RetrogeneDB ID: | retro_eeur_356 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | scaffold_268982:4030..4872(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CSGALNACT1 | ||
| Ensembl ID: | ENSEEUG00000007709 | ||
| Aliases: | None | ||
| Description: | chondroitin sulfate N-acetylgalactosaminyltransferase 1 [Source:HGNC Symbol;Acc:24290] |
Retrocopy-Parental alignment summary:
>retro_eeur_356
GTGAGGATGATTCGCCGGGGACTGCTGTCGTGGGTCTCGAGGGTGGCAGTGCTGCTTGTTCTCCTTTGCTGTGTCATCTC
CGTCCTCTACTTGCTGGCCTGCACCCCAAAAGACAACGAGGAGCAGCTGGGACTTCCCTGGGCCAATGGCCCCATAGGGA
AAGAAGGGTACCAGGCTGTCCTGCAGGAGTGGGAAGAGCAGCACCGCAACTATATCAGCAGCCTCAAGCGGCAGATCTTG
CAGCTCAAAGAGGAGCTGCAGGAGAGGAGCACGCAACTCAAGTATGCGCAGCAACAGGCCAGTGACCCTGCGGGCCTGGA
TCCAGGCCCCCCGGAGAAGACCCAGGCCGACCTGCTGGCCTTCTTGCACTCCCAGGTGGAGAGGGCGGAGGTGCATGCCG
GTGTCAAGCTGGCCACTGAGTATGCAGCCGTGCCTTTCGACAGTTTCACCCTGCAGAAAGTGTACCAATTAGAGACTGGC
CTGACTCGCCACCCCGAGGAAAAGCCAGTGAGGAAAGATAAGCGGGATGAACTGGTGGAAGCCATGGAATCTGCTCTGGA
GACCTTGAACAGCCCGGAGAAGAGCAGCCCCCATCACCGTCCTTACACCTCTTCGGATTTCATAGAAGGGATCTACCGAA
CGGAAAAGGATAAAGGCACTTTGTATGAGCTCACATTCAAAGGGGACCACAAGCATGAATTCAGAAGACTTATCTTGTTT
CGACCTTTTTGCCCCATCATGAAAGTGAAAAAGAACGACTCAACATGGCCAATATACTTATCAACGTGATCGTGCCGCTA
GCAAAGAGAGTGGACAAGTTCCAGCAGTTCATGCAGAATTTC
ORF - retro_eeur_356 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.33 % |
| Parental protein coverage: | 53.02 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | VRMIRRGLLSWVSRVAVLLVLLCCVISVLYLLACTPKGNEEQLGLPWANGPTGKEGYQAVLQEWEEQHRN |
| VRMIRRGLLSWVSRVAVLLVLLCCVISVLYLLACTPK.NEEQLGLPWANGP.GKEGYQAVLQEWEEQHRN | |
| Retrocopy | VRMIRRGLLSWVSRVAVLLVLLCCVISVLYLLACTPKDNEEQLGLPWANGPIGKEGYQAVLQEWEEQHRN |
| Parental | YISSLKRQISQLKEELQERSTQLKNAQQQASDPAGLDPGPPEKTQADLLAFLHSQVERAEVHAGVKLATE |
| YISSLKRQI.QLKEELQERSTQLK.AQQQASDPAGLDPGPPEKTQADLLAFLHSQVERAEVHAGVKLATE | |
| Retrocopy | YISSLKRQILQLKEELQERSTQLKYAQQQASDPAGLDPGPPEKTQADLLAFLHSQVERAEVHAGVKLATE |
| Parental | YAAVPCDEGALQKVYQLETGLAGHPEEKPVRKDKRDELVEAIESALETLNSPEESSPHHRPYTSSDFIEG |
| YAAVP.D...LQKVYQLETGL..HPEEKPVRKDKRDELVEA.ESALETLNSPE.SSPHHRPYTSSDFIEG | |
| Retrocopy | YAAVPFDSFTLQKVYQLETGLTRHPEEKPVRKDKRDELVEAMESALETLNSPEKSSPHHRPYTSSDFIEG |
| Parental | IYRTEKDKGTLYELTFKGDHKHEFRRLILFRPFGPIMKVK-KERLNMANTLINVIVPLAKRVDKFRQFMQ |
| IYRTEKDKGTLYELTFKGDHKHEFRRLILFRPF.PIMKVK.KERLNMAN.LINVIVPLAKRVDKF.QFMQ | |
| Retrocopy | IYRTEKDKGTLYELTFKGDHKHEFRRLILFRPFCPIMKVK<KERLNMANILINVIVPLAKRVDKFQQFMQ |
| Parental | NF |
| NF | |
| Retrocopy | NF |
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 |
|---|---|---|
| SRP017611_brain | 5 .00 RPM | 10 .15 RPM |
| SRP017611_kidney | 0 .38 RPM | 1 .69 RPM |
| SRP017611_liver | 0 .16 RPM | 0 .64 RPM |
Erinaceus europaeus was not studied using ChIP-Seq data.
Erinaceus europaeus was not studied using EST data.
Erinaceus europaeus was not studied using FANTOM5 data.
retro_eeur_356 was not experimentally validated.
Retrocopy orthology:
Erinaceus europaeus 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 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Erinaceus europaeus | ENSEEUG00000007709 | 1 retrocopy |
retro_eeur_356 ,
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