RetrogeneDB ID: | retro_ecab_1117 | ||
Retrocopylocation | Organism: | Horse (Equus caballus) | |
| Coordinates: | X:64311389..64311829(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSECAG00000012904 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ecab_1117
AGGAGAGAGAAGATTAATAAAAATGGAGAAATTCTATGAGAAATATCTGACTCAATTAGGAAAAGTGAGACAAGGATAAT
GGGTATCCCAGAAGAACAGAGGGAGAAGGAAGTAGACAGCTTATTTAGGGAAATTATAGCTGAGAACTTCCCAAACCTGT
GAAGGACCTGGATACACAAGTACATGAAGTAATAGAACTAATTATCTCACTGAAAAATGACCTTCTCCAAGGCACATTAT
ATTAAAACTGTCAAAAGTCAATGAAAAAGAAAGAATATTAAGGGCAGCCAAAGAGAAAATAAAAAACAATAATCTACAAA
GAACTCCCCATTAGGCTATCAGTAGATTTCTCAGCAGAAACTCTATAAGCCAGGAGAGAGTGAAATGACACATTCAAAAT
ATTGAAAGACAAAAATTATCAGCCAAGAATAATCTATCCA
AGGAGAGAGAAGATTAATAAAAATGGAGAAATTCTATGAGAAATATCTGACTCAATTAGGAAAAGTGAGACAAGGATAAT
GGGTATCCCAGAAGAACAGAGGGAGAAGGAAGTAGACAGCTTATTTAGGGAAATTATAGCTGAGAACTTCCCAAACCTGT
GAAGGACCTGGATACACAAGTACATGAAGTAATAGAACTAATTATCTCACTGAAAAATGACCTTCTCCAAGGCACATTAT
ATTAAAACTGTCAAAAGTCAATGAAAAAGAAAGAATATTAAGGGCAGCCAAAGAGAAAATAAAAAACAATAATCTACAAA
GAACTCCCCATTAGGCTATCAGTAGATTTCTCAGCAGAAACTCTATAAGCCAGGAGAGAGTGAAATGACACATTCAAAAT
ATTGAAAGACAAAAATTATCAGCCAAGAATAATCTATCCA
ORF - retro_ecab_1117 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 59.87 % |
| Parental protein coverage: | 83.05 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | KEKRMKKIKDSLLEKYLTIRKSNIRIIGIPEGEEKQKDTESLFKEIIAENFPNL-GKKLDLQVHE-ANRT |
| ......K....L.E....IRKS..RI.GIPE.E...K...SLF.EIIAENFPNL..K.LD.QVHE..NRT | |
| Retrocopy | RREKINKNGEIL*EISDSIRKSETRIMGIPE-EQREKEVDSLFREIIAENFPNL<VKDLDTQVHE<SNRT |
| Parental | PNYIKAKRPSPRHIVLKLVKVNDKEKILRA--ERQKKINYKRT-PIRLSADFSAETLHTKKEWNDTFETL |
| .NY...K.PSPRHI.LKL.KVN.KE.ILRA..E..K..N..RT.PIRLS.DFSAETL....E.NDTF..L | |
| Retrocopy | -NYLTEK*PSPRHIILKLSKVNEKERILRAAKEKIKNNNLQRT>PIRLSVDFSAETL*ARRE*NDTFKIL |
| Parental | RDKNFQPRILYP |
| .DKN.QPRI.YP | |
| Retrocopy | KDKNYQPRIIYP |
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 | 0 .00 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 0 .00 RPM |
| SRP021940_embryo | 0 .00 RPM | 0 .00 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 0 .00 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 0 .00 RPM |
| SRP021940_testis | 0 .00 RPM | 0 .00 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_1117 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_1117 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_1117 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 11 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000012904 | 11 retrocopies |
retro_ecab_1003, retro_ecab_1068, retro_ecab_1117 , retro_ecab_155, retro_ecab_407, retro_ecab_695, retro_ecab_702, retro_ecab_768, retro_ecab_856, retro_ecab_877, retro_ecab_906,
|