RetrogeneDB ID: | retro_ecab_877 | ||
Retrocopylocation | Organism: | Horse (Equus caballus) | |
| Coordinates: | 6:34677650..34678112(+) | ||
| 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_877
AGCATCAACAATGGCCTGGATCAAGCAGAACAATCTGTGAAGCAGAAGACAGAACCTTTGAAATGATCCAGTCAGAGGGG
AAAAAAGAAAAAAATATACAAAAGAGTGAAAGAAGCCTCCATGAACTATGGGATACCATTAACAGATACAATCTACACAT
TATTGGAGTCCCAGAAAGAGAAGAGAGGGAGAAAGGGGAAAAGAACTTATTTAAAGAAATAATCGCTGAGAACTTCCCAA
ATCTGGGGAGAGACATGGATGTCCAAGTTCAGGAAGCTAATAGGTCACCCCCAAAATTCAACTCAAAACAATCTTCTCCA
AGACACATTTTAACAAAACTATCTAAAATCAAGGACAAAGAGGATTTTAAAAGCAGCAAGAGAAAGGTAATTCTTCACAT
AAAAGGATATCCCCATAAGACTATTGGCAGATTATTTAGAAGAAACCTTGCAGACCAAGAGA
AGCATCAACAATGGCCTGGATCAAGCAGAACAATCTGTGAAGCAGAAGACAGAACCTTTGAAATGATCCAGTCAGAGGGG
AAAAAAGAAAAAAATATACAAAAGAGTGAAAGAAGCCTCCATGAACTATGGGATACCATTAACAGATACAATCTACACAT
TATTGGAGTCCCAGAAAGAGAAGAGAGGGAGAAAGGGGAAAAGAACTTATTTAAAGAAATAATCGCTGAGAACTTCCCAA
ATCTGGGGAGAGACATGGATGTCCAAGTTCAGGAAGCTAATAGGTCACCCCCAAAATTCAACTCAAAACAATCTTCTCCA
AGACACATTTTAACAAAACTATCTAAAATCAAGGACAAAGAGGATTTTAAAAGCAGCAAGAGAAAGGTAATTCTTCACAT
AAAAGGATATCCCCATAAGACTATTGGCAGATTATTTAGAAGAAACCTTGCAGACCAAGAGA
ORF - retro_ecab_877 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 52.56 % |
| Parental protein coverage: | 87.01 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | SINNRMDQAEET-CELEDRTFEIIQSEENKEKRMKKIKDSLLEKYLTIRKSNIRIIGIPEGEEKQKDTES |
| SINN..DQAE...CE.EDRTFE.IQSE........K...SL.E...TI...N..IIG.PE.EE..K.... | |
| Retrocopy | SINNGLDQAEQS<CEAEDRTFEMIQSEGXXXXXIQKSERSLHELWDTINRYNLHIIGVPEREEREKGEKN |
| Parental | LFKEIIAENFPNLGKKLDLQVHEANRTPNYIKAKRPSPRHIVLKLVKVNDKEKILRAERQKKINY-KRTP |
| LFKEIIAENFPNLG...D.QV.EANR.P.....K..SPRHI..KL.K..DKE......R.......K..P | |
| Retrocopy | LFKEIIAENFPNLGRDMDVQVQEANRSPPKFNSKQSSPRHILTKLSKIKDKEDFKSSKRKVILHI>KDIP |
| Parental | IRLSADFSAETLHTKK |
| IRL.AD...ETL.TK. | |
| Retrocopy | IRLLADYLEETLQTKR |
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_877 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_877 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_877 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,
|