RetrogeneDB ID: | retro_sscr_15 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 1:227420051..227420996(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSSSCG00000005174 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSSSCG00000029800 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_sscr_15
GTGATGCCAAATACAGCCATGAAGAAAAAGGTGCTGTTGATGGGGAAGAGCGGGTCGGGGAAGACCAGCATGAGGTCGAT
TATCTTTGCAAATTATATCGCTCGCGACACCCGGCGCCTCGGTGCCACCATTGATGTGGAGCACTCCCACGTACGATTTC
TGGGCAACCTGGTGCTGAACCTGTGGGACTGTGGCGGTCAGGACACCTTCATGGAAAATTATTTCACCAGCCAGCGAGAC
AACATTTTCCGTAATGTCGAGGTCCTGATTTACGTGTTCGACGTGGAGAGCCGCGAACTGGAAAAGGACATGCATTATTA
CCAGTCCTGTCTGGAGGCCATCCTCCAGAACTCTCCTGATGCTAAAATCTTCTGCCTGGTGCACAAAATGGATCTGGTTC
AGGAAGATCAGCGTGACCTGATTTTTAAAGAGCGAGAGGAAGACCTGAGGCGTTTGTCTCGCCCTCTCGAGTGCGCCTGT
TTCCGAACATCCATCTGGGATGAAACGCTCTACAAAGCCTGGTCTAGCATCGTCTATCAGCTGATTCCCAATGTTCAGCA
GCTGGAGATGAACCTCAGGAATTTTGCCCAAATTATTGAGGCCGATGAAGTTCTGCTGTTCGAGAGAGCAACCTTCTTGG
TCATTTCCCATTACCAGTGCAAAGAGCAGCGCGATGTCCATCGGTTCGAGAAGATCAGCAATATTATTAAGCAGTTCAAG
CTGAGCTGCAGTAAATTGGCCGCTTCCTTCCAGAGCATGGAGGTTAGGAATTCTAACTTCGCTGCTTTCATCGACATCTT
CACATCAAACACCTACGTGATGGTGGTTATGTCTGATCCCTCGATCCCTTCTGCAGCTACACTGATCAACATTCGCAATG
CCAGGAAACACTTTGAGAAGCTGGAGAGAGTGGACGGCCCCAAGCACAGCCTCCTTATGCGTTGA
ORF - retro_sscr_15 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.95 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLEAILQNSPDAKIFCLVHKMDLVQEDQRDL |
| MENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLEAILQNSPDAKIFCLVHKMDLVQEDQRDL | |
| Retrocopy | MENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLEAILQNSPDAKIFCLVHKMDLVQEDQRDL |
| Parental | IFKEREEDLRRLSRPLECSCFRTSIWDETLYKAWSSIVYQLIPNVQQLEMNLRNFAEIIEADEVLLFERA |
| IFKEREEDLRRLSRPLEC.CFRTSIWDETLYKAWSSIVYQLIPNVQQLEMNLRNFA.IIEADEVLLFERA | |
| Retrocopy | IFKEREEDLRRLSRPLECACFRTSIWDETLYKAWSSIVYQLIPNVQQLEMNLRNFAQIIEADEVLLFERA |
| Parental | TFLVISHYQCKEQRDAHRFEKISNIIKQFKLSCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDP |
| TFLVISHYQCKEQRD.HRFEKISNIIKQFKLSCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDP | |
| Retrocopy | TFLVISHYQCKEQRDVHRFEKISNIIKQFKLSCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDP |
| Parental | SIPSAATLINIRNARKHFEKLERVDGPKQCLLMR |
| SIPSAATLINIRNARKHFEKLERVDGPK..LLMR | |
| Retrocopy | SIPSAATLINIRNARKHFEKLERVDGPKHSLLMR |
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 |
|---|---|---|
| SRP014902_placenta | 65 .30 RPM | 0 .00 RPM |
| SRP014902_testis | 65 .91 RPM | 0 .00 RPM |
| SRP018288_heart | 28 .84 RPM | 0 .00 RPM |
| SRP018288_kidney | 45 .71 RPM | 0 .00 RPM |
| SRP018288_liver | 29 .26 RPM | 0 .00 RPM |
| SRP018288_lung | 58 .14 RPM | 0 .00 RPM |
| SRP018856_adipose | 72 .55 RPM | 0 .00 RPM |
| SRP035408_brain | 72 .13 RPM | 0 .00 RPM |
| SRP035408_liver | 26 .57 RPM | 0 .00 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_15 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_15 was not experimentally validated.