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 symbol: None
• Ensembl ID: ENSCSAVG00000004748
• Aliases: None
• Description: None

Sequence

>retro_csav_22
AATTCTAAAATGTCATTTACGAAAGAAGAACTGAAAAAGAAGCTGACACCTGAGCAATACAATGTTACTCAGGAGAAAGG
CACTGAAGCACCATTCACTGGAGAATATGACAAGCATTTCCAAGCTGGAGAGTATAAGTGTGTGGTTTGTGAGACAAACT
TATTCAAATCTGACGACAAATATGATGCTGGGTGTGGATGGCCTGCATTTTCAGCAGGAGATACTTCATCTATTGACGAG
CACAAAGATGAATCGCTCGGCATGATGAGAACGGAGGTTGTGTGTAACAAGTGTCAAGCCCATCTGGGCCACAAATTCAA
CGATGGACCAAAATCTACAGGCGTGAGGTACTGTATCAACAGTGCTTCTCTGAAGTTC

Alignment

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

Expression

RNA-Seq

Ciona savignyi was not studied using RNA-Seq expression data.

ChIP-Seq

Ciona savignyi was not studied using ChIP-Seq data.

EST

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

TSS

Ciona savignyi was not studied using FANTOM5 data.

Lab

retro_csav_22 was not experimentally validated.

Homology

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.

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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 ,