RetrogeneDB ID: | retro_ecab_296 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 14:44569143..44569729(+) | ||
| 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_296
AAGAAATCTAGAATGATTCAGGTGGAAGAGTAGAGAGAACTAAGATTTTTAAAAAATGAAGACATTCTATGAGAAATATG
TGAATCAATTAGGAAAATCAGCATAAGGATAATAGGTATCCCAGAAGGAGAAGAGAGGGAGAAAGGAACAGAGAGCTTAT
TTAAAGAAATAATAGCTGATAACTTCCCAAACCTGGGGAAGAAACTGGATATACAAGAACATGAAGCTAATAGAACTCCT
AAATATCTTAACACAAAAAGACCTTCTCCAAGGCACATTATATTAAAACAGCCAAAAGTCAATGACAAAGACAGAATGTT
AAGGACAGCCAGAGAGAAGAAAATAACTTATAAAGGAAATCTCATCAGGCTATCAGTGGATTTCTCAGCAGAAACTACAG
ACTAGAAGAGAGTGGAGTGATATAGTCAAAATATTGAAAGATAATAACTATCAGCAAAGAATACTCTATCCAACAAAATT
ATTCTTCAGATATGTAGGAGAAATAAAGGGTCTCCCAGGAAAATAAAAGCTGAAGGAGTTCACCACCACAAGACCAGCCT
TACAAGAAATGTTGAAAGAAGCTCTC
ORF - retro_ecab_296 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 61.42 % |
| Parental protein coverage: | 98.49 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | RNTEMLKMEEERELRLKRSEDIFQEIYNPIRKRNIRIISIPTGEERQNRRESLFKEIITENFLNLGKGLE |
| ....M...EE.RELR....EDI..EI...IRK..IRII.IP.GEER....ESLFKEII..NF.NLGK.L. | |
| Retrocopy | KKSRMIQVEE*RELRFLKNEDIL*EICESIRKISIRIIGIPEGEEREKGTESLFKEIIADNFPNLGKKLD |
| Parental | IQVKEANRTPNYINVERPSPRHILVKLAKLVMKEYIMAEAARQKKITYKGSPIRLSADFS-QTVQTRREW |
| IQ..EANRTP.Y.N..RPSPRHI..K..K...K...M...AR.KKITYKG..IRLS.DFS.Q..QTRREW | |
| Retrocopy | IQEHEANRTPKYLNTKRPSPRHIILKQPKVNDKDR-MLRTAREKKITYKGNLIRLSVDFS>QKLQTRREW |
| Parental | NDIIKILKYKNYPPRILYPVKLSFRYGREIKAFQDKQKLREFITTRPPLQEMMKTAL |
| .DI.KILK..NY..RILYP.KL.FRY..EIK....K.KL.EF.TTRP.LQEM.K.AL | |
| Retrocopy | SDIVKILKDNNYQQRILYPTKLFFRYVGEIKGLPGK*KLKEFTTTRPALQEMLKEAL |
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_296 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_296 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_296 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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