RetrogeneDB ID: | retro_ecab_147 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 1:136437928..136439224(+) | ||
| Located in intron of: | ENSECAG00000022427 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TUBAL3 | ||
| Ensembl ID: | ENSECAG00000014631 | ||
| Aliases: | None | ||
| Description: | tubulin, alpha-like 3 [Source:HGNC Symbol;Acc:23534] |
Retrocopy-Parental alignment summary:
>retro_ecab_147
AAGTGCACCTCCATCCAGTTTGGCCAGGCTGGTATCCAGATGGGCAATGCCTGCTGGGAGCTCTACTGCCAGGAACATGG
CATCCAGTCCAACGGCCAGATGCCAAGGGACAAGACCATTAGGGGAAGAGATAACTCCCTCAACACATTCTTCAGTGACA
CAGGCATTGACAAGTATGTGCCCAGAGCAGTGTTTGTAGACCTGGAACCCATGGTCATTGATGAAGTTTGCACTGGCACC
TACCATCAGCTCTTTCACCCTGAACAGCTCATCAGAGGCAAGGAAGATGCTGTCAATAACTATGCCCATGGGCACTACAC
CATTGGTAAGGTGATCATTGACCTTGTCTTGGACCAAATTTGGAAACTGGCCAGCCAGTGTATGGGTCTTCAGAGCTTCT
TGGTTTTCAACAGCTTTGGTGGGGGAACTGGTTCTGGGCTCACCTCTCTGTTGATGGAATGTCTCTGTCAACTATGGCAA
GAAGTCCAAGCTGGAGTTCTCCATTTACCAAGCCCCCAGGTTTCCACAGGTATAGTTGAGTGCCACAACTCCATCCTCAC
CACTTACACCACCCTGGAGCACTGTGATTGTGCCTTTATGGTAGACAAGGAGGCCATCTATGACATCTGTTGTAGAAGCC
TCACTATTGAGTGTCTAACCTATACTAACCTGAATAGGTTGATAGGTCAAATTGTGTCCTGCATCGCTGCTTCCCTCAGA
TTTGATGTAGCTCTGAATGTTGACCTGACAGAATTCCAGACCAACCTGGTGCCCTATCCCCGCATCCACTTCCCTCTTGC
CCTGTATGCCCCTGTCATCTTTGTTGAGAAAGCCTACCATGAATAGCTTTCTGTAGCAGAGATCAGAACGCTTCTTTTGA
GCCAGCCAACCAGATGGTGAAATGTGATCCTTGCCATGGTAAATACACGGCTTGTTGCCTGTTGTACCATGGTGATGTGG
TTCCCAAAGATGTCAATGCTGCTGTTGCCATCATCAAGACCAAGCATACCATCCAGTTTGTAGATTGGTGCCCCACTGGC
TTCAAAGTTGGCATCAATCACCAGCTTCCCACTGTGGTATCTGGTGGAGACCTGGCCAAACTACAGTGAAGTGTGTGCAT
GCTGAGCAATACCACAGCCATTGCTGAGGCCTGGGCTAGCCTGGACCACAGCTTGACCTGATGATGCCAAGCGTGTCTTT
ATTCATTGGTACGTGGGTGAGCGCATGGAAGAAGGAGAGTGTTCTGAGGGCTGTGAGGACATGGCTGCCCCTTAGAAGGA
TTACTAGGAGGTTGGT
ORF - retro_ecab_147 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 62.41 % |
| Parental protein coverage: | 99.08 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | ECLSIHIGQAGIQIGDACWELYCLEHGIQPDGGL-ENANVEHMDASFDTFFCETRAGKYVPRALFMDLEP |
| .C.SI..GQAGIQ.G.ACWELYC.EHGIQ..G...........D.S..TFF..T...KYVPRA.F.DLEP | |
| Retrocopy | KCTSIQFGQAGIQMGNACWELYCQEHGIQSNGQMPRDKTIRGRDNSLNTFFSDTGIDKYVPRAVFVDLEP |
