RetrogeneDB ID: retro_csav_24

Retrocopy location

• Organism: Pacific transparent sea squirt (Ciona savignyi)
• Coordinates: reftig_37:2915301..2915799(-)
• Located in intron of: ENSCSAVG00000008578

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_24
TATTTGTAGATTGTTATTAACATGTCTTATTTAACAGCTTCAAATGTGGCAACATACAAGGGTTATGAATTCAGTTTCTA
CACCAATAATGAATATTGGAAATCAACTTACGATGATGCAAAGCAAGCTTGTGTGGATGCTGGTGCTCGATTGGCTGAAA
TAAAGTCGGCTGATGTTCAAGACTTTATAACAACTCAACTAACTGACTTGGGTTTGGTGGAAAGTTTTAGTAATTGGAAA
CAAGGATATTGGATTGGTGGAGTGTGTGAGAGTGGAATTAACAATTGGAAATGGGAAGATGGGACCAGTATTGGCGGTAG
TAACTATGACAACTGGTTTGTCGGTTGTGGGCTCTCTGAACCCAATGGTAATGGAGCAACATACAGAACACATATTTTAC
CATTTGAAGACGGGAATTATGGCAGTCAAACTTGCAATGCTTTAGGAAAATGGGGGGATGATGGTAAAAAATCAAAAAAG
AATTATATTTGTATGAAA

Alignment

ORF - retro_csav_24 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.09 %
• Parental protein coverage: 58.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FLLFVVAVSAQTAPKVATYKGYEFSFYTNEASGKLTYDDAKQVCVDAGARLAEIKSADVQDFITTQLTDL
          .L..V...S..TA..VATYKGYEFSFYTN....K.TYDDAKQ.CVDAGARLAEIKSADVQDFITTQLTDL
Retrocopy YL*IVINMSYLTASNVATYKGYEFSFYTNNEYWKSTYDDAKQACVDAGARLAEIKSADVQDFITTQLTDL

Parental  GLVENWSSWAQGYWIGGVCGGGKDNWKWEDGTSIGNGTYQNWFNVASCSLLEPNSNKESDRICLFRFEEG
          GLVE..S.W.QGYWIGGVC..G..NWKWEDGTSIG...Y.NWF....C.L.EPN.N....R.....FE.G
Retrocopy GLVESFSNWKQGYWIGGVCESGINNWKWEDGTSIGGSNYDNWF--VGCGLSEPNGNGATYRTHILPFEDG

Parental  KYNFNTCNETLGKWGDVDKKSNMNWICMK
          .Y...TCN..LGKWGD.......N.ICMK
Retrocopy NYGSQTCN-ALGKWGDDGXXXXXNYICMK

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_24 retrocopy.

TSS

Ciona savignyi was not studied using FANTOM5 data.

Lab

retro_csav_24 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,