RetrogeneDB ID: | retro_ecab_893 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 6:2479323..2479969(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TSR3 | ||
| Ensembl ID: | ENSECAG00000013501 | ||
| Aliases: | None | ||
| Description: | TSR3, 20S rRNA accumulation, homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:14175] |
Retrocopy-Parental alignment summary:
>retro_ecab_893
CTGCTCAGCCACCTGAGTGCTCAGAATATGTCTCCTGCAGATAGGCGGCTGGTGACACAGTCAGTGGTCCCGCCATAGAC
TGCTTGTGTGCCAGACAGGAGGAAATGCCATTTGGGAAGATGACGGAGAGCCTCTTGTGGCTGCTGACCCACTGGGTGGC
TACTAACCCTGTGAAATATGGCTGGCCCTGCAAACTGTCCACTGTAGAGGTTTTTGCTGCTACCTTCTGCATCTGGAGCA
TTTTGGACCACACAGTCATTTTGCTGCAGAAGTTTAGGTGGGGCAAGGGCTGGCTGGACCTGAACCACCAGCTTCTGGAC
AAGTGTATGACCTGCAGCAGCCTATAGTGGGTGCTTGTGGCAGAGAAGGAGCTCCTGGTAGTGCCAAGGGAGCCCCAGGA
GGAGGAAGTCAATCCCTTTGATATGAATTCAGGGCAGGAGTTTGCAAACCCCAACACACCTGTGGGACACATCGGGTTGC
CCATGGACAGTGATAACAGTGACAACCATGAGTCTGAAGACTAAAGGCCCAATACCAAGGACAGAGGACACAACAGCAGT
AGCTCAGAAGATGAGGAGAGGCAGGGAAAAAGGTAGAAGCCAGTGCACCAACAGAGGTTTGGAAAGGAATCAAGAAACAG
CAAAGA
ORF - retro_ecab_893 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 56.76 % |
| Parental protein coverage: | 69.43 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | VLSPMASQYVSPADRQLVAQSGVA-VIDCSWARLDETPFGKMRGGHLRLLPHLVAANPVNYGRPCKLSCV |
| .LS....Q..SPADR.LV.QS.V...IDC..AR..E.PFGKM....L.LL.H.VA.NPV.YG.PCKLS.V | |
| Retrocopy | LLSHLSAQNMSPADRRLVTQSVVP<AIDCLCARQEEMPFGKMTESLLWLLTHWVATNPVKYGWPCKLSTV |
| Parental | EAFAATFCILGFSDLAVILL-RFKWGKGFLDLNRQLLDKYAACSGPEEVLQAEQEFLVHAKEHPEEEEID |
| E.FAATFCI....D..VILL..F.WGKG.LDLN.QLLDK...CS....VL.AE.E.LV...E.P.EEE.. | |
| Retrocopy | EVFAATFCIWSILDHTVILLQKFRWGKGWLDLNHQLLDKCMTCSSL*WVLVAEKELLVVPRE-PQEEEVN |
| Parental | PFDVDSGREFANPNRPVAGTRLPMDSGDSDGDSEDEPEEHGPDPEQEG-SGSCSEKE-GTPERGAEARAP |
| PFD..SG.EFANPN.PV....LPMDS..SD.....E.E...P.....G...S.SE.E.G......EA.AP | |
| Retrocopy | PFDMNSGQEFANPNTPVGHIGLPMDSDNSD---NHESED*RPNTKDRGHNSSSSEDE<GEAGKKVEASAP |
| Parental | TEVWKGIKKRQR |
| TEVWKGIKK.QR | |
| Retrocopy | TEVWKGIKKQQR |
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 | 14 .17 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 30 .54 RPM |
| SRP021940_embryo | 0 .00 RPM | 16 .32 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 13 .90 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 16 .44 RPM |
| SRP021940_testis | 0 .00 RPM | 17 .97 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_893 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_893 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_893 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000013501 | 1 retrocopy |
retro_ecab_893 ,
|
| Macropus eugenii | ENSMEUG00000007498 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000008158 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000011979 | 1 retrocopy |