RetrogeneDB ID: | retro_ecab_657 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 26:20345688..20346518(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DONSON | ||
| Ensembl ID: | ENSECAG00000007826 | ||
| Aliases: | None | ||
| Description: | downstream neighbor of SON [Source:HGNC Symbol;Acc:2993] |
Retrocopy-Parental alignment summary:
>retro_ecab_657
ACTCCAGATGTATCATTCTCGGATCTGATATTCCATCCTCAGAAAGTACGGGGTTACCCGTGGACTGCAGTATTAAAACC
TGACTCCTTTCACCTCTTCTCAACTTTATCTGAGAGATCATTTGAAAGCAAAGGGAAAGGCTCAAGGTATTGTCCAGCAT
TGTAGGACAATAGAAGTTATTTTGCCTCAAAGTACACAGGATCCGAAACTCTTCCCTGAGCTCCGTTGTACATTCCAGCA
CTGTCTTATCTATTGGCTCCACCCTGCCTTGCCTTGGCTACCACTGTTCCCCGATGTTGGAACTGATAGAAAATAGCGGA
AAAGACAAGTCCTTGGGCAAATGATGAAACTGTGCAACGTATTTTAATGAATAACTCGTCTGTGAGCTTTAATTCTCTGT
ATAATCTGCTGAAGACAAAACTTTATCCCAAGTTCTACATTTATATCTATGAGCTTACTATCCTGTTCCATGCAGCAGGA
TTAGCAGGAAATGATATCCTCATGGCTGTCATATCTCCTACAATTAGAGGTGTAAGACAAGGCATGGAAAAATGAAAGTA
CTACGTTTTCTCTACCTTTAATAAAAGAAAATGGTCATAAATAGAAGAAAGCCTCTGGACAAAGGGACAGGAGGAACGAG
CAATCAGTGATGAAGATGATGAAGATGGAGAAGAAAGTTTTTCCTGGCTTAAAGAGATAGGTGTGCAAGACAAAATTTTA
AAAAAAGCAGACATACTCTCTGTCAAGCTATGTAAAGAGAAACATGAATACAAAAGGATCACAGACCTGGGTCTGTTGTA
TTGGCGAATGGAATCCACGTCTTTGCTGTA
ORF - retro_ecab_657 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 61.05 % |
| Parental protein coverage: | 63.89 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | TPHVSSSE-SDILSSGSTELPVDWSIKTRLL-FTSSQPFTWADHLKAQEEAQGVVQHCRATEVTLPPSIQ |
| TP.VS.S..SDI.SS.ST.LPVD.SIKT.LL.FTSSQ.....DHLKA...AQG.VQHCR..EV.LP.S.Q | |
| Retrocopy | TPDVSFSD<SDIPSSESTGLPVDCSIKT*LL<FTSSQLYL-RDHLKAKGKAQGIVQHCRTIEVILPQSTQ |
| Parental | DPKLCTELRRAFQQSLVYWLHPAFPWLPLFPRIGADRK-MAGKASPWSADEALQDILMSDWSVSFTSLYN |
| DPKL..ELR..FQ..L.YWLHPA.PWLPLFP..G.DRK..A.K.SPW..DE..Q.ILM...SVSF.SLYN | |
| Retrocopy | DPKLFPELRCTFQHCLIYWLHPALPWLPLFPDVGTDRK<IAEKTSPWANDETVQRILMNNSSVSFNSLYN |
| Parental | LLKTKLCPYFYVCTYQFTILFRAAGLAGNDVITALISPTTRGLREAM-KNEGIEFSLPLIKENGQE-KKA |
| LLKTKL.P.FY...Y..TILF.AAGLAGND...A.ISPT.RG.R..M.KNE...FSLPLIKENG...KKA | |
| Retrocopy | LLKTKLYPKFYIYIYELTILFHAAGLAGNDILMAVISPTIRGVRQGM>KNESTTFSLPLIKENGHK*KKA |
| Parental | S-RTSLGHEEEQAMSDEDEEESFSWL-EEMGVQDKI-KKPDILSIRLRKEKHE-VQMDHRPESVVLVKGM |
| S.......E.........E...F..L..E.GVQDKI.KK.DILS..L.KEKHE..Q.DHRP.SVVL..G. | |
| Retrocopy | SGQRDRRNEQSXXXXXXXEKKVFPGL<KEIGVQDKILKKADILSVKLCKEKHE<IQKDHRPGSVVLANGI |
| Parental | NTFTL |
| ..F.. | |
| Retrocopy | HVFAV |
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 | 2 .30 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 9 .24 RPM |
| SRP021940_embryo | 0 .00 RPM | 30 .20 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 6 .59 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 7 .30 RPM |
| SRP021940_testis | 0 .00 RPM | 92 .85 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_657 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_657 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_657 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000007826 | 1 retrocopy |
retro_ecab_657 ,
|
| Echinops telfairi | ENSETEG00000019380 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000003701 | 1 retrocopy |