RetrogeneDB ID: | retro_csav_22 | ||
Retrocopy location | Organism: | Pacific transparent sea squirt (Ciona savignyi) | |
| Coordinates: | reftig_24:715943..716321(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCSAVG00000004748 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_csav_22
AATTCTAAAATGTCATTTACGAAAGAAGAACTGAAAAAGAAGCTGACACCTGAGCAATACAATGTTACTCAGGAGAAAGG
CACTGAAGCACCATTCACTGGAGAATATGACAAGCATTTCCAAGCTGGAGAGTATAAGTGTGTGGTTTGTGAGACAAACT
TATTCAAATCTGACGACAAATATGATGCTGGGTGTGGATGGCCTGCATTTTCAGCAGGAGATACTTCATCTATTGACGAG
CACAAAGATGAATCGCTCGGCATGATGAGAACGGAGGTTGTGTGTAACAAGTGTCAAGCCCATCTGGGCCACAAATTCAA
CGATGGACCAAAATCTACAGGCGTGAGGTACTGTATCAACAGTGCTTCTCTGAAGTTC
ORF - retro_csav_22 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 59.84 % |
| Parental protein coverage: | 78.88 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | DEQTAFSENDLREKLTPLQYHVTQEKGTEEPFTGEFNDNKEHGTYKCVVCGTTLFSSEEKYDSGSGWPSF |
| .....F....L..KLTP.QY.VTQEKGTE.PFTGE.......G.YKCVVC.T.LF.S..KYD.G.GWP.. | |
| Retrocopy | NSKMSFTKEELKKKLTPEQYNVTQEKGTEAPFTGEYDKHFQAGEYKCVVCETNLFKSDDKYDAGCGWPA- |
| Parental | FETTQKSAIQENVDKSEGRTRTEVVCKKCQAHLGHVFKDGPEPTGLRYCINSASLSF |
| F.....S.I.E..D.S.G..RTEVVC.KCQAHLGH.F.DGP..TG.RYCINSASL.F | |
| Retrocopy | FSAGDTSSIDEHKDESLGMMRTEVVCNKCQAHLGHKFNDGPKSTGVRYCINSASLKF |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Ciona savignyi was not studied using RNA-Seq expression data.
Ciona savignyi was not studied using ChIP-Seq data.
1 EST(s) were mapped to retro_csav_22 retrocopy
| EST ID | Start | End | Identity | Match | Mis-match | Score |
|---|---|---|---|---|---|---|
| BW521623 | 716089 | 716207 | 96.7 | 114 | 4 | 110 |
Ciona savignyi was not studied using FANTOM5 data.
retro_csav_22 was not experimentally validated.
Retrocopy orthology:
Ciona savignyi 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 | |
|---|---|---|---|
| Ciona savignyi | ENSCSAVG00000004748 | 1 retrocopy |
retro_csav_22 ,
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