RetrogeneDB ID: | retro_ecab_702 | ||
Retrocopylocation | Organism: | Horse (Equus caballus) | |
| Coordinates: | 29:15356918..15357402(-) | ||
| 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_702
ATAGAGAGCTTCTACAGAAGAGTAGATCAAATGGAAGAGAGAATAGGTGATCTAGAGGACAAGAACTTCAAAATAACTGA
AGAGAACAGAGAAAAACAGAATGAAAAAGAGTAAAGAAAGCCTACATGATCCATGAGATTCCATTAAATGTACAAATATT
TAAATAATTGGGATTCAAGAAGGAGAAGAGAGACAGAAGGAGACAGAAAGTTTATTTAAAGAAATAACAGCTGAGAACTT
CCCAAATTTGGAGAGAGACTTGGAATCTAGGTTCACAAAGCTAATAGATCACTCTATTATCTTAATGCAAAATGACCTTC
TCCAAGATACATTATAATGAAACTGTCAAAAATCAAAGATAAAGAGAGTGACCAGAGGAAAAAAAATTGTAACCTACAAA
GGAACCCCCATTAAGCTATCAGCATATTTCTCAGCAGAAACCTGACAGGCTAGAAGAGGCTGGAATGACACATTCAAAGT
ATTG
ATAGAGAGCTTCTACAGAAGAGTAGATCAAATGGAAGAGAGAATAGGTGATCTAGAGGACAAGAACTTCAAAATAACTGA
AGAGAACAGAGAAAAACAGAATGAAAAAGAGTAAAGAAAGCCTACATGATCCATGAGATTCCATTAAATGTACAAATATT
TAAATAATTGGGATTCAAGAAGGAGAAGAGAGACAGAAGGAGACAGAAAGTTTATTTAAAGAAATAACAGCTGAGAACTT
CCCAAATTTGGAGAGAGACTTGGAATCTAGGTTCACAAAGCTAATAGATCACTCTATTATCTTAATGCAAAATGACCTTC
TCCAAGATACATTATAATGAAACTGTCAAAAATCAAAGATAAAGAGAGTGACCAGAGGAAAAAAAATTGTAACCTACAAA
GGAACCCCCATTAAGCTATCAGCATATTTCTCAGCAGAAACCTGACAGGCTAGAAGAGGCTGGAATGACACATTCAAAGT
ATTG
ORF - retro_ecab_702 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 55.03 % |
| Parental protein coverage: | 93.22 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | VESINNRMDQAEETC-ELEDRTFEIIQSEENKEK-RMKKIKDSLLEKYLTIRKSNIRIIGIPEGEEKQKD |
| .ES...R.DQ.EE....LED..F.I...EEN.EK.RMKK.K.SL......I...NI.IIGI.EGEE.QK. | |
| Retrocopy | IESFYRRVDQMEERIGDLEDKNFKI--TEENREK>RMKKSKESLHDP*DSIKCTNI*IIGIQEGEERQKE |
| Parental | TESLFKEIIAENFPNL-GKKLDLQVHEANRTPNYIKAKRPSPRHIVLKLVKVNDKEKILRAERQKKINYK |
| TESLFKEI.AENFPNL.G..L...VH.ANR...Y..AK.PSPR.I..KL.K..DKE......R....N.. | |
| Retrocopy | TESLFKEITAENFPNL<GERLGI*VHKANRSLYYLNAK*PSPRYIIMKLSKIKDKES---DQRXXXCNLQ |
| Parental | R-TPIRLSADFSAETLHTKKEWNDTFETL |
| R.TPI.LSA.FSAET......WNDTF..L | |
| Retrocopy | R>TPIKLSAYFSAET*QARRGWNDTFKVL |
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_702 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_702 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_702 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,
|