| Parental | TVVDGIRTGKYRSLFHPEQLVSGKEDAANNYARGHYSVGSEIIDLVLERIRKLAKQCSGLQGFLIFRSFG |
| .V.D...TG.Y..LFHPEQL..GKEDA.NNYA.GHY..G..IIDLVL..I.KLA.QC.GLQ.FL.F.SF. | |
| Retrocopy | MVIDEVCTGTYHQLFHPEQLIRGKEDAVNNYAHGHYTIGKVIIDLVLDQIWKLASQCMGLQSFLVFNSF- |
| Parental | GGTGSGFTSLLMEQ-LSIEYSRKTKLEFSVY-PAPRISTAVVEPYNSILTTHSTIEHSDCSFMVDNEAIF |
| GG........L.....S..Y..K.KLEFS.Y.P.P..ST..VE..NSILTT..T.EH.DC.FMVD.EAI. | |
| Retrocopy | GGGTGSGLTSLLME>VSVNYGKKSKLEFSIY<PSPQVSTGIVECHNSILTTYTTLEHCDCAFMVDKEAIY |
| Parental | DICHRKLGVERPSYASINRLIGQAVSSITASLRFKGPLNVDLIEFQTNLVPYPRIHFPMTTFAPIISADK |
| DIC.R.L..E...Y...NRLIGQ.VS.I.ASLRF...LNVDL.EFQTNLVPYPRIHFP....AP.I...K | |
| Retrocopy | DICCRSLTIECLTYTNLNRLIGQIVSCIAASLRFDVALNVDLTEFQTNLVPYPRIHFPLALYAPVIFVEK |
| Parental | AYHEELSVSDITA-ACFEFSNQLVKCDPRLGKYMACCLLYRGDVVPKDVNAAIAAMKSRNSVRFVDWCPT |
| AYHE.LSV..I...A.FE..NQ.VKCDP..GKY.ACCLLY.GDVVPKDVNAA.A..K......FVDWCPT | |
| Retrocopy | AYHE*LSVAEIRT<ASFEPANQMVKCDPCHGKYTACCLLYHGDVVPKDVNAAVAIIKTKHTIQFVDWCPT |
| Parental | GFKVGINNQPPVAMPGGDLAKVQRAVCMLSNTTAIVEAWARLDH-KFDLMY-AKRAFLHWYIREGMEEGE |
| GFKVGIN.Q.P....GGDLAK.Q..VCMLSNTTAI.EAWA.LDH...DLM..AKR.F.HWY..E.MEEGE | |
| Retrocopy | GFKVGINHQLPTVVSGGDLAKLQ*SVCMLSNTTAIAEAWASLDH<QLDLMM<AKRVFIHWYVGERMEEGE |
| Parental | FSEAREDLAALEKDYEEVG |
| .SE..ED.AA..KDY.EVG | |
| Retrocopy | CSEGCEDMAAP*KDY*EVG |
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 .12 RPM | 0 .00 RPM |
| SRP021940_cerebellum | 0 .16 RPM | 0 .10 RPM |
| SRP021940_embryo | 0 .82 RPM | 0 .26 RPM |
| SRP021940_placental_villous | 0 .05 RPM | 0 .05 RPM |
| SRP021940_synovial_membrane | 0 .14 RPM | 0 .08 RPM |
| SRP021940_testis | 0 .06 RPM | 0 .26 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_147 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_147 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_147 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000005248 | 1 retrocopy | |
| Equus caballus | ENSECAG00000009504 | 1 retrocopy | |
| Equus caballus | ENSECAG00000013798 | 1 retrocopy | |
| Equus caballus | ENSECAG00000014403 | 1 retrocopy | |
| Equus caballus | ENSECAG00000014631 | 1 retrocopy |
retro_ecab_147 ,
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