RetrogeneDB ID: retro_csav_32

Retrocopy location

• Organism: Pacific transparent sea squirt (Ciona savignyi)
• Coordinates: reftig_56:796092..796603(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCSAVG00000000107
• Aliases: None
• Description: None

Sequence

>retro_csav_32
CTGTTGCTTTTTCTACACTATATCCAACATGTTTTCATTACAGTACCAAAAGTGACAACATACAAGGGGTATGAGTTCAG
TTTCTACACCAATGAAGCAAGTGGTAAATTAACCTATGATGATGCAAAGCAAGTTTGTGTGGATGCTGGTGCTAGATTGG
CTGAAATAAAGTCGACTGATGTTCAAGACTTTATTACAACTCAACTAACAGACTTGGGTTTGGTAGAAGGTTTTAGTAAC
TGGGCTCAAGGTTATTGGGTTGGTGGAGTGTGTGGGGGTGATTATGGATAATTGGAAATGGGAAAATGGAACCAATATTG
GGGGTAGTAACTATGAAAACTGGTTTGTTGGTTGTGGGATCACTGAACCCAATGGTAATAAAGCAGAAAGCAGAGCATAT
GTTTATCCATTTAAGGAGGGGAATAATGACGGTCAAACATGCACAGAAACATTGGGAACTTGGGGGGATGATGATAAGTC
CAATATGAAGAACTGGATTTGCATGAAAAGT

Alignment

ORF - retro_csav_32 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.39 %
• Parental protein coverage: 59.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQLFLLFVVAVSAQTAPKVATYKGYEFSFYTNEASGKLTYDDAKQVCVDAGARLAEIKSADVQDFITTQL
          L.LFL.....V...T.PKV.TYKGYEFSFYTNEASGKLTYDDAKQVCVDAGARLAEIKS.DVQDFITTQL
Retrocopy LLLFLHYIQHVFI-TVPKVTTYKGYEFSFYTNEASGKLTYDDAKQVCVDAGARLAEIKSTDVQDFITTQL

Parental  TDLGLVENWSSWAQGYWIGGVCGGG-KDNWKWEDGTSIGNGTYQNWFNVASCSLLEPNSNKESDRICLFR
          TDLGLVE..S.WAQGYW.GGVCGG...DNWKWE.GT.IG...Y.NWF....C...EPN.NK...R.....
Retrocopy TDLGLVEGFSNWAQGYWVGGVCGGD>MDNWKWENGTNIGGSNYENWF--VGCGITEPNGNKAESRAYVYP

Parental  FEEGKYNFNTCNETLGKWGDVDKKSNMNWICMKA
          F.EG.....TC.ETLG.WGD.DK....NWICMK.
Retrocopy FKEGNNDGQTCTETLGTWGDDDKSNMKNWICMKS

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

No EST(s) were mapped for retro_csav_32 retrocopy.

TSS

Ciona savignyi was not studied using FANTOM5 data.

Lab

retro_csav_32 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona savignyi	ENSCSAVG00000000107	2 retrocopies	retro_csav_24, retro_csav_32 ,