RetrogeneDB ID: | retro_cpor_152 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_0:33020671..33021141(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | IFT20 | ||
| Ensembl ID: | ENSCPOG00000003153 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_152
CTGGCGCACTTCCCCCTGACCACTGCTGCCACCCCTTCAAGGCAGAACTTCTCCAGGGACCTGCAAGCGGAACAGTCACG
GCCAGAGACATCCTGGGTGAAGTGCGCCTGCACTTTGATGAGCTGAATAAGCTTCAAGTGCGGGACCCAGGCTACCTGTA
GACCACAGAGCTCTAGACAGAAGGCAAAGACTCTGTGGACAAAACCGGCCAGGTTCGGAAACCAGCTGGTAGCCCAACTG
GACTTGTGGACCAACTTGCAAAAAAAGTAGAGAACGAGAAGACAAAGGTCACTGGTGCGCAGAACTTGCTCAAATCTATA
GCAAAGCAGCAAGAATCCCAACAGCAGCAACTCCAGGCACTAACAGCAGAAAAGAAAATGTAGCTAGAAAGGTATCGAGT
TGAATATGAAGCTTTGGGAAAAGCAGAAACAGAACAAAAGTAATTTACTGGCCAATTTGTTTTGCAGAAA
ORF - retro_cpor_152 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 62.89 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MTHLLLTATVTPSEQNFPRE-PRRETAMAKDILGEAGLHFDELNKLRVLDPEVTQQTIELKEECKDFVDK |
| ..H..LT...TPS.QNF.R..P...T..A.DILGE..LHFDELNKL.V.DP.....T.EL..E.KD.VDK | |
| Retrocopy | LAHFPLTTAATPSRQNFSRD<PASGTVTARDILGEVRLHFDELNKLQVRDPGYL*TT-EL*TEGKDSVDK |
| Parental | IGQFQKIVGGLIELVDQLAKEAENEKMKAIGARNLLKSIAKQREAQQQQLQALIAEKKMQLERYRVEYEA |
| .GQ..K..G....LVDQLAK..ENEK.K..GA.NLLKSIAKQ.E.QQQQLQAL.AEKKM.LERYRVEYEA | |
| Retrocopy | TGQVRKPAGSPTGLVDQLAKKVENEKTKVTGAQNLLKSIAKQQESQQQQLQALTAEKKM*LERYRVEYEA |
| Parental | LCKVEAEQNEFIDQFIFQK |
| L.K.E.EQ..F..QF..QK | |
| Retrocopy | LGKAETEQK*FTGQFVLQK |
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 | 14 .09 RPM |
| SRP017611_kidney | 0 .00 RPM | 20 .73 RPM |
| SRP017611_liver | 0 .00 RPM | 11 .71 RPM |
| SRP040447_lung | 0 .00 RPM | 12 .71 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 3 .92 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_152 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_152 was not experimentally validated.