RetrogeneDB ID: | retro_eeur_159 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | scaffold_112045:19..701(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DCP2 | ||
| Ensembl ID: | ENSEEUG00000005752 | ||
| Aliases: | None | ||
| Description: | decapping mRNA 2 [Source:HGNC Symbol;Acc:24452] |
Retrocopy-Parental alignment summary:
>retro_eeur_159
AATATTGAGTGGTTCTCCATTGTGAAATTGCCCTGCTATAGAAATGATATGACCCCAAAGTCTAAACTTAGTTTGGCACC
TAACAAATTTTTTATGGACATTCCCTTTATCAGACCTTTAAGGGACTGGCTTTCTCAGAGATTTGAAGATTCTTCAGACA
GTGACAATGGATTTTCTTCAACTGGTAGCACTCCAGCTAAGCCTACATGTGGAAAAATTGAGTCGAACCAAATTTCACCA
ATGTCAGCAATTATTTCCTGAAGGTTCTCCTGGTGACCAGTGGGTAAAGCACAAGAAGGCACTTTAGCAAAAGCCATATA
ATAATCATTAGGAGATGTCTGACCTTTTTAAAGCAAGGAATCAGAGTATGAAGGGAAACGGCAGAAAACAGTACCAGGAC
TCACCTAAATAAAAAGAAAAGAACAAATGGGGTCCACAGCCAGCCAGCCAAGCAGCAGAATTCCTTGATGAAATGTGAAA
AAAAATTCATCCACAAAAACTTCAGGATAATTTTGAAACAGATGCTGTATACGACTTATCTTGCTCCAGTGAAGACCAGT
CGCTTGAACATGCCGAGGGACAGTCATCTGTGGCATGTAATGGACATTGTAAGTTTCCCTTTTAATCCAGAGCCTTTTTG
AGTGTCAAGTTTGATCATAATGCTATAATGAAAAAATTTGAA
ORF - retro_eeur_159 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.65 % |
| Parental protein coverage: | 53.66 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | NIEWFSIEKLPCHRNDMTPKSKLGLAPNKFFMAIPFIRPLKDWLSRRFGDSSDSDNGFSSTGSTPAKPT- |
| NIEWFSI.KLPC.RNDMTPKSKL.LAPNKFFM.IPFIRPL.DWLS.RF.DSSDSDNGFSSTGSTPAKPT. | |
| Retrocopy | NIEWFSIVKLPCYRNDMTPKSKLSLAPNKFFMDIPFIRPLRDWLSQRFEDSSDSDNGFSSTGSTPAKPT> |
| Parental | VEKLSRTKFRHCQQLFPEGSPGDQWVKHKQPLQQKPYNNHSEMFDLFKAKNQSMKGNGRKQYQDSP-NQK |
| VEKLSRTKF..CQQLFPEGSPGDQWVKHK..L.QKPYNNH.EM.DLFKA.NQSMKGNGRKQYQDSP.N.K | |
| Retrocopy | VEKLSRTKFHQCQQLFPEGSPGDQWVKHKKAL*QKPYNNH*EMSDLFKARNQSMKGNGRKQYQDSP>NKK |
| Parental | KRTNGVHSQPTKQQNSLMKCEKKL-HPRKLQDNFETDAVYELSCSSEDQLLEHAEGQPSVACNGHCKFPF |
| KRTNGVHSQP.KQQNSLMKC.....HP.KLQDNFETDAVY.LSCSSEDQ.LEHAEGQ.SVACNGHCKFPF | |
| Retrocopy | KRTNGVHSQPAKQQNSLMKCXXXF<HPQKLQDNFETDAVYDLSCSSEDQSLEHAEGQSSVACNGHCKFPF |
| Parental | SSRAFLSFKFDHNAIMKNLD |
| .SRAFLS.KFDHNAIMK... | |
| Retrocopy | *SRAFLSVKFDHNAIMKKFE |
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 | 0 .32 RPM | 22 .08 RPM |
| SRP017611_kidney | 0 .38 RPM | 5 .63 RPM |
| SRP017611_liver | 0 .16 RPM | 5 .14 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_159 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 | ENSEEUG00000005752 | 1 retrocopy |
retro_eeur_159 ,
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