RetrogeneDB ID: | retro_ecab_1055 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | X:24200046..24200784(+) | ||
| Located in intron of: | ENSECAG00000020894 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TRPT1 | ||
| Ensembl ID: | ENSECAG00000009917 | ||
| Aliases: | None | ||
| Description: | tRNA phosphotransferase 1 [Source:HGNC Symbol;Acc:20316] |
Retrocopy-Parental alignment summary:
>retro_ecab_1055
ATGAACTCCTCTGGCGGAAGGAGGCAGGAAGCAGCAGGGCCTGGGGGCAGAAGTACTCACAGATCCCAAGAATCAGATGT
GCAACTGTCCAAGGCTCTGCCCTGCGCCCTGTGCCACGGGGCCCTGAAGCTGAGGTTTCCCACGGGGGCCAACAGCTTTG
TGCCCCTGGGCGCCCTCCTGCAGCTCCCCAGTTCCGAAGCATCTCAGCTAAAGGTGTGCACTGTGTGGTGGACACCAAAG
GGAAGCAGCGCTTTGCCCTGCAGCTGGGGGACTCCAGCACTGGCCTTCTCATCCAGGCCAATCAGGGACACTCTCTGTAG
GTACCTTAGTTGGAGTTGATGCCCCTGGGGACCCCACAGGCCCTGCCCTGATGCTCATCCATGGCACATTCTGGCAGCAC
TGGCCATCCATCTTGCTCAAGGGCCTGTCCTGCTGGGGAAGGATGCACATCCACCTGGCCCTAGGACTGCCTGGGGATCC
TGGTGTCAGTGGCATGTGGTCAAACTGCAGACGGGTCATGTTCATCAACAGGCCCCTGGCCCTGGCAGATGGAGCCCTTT
TCTTCAGCTCTGCCAATGAAGTGATTCTGACTCCAGGGAAAGCTGATGGCTTCCTGCTTCCCAAGTACTTCAAGGAGGCC
CTGCAGCTATGCCCTACCGAAACCCTCTCTCCTTGGCTGATAATGAAAAGACAGAGTGTCAGAGTGGCCCTGAGCACAGC
TCCAGAGGAAGAAGGATA
ORF - retro_ecab_1055 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 74.31 % |
| Parental protein coverage: | 98.81 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MDTSGGRRQEAGGPRGRKARRPREQDRDMQLSKALSYALRHGALKLGLPMGADGFVPLGALLQLP-QFRS |
| M..SGGRRQEA.GP.GR...R...Q..D.QLSKAL..AL.HGALKL..P.GA..FVPLGALLQLP.QFRS | |
| Retrocopy | MNSSGGRRQEAAGPGGRSTHR--SQESDVQLSKALPCALCHGALKLRFPTGANSFVPLGALLQLP<QFRS |
| Parental | FSAEDVQRVVATNAKQRFALQPGDPSTGPLIRANQGHSLQVPELELMPLETPQALP-PMLIHGTFWQHWP |
| .SA..V..VV.T..KQRFALQ.GD.STG.LI.ANQGHSL.VP.LELMPL.TPQALP..MLIHGTFWQHWP | |
| Retrocopy | ISAKGVHCVVDTKGKQRFALQLGDSSTGLLIQANQGHSL*VP*LELMPLGTPQALP<LMLIHGTFWQHWP |
| Parental | SILLKGLSCRGRTHIHLATGLPGDPGVISGIRPNCEVAVFINGPLALADGIPFFRSANGVILTPGDADGF |
| SILLKGLSC.GR.HIHLA.GLPGDPGV.SG...NC....FIN.PLALADG..FF.SAN.VILTPG.ADGF | |
| Retrocopy | SILLKGLSCWGRMHIHLALGLPGDPGV-SGMWSNCRRVMFINRPLALADGALFFSSANEVILTPGKADGF |
| Parental | LFPKYFKEALQLRPT-RKPLSLAGDEETECQSGPKHSSRGRRM |
| L.PKYFKEALQL.PT.R.PLSLA..E.TECQSGP.HSSRGRR. | |
| Retrocopy | LLPKYFKEALQLCPT<RNPLSLADNEKTECQSGPEHSSRGRRI |
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 | 9 .68 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 14 .39 RPM |
| SRP021940_embryo | 0 .00 RPM | 11 .89 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 6 .16 RPM |
| SRP021940_synovial_membrane | 0 .05 RPM | 9 .03 RPM |
| SRP021940_testis | 0 .00 RPM | 19 .31 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_1055 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_1055 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_1055 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 | ENSECAG00000009917 | 1 retrocopy |
retro_ecab_1055 ,
|
| Sus scrofa | ENSSSCG00000013040 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000010252 | 1 retrocopy |