RetrogeneDB ID: | retro_ecab_908 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 6:57773299..57773865(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSECAG00000018840 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ecab_908
TTGGAGGAGAGAAATATAGAAATGCTTCAGATGGAGGAGGAGAGAGTACTAAGACTAAAAAGAAATGAAGGAATTCTCTG
AGAAATATCTGACTCTATTAAGAAAGGCAACATAAGGATTATAGGTATTCCAGAGGAAGAAGGGAGGGAGAAAGGAGAAG
ACAGCTTGTGCAAAGAAATAATAGCTGAGAACTTCCCAAACCTGAGAAAGAAGTTGGAATTACAGGTAAAATAAGCTAAT
AGAACTCCTAACTACATTAATGTAAAAAGACCTCTCCAAGCATAAGGTAGTAAAACTGGCAAAAGTCAATGACAAAGAAA
AAACATTAAGGGCAGCAAGGCAGAAGAAAATATCTTACAAAGGAACTCCTATCAGGATTTCAGCAGATTTCTCAGCAGAC
CTCACATACTAGGAGAGAGTTGAATGATATATTCAAATCTTTGGAACACAAAAACTTTCAGCCAAGAATACTCTATCCAG
CGAAAATATCCTTCAGATATGATGGAGAAATAATATCTTTCCCAGATAAACAAAAGCTGAGGGAGGTCGTTATCACAAGA
TCTCCC
ORF - retro_ecab_908 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 65.28 % |
| Parental protein coverage: | 95.48 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | LEDRNTEMLKMEEERELRLKRSEDIFQEIYNPIRKRNIRIISIPTGEERQNRRESLFKEIITENFLNLGK |
| LE.RN.EML.MEEER.LRLKR.E.I..EI...I.K.NIRII.IP..E.R.....SL.KEII.ENF.NL.K | |
| Retrocopy | LEERNIEMLQMEEERVLRLKRNEGIL*EISDSIKKGNIRIIGIPEEEGREKGEDSLCKEIIAENFPNLRK |
| Parental | GLEIQVKEANRTPNYINVERP-SP-RHILVKLAKLVMKEYIMAEAARQKKITYKGSPIRLSADFS-QTVQ |
| .LE.QVK.ANRTPNYINV.RP.SP..H..VKLAK...KE.....AARQKKI.YKG.PIR.SADFS.QT.. | |
| Retrocopy | KLELQVK*ANRTPNYINVKRP<SP<KHKVVKLAKVNDKEKTL-RAARQKKISYKGTPIRISADFS>QTSH |
| Parental | TRREWNDIIKILKYKNYPPRILYPVKLSFRYGREIKAFQDKQKLREFITTRPP |
| TRRE.NDI.K.L..KN..PRILYP.K.SFRY..EI..F.DKQKLRE...TR.P | |
| Retrocopy | TRRELNDIFKSLEHKNFQPRILYPAKISFRYDGEIISFPDKQKLREVVITRSP |
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 .03 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_908 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_908 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_908 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 28 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000018840 | 28 retrocopies |
retro_ecab_1000, retro_ecab_1011, retro_ecab_1045, retro_ecab_1062, retro_ecab_1076, retro_ecab_221, retro_ecab_243, retro_ecab_296, retro_ecab_322, retro_ecab_327, retro_ecab_424, retro_ecab_482, retro_ecab_498, retro_ecab_523, retro_ecab_545, retro_ecab_564, retro_ecab_571, retro_ecab_663, retro_ecab_718, retro_ecab_742, retro_ecab_763, retro_ecab_787, retro_ecab_790, retro_ecab_824, retro_ecab_902, retro_ecab_908 , retro_ecab_928, retro_ecab_929,
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