RetrogeneDB ID: | retro_ecab_644 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 25:11314013..11314328(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ATP5J | ||
| Ensembl ID: | ENSECAG00000017858 | ||
| Aliases: | None | ||
| Description: | ATP synthase, H+ transporting, mitochondrial Fo complex, subunit F6 [Source:HGNC Symbol;Acc:847] |
Retrocopy-Parental alignment summary:
>retro_ecab_644
CGGAAGGTCCACGGGTTCTGCCTTGTCTTTCCACCAGCTCTCTCAGTCCATTTGTGGAAGACCATTGGTGTTATGGCAGT
GGCGTTTAATAAGGAATTTGATCCTGTACAGAAACTCTTTGGGGGCAAGATTAGAGAATATGAATCTAAGCACGCATCAT
CTTGAGGACGTTTTTATATTGACCCAGAGGATCAGCAAGAGCTGGAGAGGGAGATTTTTAAGCTTAAACAGACGTTCAGC
AAGGCAGACAGAAATACCCTGGCTAACTTCAAATTTGCAGACCCCAAATTTGAAAGCATGGAAAAACTGCAGACC
ORF - retro_ecab_644 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 57.14 % |
| Parental protein coverage: | 97.2 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | RRLFRLSSVVQSAISVHLRRNIGVTAVAF-KELDPIQKLFVDKIREYRTKRQTSGGPVDIGPEYQQDLER |
| R.......V...A.SVHL...IGV.AVAF.KE.DP.QKLF..KIREY..K...S.G...I.PE.QQ.LER | |
| Retrocopy | RKVHGFCLVFPPALSVHLWKTIGVMAVAFNKEFDPVQKLFGGKIREYESKHASS*GRFYIDPEDQQELER |
| Parental | ELFKLKQMYGKADMNTFPNFKFEDPKFEVFDKPQS |
| E.FKLKQ...KAD.NT..NFKF.DPKFE...K.Q. | |
| Retrocopy | EIFKLKQTFSKADRNTLANFKFADPKFESMEKLQT |
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 |
|---|---|---|
| SRP021940_articular_cartilage | 0 .00 RPM | 17 .83 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 33 .91 RPM |
| SRP021940_embryo | 0 .00 RPM | 37 .77 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 32 .19 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 19 .49 RPM |
| SRP021940_testis | 0 .00 RPM | 31 .27 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_644 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_644 was not experimentally validated.