RetrogeneDB ID: | retro_ecab_249 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 11:3802215..3802824(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PPCDC | ||
| Ensembl ID: | ENSECAG00000019339 | ||
| Aliases: | None | ||
| Description: | phosphopantothenoylcysteine decarboxylase [Source:HGNC Symbol;Acc:28107] |
Retrocopy-Parental alignment summary:
>retro_ecab_249
ATGGAAGCAAGGGCCTCGTGTCCAGCTGCTGCCCCCTCGGTGGAGGGACAGTTCCGTGTTCTCGTGGGTGTCACTGGGAG
TGTTGCAGCTCTGAAGTTGCCCCTTCTGGTGCGAAGGCTTTTGGATATTCCTGGCCTGGAAGTAGCAGTAGTTAAAACTG
AGAGAGCCAAACATTTCTACACTCCCAGGATGTTCCTGTCACCCTCGACAGCAATGCTGATGGATGGGAGATGTGGCAGC
GCCGATCTGATCCACTTCTCCACATTGACCTGCGGCAGTGCGCAGACCTGATGCTGGTGGCTCCTCTTGATGCCAATACT
CTGGGGAAGGTGGCTAGAGGCATCTGTGACAACTTGCTTACCTGTGTCATCCGGGCCTGGGACTGCAGCAAGCCTCTGCT
CTTCTGCCCGGCGATGAACACTGCCTGTGGGAGCACCCCATCACCGCGCAGCAGGGGGGCCAGCTCAAGGCCTTCGCTAC
GTCGAGATTCCCTGTGTGGCCAAGAAGCTGGTGTGTGGAGACCAACATCTGGGGGCCATGGCTGCAGTGGGCACCATTGT
GGACAGAGTGAAAGAGATCCTCCCCCTTCACAGTGGCTTCCAGCAGAGT
ORF - retro_ecab_249 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.92 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MEARASCPAAAPLVERQFHVLVGVTGSVAALKLPLLVSRLLDIPGLEVAVVTTERAKHFYTP-QDVPVTL |
| MEARASCPAAAP.VE.QF.VLVGVTGSVAALKLPLLV.RLLDIPGLEVAVV.TERAKHFYTP.QDVPVTL | |
| Retrocopy | MEARASCPAAAPSVEGQFRVLVGVTGSVAALKLPLLVRRLLDIPGLEVAVVKTERAKHFYTP<QDVPVTL |
| Parental | YSDADEWEMWKRRSDPVLHIDLRKWADLMLVAPLDANTLGKVASGICDNLLTCVIRAWDRSKPLLFCPAM |
| .S.AD.WEMW.RRSDP.LHIDLR..ADLMLVAPLDANTLGKVA.GICDNLLTCVIRAWD.SKPLLFCPAM | |
| Retrocopy | DSNADGWEMWQRRSDPLLHIDLRQCADLMLVAPLDANTLGKVARGICDNLLTCVIRAWDCSKPLLFCPAM |
| Parental | NTA-MWEHPITAQQVGQLKAFG-YVEIPCVAKKLVCGDQGLGAMAEVGTIVDKVKEILSLHGGFQQS |
| NTA..WEHPITAQQ.GQLKAF..YVEIPCVAKKLVCGDQ.LGAMA.VGTIVD.VKEIL.LH.GFQQS | |
| Retrocopy | NTA<LWEHPITAQQGGQLKAFA<YVEIPCVAKKLVCGDQHLGAMAAVGTIVDRVKEILPLHSGFQQS |
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 | 0 .59 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 2 .44 RPM |
| SRP021940_embryo | 0 .00 RPM | 1 .53 RPM |
| SRP021940_placental_villous | 0 .05 RPM | 1 .64 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 1 .51 RPM |
| SRP021940_testis | 0 .00 RPM | 11 .19 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_249 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_249 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_249 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000019339 | 1 retrocopy |
retro_ecab_249 ,
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