RetrogeneDB ID: | retro_cpor_1254 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_6:38846530..38847358(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCPOG00000027382 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TRUB1 | ||
| Ensembl ID: | ENSCPOG00000005617 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_1254
ATGGCAGTTGCTGAAGCTGTGGTGCTTTCCTCGCCTTTGAAAACAGACATAGCCCCGATCTTAGACGCTGCAGAAACAGG
CTCAACATTGGCCAGGAAGTCTGTAGCAATAGCTGCGGCCGCAAATATTGCGGCCGCGGCCAGAACTGGAGCTGAAACAA
AGGTCACCAAGGCCCCTTTGGCTACTAAACTGCTGTCTCTCAGCGGCGTGTTCGCAGTGCACAAGCCCAAAGGGCCCACT
TCAGCCGAGCTGCTGAATCGGTTGAAAGAGAAGCTGCTGGCAGAAGCTGGTATGCCTTCTTCAGAATGGACCAAGAGGGA
AAAACAGACCTTGAAAATTGGGCATGGAGGAACTCTAGACAGCGCAGCCCGAGGTGTTCTGGTCATTGGAATTGGAAGGG
GAACAAAAATGTTGACCAGTATGTTGTCAGGTTCTAAGAGGTATATCGCCATTGGAGAACTGGGAAAGGCCACCGACACA
CTAGATTCTACGGGGAAAGTGACCGAAGAGAAACCTTATGATAAAATAACACAAGAGGATATTGAAAGTATTCTACAGAA
GTTTACTGGAAATATAATGCAGACACCCCCTCTCTATTCTGCATTAAAGAAAGATGGGCAGAGACTTTCAACTTTAATGA
AGAGACGAAAAGTAGTAGAAGCAAAACCTGCCAGGCCGGTTACTGTATACAGTATCTCCCTTGAAAAATTCCAGCCACCA
TTTTTTACATTAGATGTTGAATGTGGAGGTGGTTTTTACATCAGAAGCTTGGTCAGTGACATTGGCAAAGCGCTGTCTTC
CTGTGCCAGTGTACTGGAGCTGACCAGG
ORF - retro_cpor_1254 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.1 % |
| Parental protein coverage: | 79.08 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAVAEAVVLSSPLKTDVAPILDAAETGSTMARKSVATAAAASIAATARTGAETKVTKAPLATKLLSLSGV |
| MAVAEAVVLSSPLKTD.APILDAAETGST.ARKSVA.AAAA.IAA.ARTGAETKVTKAPLATKLLSLSGV | |
| Retrocopy | MAVAEAVVLSSPLKTDIAPILDAAETGSTLARKSVAIAAAANIAAAARTGAETKVTKAPLATKLLSLSGV |
| Parental | FAVHKPKGPTSAELLNRLKEKLLAEAGMPSSEWTKRKKQTLKIGHGGTLDSAARGVLVIGIGRGTKMLTS |
| FAVHKPKGPTSAELLNRLKEKLLAEAGMPSSEWTKR.KQTLKIGHGGTLDSAARGVLVIGIGRGTKMLTS | |
| Retrocopy | FAVHKPKGPTSAELLNRLKEKLLAEAGMPSSEWTKREKQTLKIGHGGTLDSAARGVLVIGIGRGTKMLTS |
| Parental | MLSGSKRYIAIGELGKATDTLDSTGKVTEEKPYDKITQEDIENILQKFTGNIMQTPPLYSALKKDGQRLS |
| MLSGSKRYIAIGELGKATDTLDSTGKVTEEKPYDKITQEDIE.ILQKFTGNIMQTPPLYSALKKDGQRLS | |
| Retrocopy | MLSGSKRYIAIGELGKATDTLDSTGKVTEEKPYDKITQEDIESILQKFTGNIMQTPPLYSALKKDGQRLS |
| Parental | TLMKRGKVVEAKPARPVTVYSISLEKFQPPFFTLDVECGGGFYIRSLVSDIGKALSSCASVLELTR |
| TLMKR.KVVEAKPARPVTVYSISLEKFQPPFFTLDVECGGGFYIRSLVSDIGKALSSCASVLELTR | |
| Retrocopy | TLMKRRKVVEAKPARPVTVYSISLEKFQPPFFTLDVECGGGFYIRSLVSDIGKALSSCASVLELTR |
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 | 4 .14 RPM |
| SRP017611_kidney | 0 .10 RPM | 4 .08 RPM |
| SRP017611_liver | 0 .04 RPM | 2 .87 RPM |
| SRP040447_lung | 0 .03 RPM | 3 .00 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 2 .26 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1254 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1254 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 | ENSCPOG00000005617 | 1 retrocopy |
retro_cpor_1254 ,
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