RetrogeneDB ID: retro_csav_7

Retrocopy location

• Organism: Pacific transparent sea squirt (Ciona savignyi)
• Coordinates: reftig_726:33665..34748(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCSAVG00000001829
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCSAVG00000003785
• Aliases: None
• Description: None

Sequence

>retro_csav_7
TACAACTTGGGAAGTCGTGGAAATGAGTTATCGACTCGAAAGATCATTTTCGCCAACTTCAACCAGGATTGCACCTCGCT
GGCTGTGGGGACCAAACATGGATACAAACTATTCGCGCTGAACTCCGTGGATACGTTGGATGTGATTTACGACAATGAGA
GCGAAACAGAAGACGTTTGTTTGGTCGATCGCTTGTTCTCAAGCAGCCTGGTTGCGATCGTGAGTCTCATGTCCCCGCGG
AAGCTGAAGGTCTGCCATTTCAAGAAAGGAACCGAGATCTGCAATTACAGCTACTCGAACACGATACTCGGGGTGAAACT
GAATCGAATCCGACTTGTGGTGGTCCTCGAAGAGAGCTTGTACATTCACAACATCAGAGACATGAAAGTGTTGCACACCA
TACGCGATACACCCAGCAATCCTAAAGGTCTCTGCTGCCTCAGTGTCAACAATGATAATTCCTTCCTTGTCTACCCAGGT
AGTAGCATAACAGGGGAAGTACAAATATTCGACGTCACCACCCTCAATGCAGTAAGCACCATCAACGCACACGATAGTCC
TCTCGCTGCTATGGCGTTCAATTCCACAGCAACTAAACTGGCAACAGCCTCCTGCAAAGGAACTGTGATCAGAGTGTTCT
CGGTGCCTGATGGACAAAAACTCTTTGAGTTCCGACGAGGGGTGAAGCGATGCGTTTCCATCGGATCCCTTGCGTTCAGC
CCCGATTCCCTCTTCCTCTGCGCCTCCAGCAACACCGAAACCGTCCACATTTTCAAACTGGAGCAAATGGGAGCTGAGAA
AGCTCCAGTGGCGGACGAATCGTCATCCTGGATGGGATATTTCAACAAAGTATTGAGCAATTCTGCCAGTTACCTTCCAA
GTCAGGTTTCCGAGGTTTTGAACCAAGGACGTGACTTCGCGACGGTGAAACTCTCGTTCCAGGGGTCGAGGAATGTTTGT
GCGATCACCACCCTGCAGAAGCTCCCTCGTGTGCTGGTGGCTGACGAGGACGGCTTCTTGTACATCTACAACCTCGACCC
GATGGATGGTGGGGAGTGCGCGTTGCTTCGACAGCACAACCTC

Alignment

ORF - retro_csav_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.92 %
• Parental protein coverage: 55.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLFANFNQDFTSLAVGGRYGYRILALNSVDNLEEIHSEE--ISDVCLVERLFSSSLVAHVSLASPRKLKV
          ..FANFNQD.TSLAVG...GY...ALNSVD.L..I...E....DVCLV.RLFSSSLVA.VSL.SPRKLKV
Retrocopy IIFANFNQDCTSLAVGTKHGYKLFALNSVDTLDVIYDNESETEDVCLVDRLFSSSLVAIVSLMSPRKLKV

Parental  CHFKKKTEICNYSYSNTILAVKLNRIRLVVLVEESLYIHNIHDMKVLHTIRDTPSNPLGICALSGNNDNA
          CHFKK.TEICNYSYSNTIL.VKLNRIRLVV..EESLYIHNI.DMKVLHTIRDTPSNP.G.C.LS.NNDN.
Retrocopy CHFKKGTEICNYSYSNTILGVKLNRIRLVVVLEESLYIHNIRDMKVLHTIRDTPSNPKGLCCLSVNNDNS

Parental  LLAYPGSPHTGEVQIFDVANLKAVTMIHAHNNPLAALAFNRLATQLATASDKGTVIRVFSVVNGNKLFEF
          .L.YPGS..TGEVQIFDV..L.AV..I.AH..PLAA.AFN..AT.LATAS.KGTVIRVFSV..G.KLFEF
Retrocopy FLVYPGSSITGEVQIFDVTTLNAVSTINAHDSPLAAMAFNSTATKLATASCKGTVIRVFSVPDGQKLFEF

Parental  RRGMKRCVSICSLAFSADSLFLAASSNTETVHLFKLE
          RRG.KRCVSI.SLAFS.DSLFL.ASSNTETVH.FKLE
Retrocopy RRGVKRCVSIGSLAFSPDSLFLCASSNTETVHIFKLE

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_7 retrocopy.

TSS

Ciona savignyi was not studied using FANTOM5 data.

Lab

retro_csav_7 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona savignyi	ENSCSAVG00000003785	1 retrocopy	retro_csav_7 ,
Monodelphis domestica	ENSMODG00000000956	1 retrocopy	retro_mdom_172,