RetrogeneDB ID: | retro_cpor_809 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_29:4820446..4821271(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RBM46 | ||
| Ensembl ID: | ENSCPOG00000010284 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_809
ATGAATGAAGACAATATGGATGGAACCAATGGATGCAGCAACATTTGAACTGGTATTCAGAATGAAGCGGCACTGCTTGC
TTTGATGGAGAAGCCTGGGTACAACTTGGTTCAAGAAAATGGACAAAGGAAATTCAGTGGTCCTCCTTCAGGCTGGGAAG
TTCCACCTTCATCTAGAAGATATGAAGTTTCTGTAGGAAAAATACCCTGCAATATTTATGAAGATGAGTTAGTTTCTGTA
TTTGAAAGAGCTGGGAAGATATATGAATTGCAACTTACGATGGAATTTAATGGTGAAAATAGGAGTTATGCTTTTGTGAT
GTATACTACAAAAGAAGAAGACCAGTTGGCTATCAGAATTCTTAATAATTATGAGATTCAACCAGGAAAGTTTATTGGTG
TTTGTGTGAGCTTGGGTGATTACAGATTATTTATTGGAGCTATTCCCAAGGAAAAGAAGAAAGAAGAAATTTTGGATGTA
ACGAAGAAAGTTACAGGAGTTGTAGATGCCATTGTTTATCCAAGTGCAATTGACAAGACCAAAAATCATGATTTTGCTTT
TGTTGAGTGTGAATCTCACAGAGCTGCTGCTATGGCTAGGAGAAAATTAATTCCAGGTGCCTTCCATCTGTGGGGCCATA
TTATTTAGATGGTTTGGGCTGATGCAGAGAAAGAACTTGAAGAGGAAACCATGCAAAGAGTTGAAGTTCTCTTTGTAAGA
AATTTAATAATCTCAACTACAGAGGAAACAAAGCACAATTTAGTAAATTCAAAGTAGGTGCTGTTGAAGGAGTCGAAAAA
TTTAAGAGATTATGCTTTTGTTCAC
ORF - retro_cpor_809 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 76.98 % |
| Parental protein coverage: | 51.96 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MNEENMDGTNGCSKVRTGIQNEAALLALMEKTGYNMVQENGQRKFGGPPPAGWEGPPPPRGCEVFVGKIP |
| MNE.NMDGTNGCS...TGIQNEAALLALMEK.GYN.VQENGQRKF.GPP..GWE.PP..R..EV.VGKIP | |
| Retrocopy | MNEDNMDGTNGCSNI*TGIQNEAALLALMEKPGYNLVQENGQRKFSGPP-SGWEVPPSSRRYEVSVGKIP |
| Parental | RDMYEDELVPVFERAGKIYEFRLMMEFSGENRGYAFVMYTTKEEAQLAIRILNNYEIRPGKFIGVCVSLD |
| ...YEDELV.VFERAGKIYE..L.MEF.GENR.YAFVMYTTKEE.QLAIRILNNYEI.PGKFIGVCVSL. | |
| Retrocopy | CNIYEDELVSVFERAGKIYELQLTMEFNGENRSYAFVMYTTKEEDQLAIRILNNYEIQPGKFIGVCVSLG |
| Parental | NCRLFIGAIPKEKKKEEILDEMKKVTEGVVDVIVYPSATDKTKNRGFAFVKYESHRAAAMARRKLIPGTF |
| ..RLFIGAIPKEKKKEEILD..KKVT.GVVD.IVYPSA.DKTKN..FAFV..ESHRAAAMARRKLIPG.F | |
| Retrocopy | DYRLFIGAIPKEKKKEEILDVTKKVT-GVVDAIVYPSAIDKTKNHDFAFVECESHRAAAMARRKLIPGAF |
| Parental | QLWGHTIQVDWADPEKEVDEETMQRVKVLFVRNLMISTTEETIKAEFNKFKPGAVERVKKLRDYAFVH |
| .LWGH.I...WAD.EKE..EETMQRV.VLFVRNL.ISTTEET.K......K.......K.LRDYAFVH | |
| Retrocopy | HLWGHII*MVWADAEKELEEETMQRVEVLFVRNLIISTTEET-KHNLVNSK*VLLKESKNLRDYAFVH |
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 .06 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .13 RPM |
| SRP040447_lung | 0 .00 RPM | 0 .15 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 0 .03 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_809 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_809 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 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000010284 | 1 retrocopy |
retro_cpor_809 ,
|
| Tursiops truncatus | ENSTTRG00000001239 | 1 retrocopy |