RetrogeneDB ID: | retro_ecab_944 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 7:4145055..4145793(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LANCL1 | ||
| Ensembl ID: | ENSECAG00000009197 | ||
| Aliases: | None | ||
| Description: | LanC lantibiotic synthetase component C-like 1 (bacterial) [Source:HGNC Symbol;Acc:6508] |
Retrocopy-Parental alignment summary:
>retro_ecab_944
GGACCGATGGGCCACATCCATGCTCTTCTCTTTGCCAATAAGCACTTTGGAGTGGAAAAGATTCCTCAAAGCCACATTCA
GTAGATTTGTGAAACAGTCTTAACCTCTGGAGAAAACCTAGCTAGAAAGAAGAATTTAACAGCAAAGACTCCACTGGTGT
ATGAATGGTACCAAGAATATTACGTGGGGGCTGCTCACGGCCTGGCAGGAATTTACTACCTCCTGATGCAGCCCAGCCTT
CAGGTGAGCCATGCGAAGTTACATAGTTTGGTCAAGCCCAGTGTAGACTATGTCTGCCAGCTGAAATTCCCTTCTGGCCA
TTGCCCTCCACGTGTGGACAATACTCAAGATCTGCTAGTCCACTGGTGCCACGGTGCCCCTGGGGTAATCTACATGCTCA
TCCAGGCCTATAAGGTGTTCAGAGAGGAGCGCTATCTCAGCGACGCCCGGCAGAGCGCTGACCTGACCTGGCAGTACGGG
CTGCTGAAGAAGGGCTACTGGCTGTGCCACGGCGCTGCGGGCAACGCCGACGCCTTCCTGGCGCTGTTCAACCTCACACA
GGCCAGGAAGTACCTGTACAGGGCCTGCAAGTTCGCTGAGTGATGCTTGGATTACGGAGAACATGGGTGCAGAACACCGG
ACAACCCCTTCTCCCTCTTTGAAGGAATGGCTGGAACAATCTATTTCCTGGCTGACCTGCTAGTGCCAGAGAAAGCCTGG
TTCCCTGCATTTGAACTG
ORF - retro_ecab_944 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.65 % |
| Parental protein coverage: | 61.65 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | GRMGYIYALLFVNKHFGVEKIPQSHIQQICETVLTSGENLARKRNFTAKTPLMYEWYQEYYVGAAHGLAG |
| G.MG.I.ALLF.NKHFGVEKIPQSHIQ.ICETVLTSGENLARK.N.TAKTPL.YEWYQEYYVGAAHGLAG | |
| Retrocopy | GPMGHIHALLFANKHFGVEKIPQSHIQ*ICETVLTSGENLARKKNLTAKTPLVYEWYQEYYVGAAHGLAG |
| Parental | IYYFLMQPSLQVSHAKLHSLVKPSVDYVCQLKFPSGNYPPCVDDTRDLLVHWCHGAPGVIYMLIQAWKVF |
| IYY.LMQPSLQVSHAKLHSLVKPSVDYVCQLKFPSG..PP.VD.T.DLLVHWCHGAPGVIYMLIQA.KVF | |
| Retrocopy | IYYLLMQPSLQVSHAKLHSLVKPSVDYVCQLKFPSGHCPPRVDNTQDLLVHWCHGAPGVIYMLIQAYKVF |
| Parental | REERYLTDARQSADLIWQYGLLKKGYGLCHGAAGNAYAFLALFNLTQDRKYLYRACKFAEWCLDYGEHGC |
| REERYL.DARQSADL.WQYGLLKKGY.LCHGAAGNA.AFLALFNLTQ.RKYLYRACKFAE.CLDYGEHGC | |
| Retrocopy | REERYLSDARQSADLTWQYGLLKKGYWLCHGAAGNADAFLALFNLTQARKYLYRACKFAE*CLDYGEHGC |
| Parental | RTPDTPFSLFEGMAGTIYFLADLLVPEKARFPAFEL |
| RTPD.PFSLFEGMAGTIYFLADLLVPEKA.FPAFEL | |
| Retrocopy | RTPDNPFSLFEGMAGTIYFLADLLVPEKAWFPAFEL |
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 | 19 .48 RPM |
| SRP021940_cerebellum | 0 .05 RPM | 172 .78 RPM |
| SRP021940_embryo | 0 .05 RPM | 45 .67 RPM |
| SRP021940_placental_villous | 0 .05 RPM | 18 .47 RPM |
| SRP021940_synovial_membrane | 0 .03 RPM | 24 .02 RPM |
| SRP021940_testis | 5 .82 RPM | 299 .77 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_944 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_944 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_944 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 | ENSECAG00000009197 | 1 retrocopy |
retro_ecab_944 ,
|
| Otolemur garnettii | ENSOGAG00000005620 | 1 retrocopy |