RetrogeneDB ID: | retro_ecab_902 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 6:41975113..41975642(-) | ||
| Located in intron of: | ENSECAG00000008029 | ||
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_902
AATGAAGAAATTCTCCAAGAAATATCTGACTCAATAAGGAAATACAACCTAAGACCTATAGGTATTCCAGAGGGAGAAGT
GAGGGAGAAAGGAGCAAGAGAGCTTGTTCAAAGAAATAATATGAGAACTTCCCAAACCTGGGGGAGGACTTGACTTACAA
GTACATGAAGCCAATAGAACTCCTAATTAAGTCAATGCAAAAAGACCTCTACAAGGCATGCAACAGTAAAACTGACAAAA
GTTAAGGACAAAGAAAAAACATTAAGGGCAACAGGGCAAAAGGAAATAACCTACAAAGGAACCCCTATCAGGTTTTCAGC
AGACTTCTCCGCAAACTTTACAAACTAGGAGAGAATGGAATAATATATTCAGAATAATAAAAAACAAAGACTTTCAGCCA
AGAATAGTCTATTCAGCAAAACTAACCTTCAGATATGATGGAGAAATAAAAATTTTCCCAGATAAACAAAAGTTAAAGGA
GTTCATCGCAACTAGACATCTGTTACAAGAAATGATGAAGGAACACCTC
ORF - retro_ecab_902 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 56.59 % |
| Parental protein coverage: | 89.45 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | SEDIFQEIYNPIRKRNIRIISIPT-GEERQNRRESLFKEIITENFLNLGK-GLEIQVKEANRTPNYINVE |
| .E.I.QEI...IRK.N.R.I.IP..G.....R..........ENF.NLG..GL..QV.EANRTPN..N.. | |
| Retrocopy | NEEILQEISDSIRKYNLRPIGIPE<GRSEGERSKRACSKK*YENFPNLGE<GLDLQVHEANRTPN*VNAK |
| Parental | RP-SPRHILVKLAKLVMKEYIMAEAARQKKITYKGSPIRLSADFS-QTVQTRREWNDIIKILKYKNYPPR |
| RP.S.RH..VKL.K...KE.....A..QK.ITYKG.PIR.SADFS.QT.QTRREWN.I..I.K.K...PR | |
| Retrocopy | RP<STRHATVKLTKVKDKEKTL-RATGQKEITYKGTPIRFSADFS>QTLQTRREWNNIFRIIKNKDFQPR |
| Parental | ILYPVKLSFRYGREIKAFQDKQKLREFITTRPPLQEMMKTAL |
| I.Y..KL.FRY..EIK.F.DKQKL.EFI.TR..LQEMMK..L | |
| Retrocopy | IVYSAKLTFRYDGEIKIFPDKQKLKEFIATRHLLQEMMKEHL |
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_902 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_902 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_902 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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