RetrogeneDB ID: retro_cint_20

Retrocopy location

• Organism: Vase tunicate (Ciona intestinalis)
• Coordinates: 5:3122588..3123557(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCING00000018489
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCING00000009936
• Aliases: None
• Description: None

Sequence

>retro_cint_20
ATGGGTACTAAAGTATCGCGTAACGATTTTGAATGGGTTTACACCGACCAACCGCACGGAGATCGAAGAAGAGCAATGCT
TAAGAAGTATCCTCAAATCAAGAAGCTATTCTGTATCGACGCACACTTCAAATACGTGGTGGCAGCCATGGTAGCCGCGC
AAGTTATAGCGTGTTACTTTGTGAAGGACATGAGCTGGCCATGGATATTGGCCCTTGCTTATTTCTTTGGTGGTACCATT
AATCATTCACTTACACTTGCTATCCATGATATATCCCATAACACTGCATATGGCTACCAGCATGCCAAGTGGAATAGATA
TTTCGGCATGTTTGCCAATTTACCAATTGGTGTGCCTATGTCAATCAGTTTTAAAAAATATCACATTGATCATCATAGAT
ATCTAGGTGGAGATGTACTGGATGTTGATCTGCCGACACCAATAGAAGGATATTTATTCCGGAACAGTTTTTTGAAACTA
ATTTGGTTAATTTTGAACCCACTTTTCTACGTACTGAGACCATTAGCTGTAAATCCCAAACCACTGACAGTACTGGAGCT
TCACAATGCTGTTATTCAAGTTATATTCGATGGACTCATAATGTACTTCTTTGGGTATAAAGCTGTACTTTATCTGGTAG
TTGGCACTTTGATTTCAATGGGAATCCACCCTATTACCGGGCACTTTATTTCAGAGCATTACATGTACACAAAAGGCCAT
GAAACTTATTCTTATTATGGAATTTTGAATCTTATAACATTTAATGTAGGATATCATATGGAGCATCATGATTTTCCTGC
CATTCCCAGTTCAAAGTTGCCGCTGATGAAAAAAATTGCTCCCGATTTTTACGATGACTTGCCAAGCTATACTTCATGGT
GCAAGGTGCTGTGGGACTTTGTTTTTGATCCAGCTATTGGACCCTTTGCCAGGGTAAGAAGAGAAATTGAGTTAGAGCAA
TCGAAGATG

Alignment

ORF - retro_cint_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.32 %
• Parental protein coverage: 97.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGNIVQRSSYEWVCTDEPHATRRRAMLEKYPDLKKLMTVNPHFKWVVAAEVAFQLMMCYFVKDLSWPLLI
          MG..V.R...EWV.TD.PH..RRRAML.KYP..KKL.....HFK.VVAA.VA.Q...CYFVKD.SWP...
Retrocopy MGTKVSRNDFEWVYTDQPHGDRRRAMLKKYPQIKKLFCIDAHFKYVVAAMVAAQVIACYFVKDMSWPWIL

Parental  ITTYFIGGTINHSLTLAVHELSHNRAFGHGKHAMWNRVLAFVANFPVGVPFCVSFKKYHLEHHRQLGVDG
          ...YF.GGTINHSLTLA.H..SHN.A.G...HA.WNR.....AN.P.GVP...SFKKYH..HHR.LG.D.
Retrocopy ALAYFFGGTINHSLTLAIHDISHNTAYGY-QHAKWNRYFGMFANLPIGVPMSISFKKYHIDHHRYLGGDV

Parental  LDTDIPMEIEGNFFRTTGLKLLWVILQPLLYSARPLFINPKPLNRLDYLNLSLQILFNSLLLSSWGIKPV
          LD.D.P..IEG..FR...LKL.W.IL.PL.Y..RPL..NPKPL..L...N...Q..F..L.....G.K.V
Retrocopy LDVDLPTPIEGYLFRNSFLKLIWLILNPLFYVLRPLAVNPKPLTVLELHNAVIQVIFDGLIMYFFGYKAV

Parental  AYLLLGTAFGLGLHPLAGHFIAEHYMFLKGHETYSYYGPLNILTFNVGYHMEHHDFPSITGSKLPLVRKI
          .YL..GT....G.HP..GHFI.EHYM..KGHETYSYYG.LN..TFNVGYHMEHHDFP.I..SKLPL..KI
Retrocopy LYLVVGTLISMGIHPITGHFISEHYMYTKGHETYSYYGILNLITFNVGYHMEHHDFPAIPSSKLPLMKKI

Parental  APDFYDDLPQYSSWPKVIYDFVTDSTIGPYSRIKR
          APDFYDDLP.Y.SW.KV..DFV.D..IGP..R..R
Retrocopy APDFYDDLPSYTSWCKVLWDFVFDPAIGPFARVRR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

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

ChIP-Seq

Ciona intestinalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cint_20 retrocopy.

TSS

Ciona intestinalis was not studied using FANTOM5 data.

Lab

retro_cint_20 was not experimentally validated.

Homology

Retrocopy orthology:

Ciona intestinalis 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,