RetrogeneDB ID: | retro_cpor_847 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_3:9033587..9034238(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ZC4H2 | ||
| Ensembl ID: | ENSCPOG00000019721 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_847
ATGTGCAAACTGGAAAGCATTAAAGAGATCAGGAACAAAACTCTGCAGATGGAGATGATCAAGGCTCGACTGAAGGCTGA
ATTTGAGGCACTTGAGTCAGAGGAACGGCACCTGAAAGAATACAAGCAGGAGATGGACCTCCTGTTACAGGAGAAGATGG
CCCATGTGGAGGAACTCCGACTTATCCACGCTGACATCAATGTGATGGAAAACACCATTAAACAGTCTGAAAATGACCTT
AACAAGCTGCTAGAGTCTACAAGGCGACTGCATGAGGAGTATAAGCCTCTGAAGGAACATGTGGATGCTCTACATATGAC
TTTGGGCTTGCAGAGGCTTCCTGACTTGTGTGAAGAGGAGGAGAAGCTCTCTTTGGATTACTTTGAGAAACAGAAAGCAG
AATGGCAGACAGAGCCTCAGGAGCCCCCTATCCCTGAGTCCTTGGCTGCTGCAGCTGCTGTTGCCCAACAACTCCAAGTG
GCTAGATAGCAGGACACTCGACAGACAGCCACCTTCAGGCAGCAGCCTCCACCTATGAAGGCCTGTTTGTCATGCCACCA
GCAAATTCACCGGAATGCACCCATATGCCCTCTGTGCAAAGCCAAAAGTCGGTCCCGGAACCCCAAGAAGCCCAAACGGA
AGCAGGATGAA
ORF - retro_cpor_847 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 95.39 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ICFLESISYLKNKTLQMEKIKARLKAEFEALESEERHLKEYKQEMDLLLQEKMAHVEELRLIHADINVME |
| .C.LESI....NKTLQME.IKARLKAEFEALESEERHLKEYKQEMDLLLQEKMAHVEELRLIHADINVME | |
| Retrocopy | MCKLESIKEIRNKTLQMEMIKARLKAEFEALESEERHLKEYKQEMDLLLQEKMAHVEELRLIHADINVME |
| Parental | NTIKQSENDLNKLLESTRRLHEEYKPLKEHVDALRMTLGLQRLPDLCEEEEKLSLDYFEKQKAEWQTEPQ |
| NTIKQSENDLNKLLESTRRLHEEYKPLKEHVDAL.MTLGLQRLPDLCEEEEKLSLDYFEKQKAEWQTEPQ | |
| Retrocopy | NTIKQSENDLNKLLESTRRLHEEYKPLKEHVDALHMTLGLQRLPDLCEEEEKLSLDYFEKQKAEWQTEPQ |
| Parental | EPPIPESLAAAAAAAQQLQVARKQDTRQTATFRQQPPPMKACLSCHQQIHRNAPICPLCKAKSRSRNPKK |
| EPPIPESLAAAAA.AQQLQVAR.QDTRQTATFRQQPPPMKACLSCHQQIHRNAPICPLCKAKSRSRNPKK | |
| Retrocopy | EPPIPESLAAAAAVAQQLQVAR*QDTRQTATFRQQPPPMKACLSCHQQIHRNAPICPLCKAKSRSRNPKK |
| Parental | PKRKQDE |
| PKRKQDE | |
| Retrocopy | PKRKQDE |
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 .06 RPM | 5 .64 RPM |
| SRP017611_kidney | 0 .00 RPM | 4 .19 RPM |
| SRP017611_liver | 0 .26 RPM | 2 .96 RPM |
| SRP040447_lung | 0 .00 RPM | 4 .16 RPM |
| SRP040447_skeletal_muscle | 0 .01 RPM | 1 .19 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_847 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_847 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 | ENSCPOG00000019721 | 1 retrocopy |
retro_cpor_847 ,
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