RetrogeneDB ID: | retro_etel_2052 | ||
Retrocopy location | Organism: | Lesser hedgehog tenrec (Echinops telfairi) | |
| Coordinates: | scaffold_42584:221..1063(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSETEG00000009460 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RAB40C | ||
| Ensembl ID: | ENSETEG00000005311 | ||
| Aliases: | None | ||
| Description: | RAB40C, member RAS oncogene family [Source:HGNC Symbol;Acc:18285] |
Retrocopy-Parental alignment summary:
>retro_etel_2052
ATGGGGACGCAGGGCAGCCCGGTGAAAGAGCTACGACTACCTGCTCAAGTTTCTGCTGGTGGGCGATAGCGACGTGGGCA
AGGGCGAGATCCTGGAGAGCCTGCAGGACGGCGCCTCCGAGTCGCCCTACGCTTACAGCAACGGCATTGACTACAAAACC
ACCACCATCCTGCTGGACGGCCGCCGAGTGAAGCTGGAGCTCTGGGACACCTCAGGCCAGGGCAGGTTCTGCACCATGTT
CAGGTCCTACTCCCGCGGCGCACAGGGCATCCTCCTAGTGTACGACATCACTAACCGCTGGTCCTTTGACGGCATCGACC
GGTGGATCAGGGCGATTGATGAGCACGCACCCGGGGTCCCCCGGATCCTGGTAGGGAACCGGCTGCACCTGGCCTTCAAG
CGGCAGGTGCCCACAGAGCAGGCGCGCGCCTACGCCGAGAAGAACTGCATGACCTTCTTTGAGGTCAGCCCGCTGTGCAA
CTTCAACGTGACGGAGTCCTTCACGGAGCTCTCGCGCATCGTGCTCATGCGCCACGGCATGGAGAAGATCTGGAGGCCCA
ACCGAGTGTTCAGTCTGCAGGACCTGTGCTGCCGTGCCATCGTGTCCTGTACGCCGGTCCACCTCATCGACAAGCTCCCG
CTGCCCGTCACCATTAAGAGCCACCTCAAGTCCTTCTCCATGGCCAACGGCATGAACGCCGTCATGATGCACGGCCGCTC
CTACTCGCTGGCGGGCGGGGGCGGGGGCGGGGGCAGCAAGGGCAGCAGCCTCAAACGCTCCCGCTCTATCCGCCCCTCCC
AGAGCCTCCCCCCAGAACTGCTCCCGCAGCAACTGTAAGATC
ORF - retro_etel_2052 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.97 % |
| Parental protein coverage: | 99.64 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MGTQGSPVK-SYDYLLKFLLVGDSDVGKGEILESLQDGASESPYAYSNGIDYKTTTILLDGRRVKLEIWD |
| MGTQGSPVK.SYDYLLKFLLVGDSDVGKGEILESLQDGASESPYAYSNGIDYKTTTILLDGRRVKLE.WD | |
| Retrocopy | MGTQGSPVK>SYDYLLKFLLVGDSDVGKGEILESLQDGASESPYAYSNGIDYKTTTILLDGRRVKLELWD |
| Parental | TSGQGRFCTIFRSYSRGAQGILLVYDITNRWSFDGIDRWIREIDEHAPGVPRILVGNRLHLAFKRQVPTE |
| TSGQGRFCT.FRSYSRGAQGILLVYDITNRWSFDGIDRWIR.IDEHAPGVPRILVGNRLHLAFKRQVPTE | |
| Retrocopy | TSGQGRFCTMFRSYSRGAQGILLVYDITNRWSFDGIDRWIRAIDEHAPGVPRILVGNRLHLAFKRQVPTE |
| Parental | QARAYAEKNCMTFFEVSPLCNFNVTESFTELSRIVLMRHGMEKIWRPNRVFSLQDLCCRAIVSCTPVHLI |
| QARAYAEKNCMTFFEVSPLCNFNVTESFTELSRIVLMRHGMEKIWRPNRVFSLQDLCCRAIVSCTPVHLI | |
| Retrocopy | QARAYAEKNCMTFFEVSPLCNFNVTESFTELSRIVLMRHGMEKIWRPNRVFSLQDLCCRAIVSCTPVHLI |
| Parental | DKLPLPVTIKSHLKSFSMANGMNAVMMHGRSYSLAGGGGGGGSKGSSLKRSRSIR-PPQSPPQNCSRSNC |
| DKLPLPVTIKSHLKSFSMANGMNAVMMHGRSYS.........SKGSSLKRSRSIR.PP...PQNCSRSNC | |
| Retrocopy | DKLPLPVTIKSHLKSFSMANGMNAVMMHGRSYSXXXXXXXXXSKGSSLKRSRSIR>PPRASPQNCSRSNC |
| Parental | KI |
| KI | |
| Retrocopy | KI |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Echinops telfairi was not studied using RNA-Seq expression data.
Echinops telfairi was not studied using ChIP-Seq data.
Echinops telfairi was not studied using EST data.
Echinops telfairi was not studied using FANTOM5 data.
retro_etel_2052 was not experimentally validated.
Retrocopy orthology:
Echinops telfairi does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000036629 | 1 retrocopy | |
| Echinops telfairi | ENSETEG00000005311 | 1 retrocopy |
retro_etel_2052 ,
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