RetrogeneDB ID: retro_csav_21

Retrocopy location

• Organism: Pacific transparent sea squirt (Ciona savignyi)
• Coordinates: reftig_220:574874..575816(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCSAVG00000006912
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCSAVG00000004129
• Aliases: None
• Description: None

Sequence

>retro_csav_21
ATGGGTTCCAAAGTGTCACGTGAGGATTTCGAGTGGGTTTATACGGATCAGCCCCACGGGGATCGACGGAAAGTGATGCT
TAAGAAGTACCCTCAAATCAAGAAGTTATTTTGCACTGATTCCCACTTCACATACGTAGTAACAGCCATGGTTGCGGCAC
AAGTCATAGCTTGTTATTTTGTGAAAGACATGAGCTGGCCTTGGATTTTCGCACTTGCTTATTTCTTCGGTGGAACCATA
AACCACTCGCTGACCCTCGCGATTCATGATATTTCCCACAACACGGCTTTTGGATACAACAATGCGATATGGAACCGGTA
TTTCGGGATGTTAGCAAACTTACCCATCGGAGTTCCAATGTCAATAAGTTTCAAGAAATACCATGTTGACCACCATCGTT
ATTTAGGGGGTGATGTGCTTGATGTGGACCTTCCAACACCTTTGGAAGGATATCTTTTCCGCAACAGTTTTTTGAAGATG
ATCTGGCTTATTTTAAATCCCTTGTTTTATGTGCTTCGGCCGTTAGCTGTTAATCCCAAACCAATGACCTTGCTTGAGTT
ACATAACGCTGTTGTACAGATAATATTTGATGGCCTCATTTTATATTTCTTTGGTTACAAACCAGTTATTTACTTGATCC
TTGGCACATTGCTGTCCATGGGTCTCCACCCAATTACCGGCCACTTTATATCTGAGCACTACATGTACACAAAAGGTTTT
GAAACTTACTCGTACTATGGCTGTTTGAACCTGGTGACATTCAACGTGGGTTACCACATGGAGCATCATGATTTCCCTGC
CATCCCAGGTTCCAAGTTGCCGCTGATGAAGAAGATCGCTCCGGATTATTATGACGAGCTCCCGAGTTACACTTCCTGGT
GCAAGGTCTTGTGGGACTTTGTTTTTGACCCTGCCATTGGACCCTTCGCAAGAGTCCGACGT

Alignment

ORF - retro_csav_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.0 %
• Parental protein coverage: 98.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGNYVTRTSYEWVYTDEPHASRRKEILEKYPDMKKLMKVNPHFKWVVAAEIAFQMIMCYLVKDASWLWVF
          MG..V.R...EWVYTD.PH..RRK..L.KYP..KKL.....HF..VV.A..A.Q.I.CY.VKD.SW.W.F
Retrocopy MGSKVSREDFEWVYTDQPHGDRRKVMLKKYPQIKKLFCTDSHFTYVVTAMVAAQVIACYFVKDMSWPWIF

Parental  VITYVIGGTVNHSLTLAVHELSHNRAFGHGKHAIWNRVLAFIANLPIGVPFCVSFKKYHLEHHRKLGVDG
          ...Y..GGT.NHSLTLA.H..SHN.AFG....AIWNR.....ANLPIGVP...SFKKYH..HHR.LG.D.
Retrocopy ALAYFFGGTINHSLTLAIHDISHNTAFGYN-NAIWNRYFGMLANLPIGVPMSISFKKYHVDHHRYLGGDV

Parental  VDTDIPMPIEGKLFRTTARKLLWVILQPFLYSLRPLFINPKPLNRLDYFNLVLQILFNGFIVHSLGAKPL
          .D.D.P.P.EG.LFR....K..W.IL.P..Y.LRPL..NPKP...L...N.V.QI.F.G.I....G.KP.
Retrocopy LDVDLPTPLEGYLFRNSFLKMIWLILNPLFYVLRPLAVNPKPMTLLELHNAVVQIIFDGLILYFFGYKPV

Parental  VYLILGTFLGLGLHPISGHFIAEHYMFLKGHETYSYYGPLNTLTFNVGYHVEHHDFPSITGSRLPLVKQI
          .YLILGT.L..GLHPI.GHFI.EHYM..KG.ETYSYYG.LN..TFNVGYH.EHHDFP.I.GS.LPL.K.I
Retrocopy IYLILGTLLSMGLHPITGHFISEHYMYTKGFETYSYYGCLNLVTFNVGYHMEHHDFPAIPGSKLPLMKKI

Parental  APEFYDHLPMYSSWTKVIHDFVTDPSIGPYSRIKR
          AP..YD.LP.Y.SW.KV..DFV.DP.IGP..R..R
Retrocopy APDYYDELPSYTSWCKVLWDFVFDPAIGPFARVRR

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

3 EST(s) were mapped to retro_csav_21 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BW538930	574836	575301	97.9	455	10	445
BW571205	574832	575317	97.8	475	8	465
BW588995	574814	575269	97.9	445	10	435

TSS

Ciona savignyi was not studied using FANTOM5 data.

Lab

retro_csav_21 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 intestinalis	ENSCING00000009936	1 retrocopy	retro_cint_20,
Ciona savignyi	ENSCSAVG00000004129	1 retrocopy	retro_csav_21 ,