RetrogeneDB ID: | retro_ecab_787 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 4:51183186..51183776(+) | ||
| 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_787
GTAGAGGATAAAAATATATAAGCTTTGCAGGTGGAGGAGGAGAAAACTTAGATTTTGAAAAAATGAAGGAATTCTTTGAG
AAATATCTGAGTCAACAAGGGAAAGCAACATAAGGATTATAGGTGTTCCAGAGGGAGAAGGGAGAGAGAAAGGAGCAGAG
AGCTTGTTCAAAGAAATAGCCGCTGAGAACTTCCCAAACCTGGGGAAGAAACCAGACTTACAAATACATGAAGCCAATAG
AACTCCTAATTACATCAATGCTAAAGGACCTTCTGCAAGGCATATAATAGTAAAACTGGCAAAAGTCAATGACAAAGAAA
AAATATTAAGTGCAGCAAGGCAGAAGAAAATACAAAGGAACCCCTATCAGGCTTTCAGAGGATATCTCAGCAGAAACCTT
ACAGGCTAGCAGAGAATGGAATGATATATTCAAAATACTGAAAGACAAAAAATTTTCAGCCAAGAATACTGTATCCAGTA
AAACTATCTTTCAGATCCTATGGAGAAATAAAGCTTTCTCAGATAAACAAAAGCTAAGGGAGTTCATTGCCACCATACCT
CCCCTACAAAAAATGATGAAGGATGCCCTC
ORF - retro_ecab_787 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 59.31 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | LEDRNTEMLKMEEE-RELRLKRSEDIFQEIYNPIRKRNIRIISIPTGEERQNRRESLFKEIITENFLNLG |
| .ED.N...L...EE.R.LR....E.I..EI....R..NIRII..P.GE.R....ESLFKEI..ENF.NLG | |
| Retrocopy | VEDKNI*ALQV-EE>RKLRF*KNEGIL*EISESTRESNIRIIGVPEGEGREKGAESLFKEIAAENFPNLG |
| Parental | KGLEIQVKEANRTPNYINVERPSPRHILVKLA-KLVMKEYIMAEAARQKKITYKGSPIRLSADFS-QTVQ |
| K....Q..EANRTPNYIN...PS.RHI.VKLA.K...K........R.K...YKG.PIRLS.D.S..T.Q | |
| Retrocopy | KKPDLQIHEANRTPNYINAKGPSARHIIVKLA>KSMTKKKY*VQQGRRK---YKGTPIRLSEDISAETLQ |
| Parental | TRREWNDIIKILK-YKNYPPRILYPVKLSFRYGREI-KAFQDKQKLREFITTRPPLQEMMKTAL |
| ..REWNDI.KILK..KN..PRILYPVKLSFR...EI.KAF.DKQKLREFI.T.PPLQ.MMK.AL | |
| Retrocopy | ASREWNDIFKILK>TKNFQPRILYPVKLSFRSYGEI<KAFSDKQKLREFIATIPPLQKMMKDAL |
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_787 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_787 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_787 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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