RetrogeneDB ID: | retro_eeur_509 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | scaffold_331248:7586..8492(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SYT2 | ||
| Ensembl ID: | ENSEEUG00000015136 | ||
| Aliases: | None | ||
| Description: | synaptotagmin II [Source:HGNC Symbol;Acc:11510] |
Retrocopy-Parental alignment summary:
>retro_eeur_509
GATGACGATGCTGAAACTGGACTGACTGATGGAGAAGAAAAGGAAGAACCCAAAGAGGAGGAGAAATTGGGGAAACTTCA
ATACTCACTGGACTACGATTTCCAAAATAACCAGCTGCTGGTGGGGATCATTCAGGCTGCTGAGCTGCCTGCCCTGGACA
TGGGAGGCACGTCGGATCCTTATGTCAAAGTGTTTCTGCTACCAGACAAGAAGAAGAAGTTTGAGACAAAAGTCCATCGC
AAGACCTTTAACCCTGTCTTCAATGAGAAGTTTACCTTCAAGTTTCCCTACTCAGAACTGGGCGGCAAGACCCTGGTGAT
GGCAGTGTAGGATTTTGACGCCTTCTCCAAACATGACATCATCGGGGAATTTAAAGTCCCCATGAACACGGTAGACTGCG
GCCATGTAACAGAGGAGTGGCATGATGTGCAGAGTGCCGAGAAGGAAGAGCAAGAGAAACTGGGTGATATCTGCTTTTCC
CTTGCTACGTACCTACTGCCAGCAAGCTGACTATCGTCATTCTGAAGGCGAAGAACCTGGAGAAGATGGATGTGGGGGGC
CTATCTTATCCTTATGTGAAAATTCATCTGATGCAAAATGGCAAGAGACTGAAGAAGAAAAAGACAACAATTAAAAAGAA
CACACTTAACCCCTACTACAACGAGTCATTTAGCTTTGAAGTCCCTTTTGAGCAAATCCAGAAAGTGCAAGTGGTGGTAA
CTGTTTTGGACTATGACAAGATTGGCGAGAATGATGCCATCGGTAAGGTCTTTGTGGGCTACAGTAGCACCGGGGTGGAG
CTGTGACATTGGTCAGACATGCTTGGCCAACCCCAGGTGACCCATTGCCCAGTGGTACACCCTGCAGGTGGAGGAGGAAG
TGGATGCCATGCTGGCTGTCAAGAAG
ORF - retro_eeur_509 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.34 % |
| Parental protein coverage: | 72.14 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | DDDAETGLTEGEGEGEEEKEPENLGKLQFSLDYDFQANQLTVGVLQAAELPALDMGGTSDPYVKVFLLPD |
| DDDAETGLT.GE.E.EE.KE.E.LGKLQ.SLDYDFQ.NQL.VG..QAAELPALDMGGTSDPYVKVFLLPD | |
| Retrocopy | DDDAETGLTDGE-EKEEPKEEEKLGKLQYSLDYDFQNNQLLVGIIQAAELPALDMGGTSDPYVKVFLLPD |
| Parental | KKKKYETKVHRKTLNPAFNETFTFKVPYQELGGKTLVMAIYDFDRFSKHDIIGEVKVPMNTVDLGQPIEE |
| KKKK.ETKVHRKT.NP.FNE.FTFK.PY.ELGGKTLVMA..DFD.FSKHDIIGE.KVPMNTVD.G...EE | |
| Retrocopy | KKKKFETKVHRKTFNPVFNEKFTFKFPYSELGGKTLVMAV*DFDAFSKHDIIGEFKVPMNTVDCGHVTEE |
| Parental | WRDLQGGEKEEPEKLGDICTSLR-YVPTAGKLTVCDLEAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKK |
| W.D.Q..EKEE.EKLGDIC.SL..YVPTA.KLT...L.AKNL.KMDVGGLS.PYVKIHLMQNGKRLKKKK | |
| Retrocopy | WHDVQSAEKEEQEKLGDICFSLA<YVPTASKLTIVILKAKNLEKMDVGGLSYPYVKIHLMQNGKRLKKKK |
| Parental | TTVKKKTLNPYFNESFSFEIPFEQIQKVQVVVTVLDYDKLGKNEAIGKIFVGSNATGTELRHWSDM-LAN |
| TT.KK.TLNPY.NESFSFE.PFEQIQKVQVVVTVLDYDK.G.N.AIGK.FVG...TG.EL.HWSDM.LAN | |
| Retrocopy | TTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGENDAIGKVFVGYSSTGVEL*HWSDM>LAN |
| Parental | PRRPIAQWHSLKPEEEVDALLGKNK |
| PR.PIAQW..L..EEEVDA.L...K | |
| Retrocopy | PR*PIAQWYTLQVEEEVDAMLAVKK |
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 | 241 .56 RPM | 68 .81 RPM |
| SRP017611_kidney | 0 .38 RPM | 1 .13 RPM |
| SRP017611_liver | 0 .00 RPM | 1 .13 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_509 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 | ENSEEUG00000015136 | 1 retrocopy |
retro_eeur_509 ,
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