RetrogeneDB ID: | retro_ecab_980 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 8:80798639..80799414(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | YARS2 | ||
| Ensembl ID: | ENSECAG00000011140 | ||
| Aliases: | None | ||
| Description: | tyrosyl-tRNA synthetase 2, mitochondrial [Source:HGNC Symbol;Acc:24249] |
Retrocopy-Parental alignment summary:
>retro_ecab_980
CAGACACGGCTGAAGACTCCTAGAGACATGAGCGCCAAGTTCTAATACCAGGTGCCCCAGGCTTGTGACTTCCATCATCA
GTTCCAGAGTATGGATGGTGGGTCCAGCTGGTGGACCTGATCAGCTGGGCAACATCATGTCCAGATACAAGTCAATCCAC
AAGTTGACTAGAGAAGACCATTTGGCATCCCTGTTGCTCTAATTACAAGCACAGCTGGAGCAGAACTGGGAAAGTCAGTG
GCAGTGCTGTCTGGATAAACAGAGATGAGACATCTCCATTTGAATTGTACCATTTCTTTGTCAGGGAGAAAGATGATTTG
GAAGAAAGGTAGCCGAAGCTCCTCACTTTTCTGCCGCTTCCAGAGCTTGACCACGTAATGTGGCTGCATGTCAAAGAGCC
ACAAAAGCAGGGTCCTCGGAAACGACTGGCTGCAGAAGTAACAAAGCTTGTACATGGACAGGAAGGGCTGGCTTCTGCTA
AAATGTGTAAACAAGCACTTTGTCATCGTTGTACAGACACACTGGAGGTCATGTCTGATCAAGAGATGAAAGAGTGTTTA
AAGAAGCTTCATTTTCTGAATTAGTTCTTGACCCTGGAGCAAGCGGCTGAGATACATGCCACAAAGCAAATGCCATTCCA
GATGGTCCCCGAAGGTATCAGGTGATAACACAGGGCAGAGTCAGTATAAGTCACAGATGAGTAACAAATCCTGAGAGTGT
TTTAGTGGTTGGACAACATATTCTTAAGAATGGACTGTCAGTAGAGGAAGATGGG
ORF - retro_ecab_980 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 72.56 % |
| Parental protein coverage: | 54.6 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | QTRLKSPEGMSLAEFLYQVLQAYDFYYLFQ-RYGCRVQL-GGSDQLGNIMSGYEFIHKLTGED-VFGITV |
| QTRLK.P..MS.A.F.YQV.QA.DF...FQ..YG..VQL.GG.DQLGNIMS.Y..IHKLT.ED..FGI.V | |
| Retrocopy | QTRLKTPRDMS-AKF*YQVPQACDFHHQFQ<EYGWWVQL<GGPDQLGNIMSRYKSIHKLTRED<PFGIPV |
| Parental | PLITSTTGAKLGKS-AGNAVWLNRDKTSPFELYQFFVRQQDDSVERYLKLFTFLPLPEIDHIMQQHVKEP |
| .LITST.GA.LGKS..G.AVW.NRD.TSPFELY.FFVR..DD..ER..KL.TFLPLPE.DH.M..HVKEP | |
| Retrocopy | ALITSTAGAELGKS<SGSAVWINRDETSPFELYHFFVREKDDLEER*PKLLTFLPLPELDHVMWLHVKEP |
| Parental | EKWGPQKRLAAEVTKLVHGQEGLDSAKRCTQALYHSSIDALEVMSDQELKE-LFKEASFSELVLDPGTSV |
| .K.GP.KRLAAEVTKLVHGQEGL.SAK.C.QAL.H...D.LEVMSDQE.KE..FKEASFSELVLDPG.S. | |
| Retrocopy | QKQGPRKRLAAEVTKLVHGQEGLASAKMCKQALCHRCTDTLEVMSDQEMKE<VFKEASFSELVLDPGASG |
| Parental | LDTCRKANAIPDGPRGYRMITEGGVSINHRQVTNPESVLVVGQHILKNGLSLLKIG |
| .DTC.KANAIPDGPR.Y..IT.G.VSI.HR.VTNPESVLVVGQHILKNGLS....G | |
| Retrocopy | *DTCHKANAIPDGPRRYQVITQGRVSISHR*VTNPESVLVVGQHILKNGLSVEEDG |
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 .06 RPM | 3 .48 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 7 .22 RPM |
| SRP021940_embryo | 0 .00 RPM | 11 .10 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 7 .12 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 6 .09 RPM |
| SRP021940_testis | 0 .00 RPM | 15 .79 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_980 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_980 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_980 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000011140 | 1 retrocopy |
retro_ecab_980 ,
|
| Myotis lucifugus | ENSMLUG00000001614 | 1 retrocopy |