNI.N.VYAVA.....ML..E.Q.P.MRNRQ....SP.Q.....L | |
| Retrocopy | ENCTPNASLAWLPPNSFDTTMSDRSYNIHNDVYAVAYTFQVMLSEEVQSP*MRNRQDDV-SPSQVIRVLL |
| Parental | KNIQFSNSAGDQV |
| ...Q....A..Q. | |
| Retrocopy | DGMQCHQCASVQL |
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 .00 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .00 RPM |
| SRP040447_lung | 0 .00 RPM | 0 .00 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 0 .00 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1533 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1533 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 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000023395 | 2 retrocopies |
retro_cpor_1533 , retro_cpor_1534,
|