RetrogeneDB ID: retro_cint_11

Retrocopy location

• Organism: Vase tunicate (Ciona intestinalis)
• Coordinates: HT000074.1:187642..188548(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCING00000003470
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCING00000003072
• Aliases: None
• Description: None

Sequence

>retro_cint_11
ATGTCAAACGTCACTTCAAAGTCAATGTCAAAGAAATTCTGTGAAAAAAATGAAGAAAAAGGTAATTGCTGCAAATACTG
CGACAAAGTATTTCGTTTTCCTTCAAAGCTTGTTATTCACTTGAGAACACATACTGGAGAAAAACTTTTTCAATGCGATA
TTTGTGACAAATCATTTACAATAAATGGTAGCTTAAGACGTCACCAAAAAGTCCACACTGGTGAGAACCCATACACGTGC
AATATTTGTGACAAACCGTTTACTACAACTAATAGATTAAACACTCACCAAAGAATTCACACTGGTGAGAAGCCTTACAA
ATGCGCCTTTTGTGACAAATCTTTTTCTGAAAGTGGTAGCTTAAGATGCCACCAAAGGGTCCACACTGGTGAGAAGCCAT
ACAAATGCGACATTTGTGAAAGGACGTTTTCTGAAAATGGTAGCTTAAGAAGCCACCAGAGAGTTCACACTGGTGAGAAG
CCATACAAATGCGACATCTGTGACAAATCGTTTGTTCAACAATGTCATTTAAGAAGGCACCAAAGGGTTCACACTGGTGA
GAAGCCTTACAAATGCGACATTTGTGAAAAATCTTTTGTTCAAAGTGGTAACCTAAAAACCCACCAAAGGGTTCACACTG
GTGAGAAGCCATACAAGTGCGACATTTGTGGAAAATCGTTTTCTGATGGCAGCATCTTAAGAAGTCATCAAAGAACCCAC
ACTGGTGAGAAGCTACACAAATGCAACATTTGTAAAAAATGTTTCGGTGAAAATAGTAAATTAAGAAGACACCAACGAGT
TCACATTGGTGAAAAGCCATACAAATGCGACATTTGTGAAATATCGTTTGTTCAAAGTTGTAACTTAAGAAGGCATCAAG
GAATTCATGGTGAGAAGCCATGTTAA

Alignment

ORF - retro_cint_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.41 %
• Parental protein coverage: 99.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSEVSSKSVLKKFSRKTKQKEICCKYCDKVYNCHSKLVIHVRTHTGEKPFKCDICEKSFSGNSSLKIHQR
          MS.V.SKS..KKF..K...K..CCKYCDKV....SKLVIH.RTHTGEK.F.CDIC.KSF..N.SL..HQ.
Retrocopy MSNVTSKSMSKKFCEKNEEKGNCCKYCDKVFRFPSKLVIHLRTHTGEKLFQCDICDKSFTINGSLRRHQK

Parental  THTGEKPYICNICEKAFTTNGHLKSHQRMHTGEKPYQCKLCEKSFAANRTLRDHQAVHTGKKAYQCNICE
          .HTGE.PY.CNIC.K.FTT...L..HQR.HTGEKPY.C..C.KSF.....LR.HQ.VHTG.K.Y.C.ICE
Retrocopy VHTGENPYTCNICDKPFTTTNRLNTHQRIHTGEKPYKCAFCDKSFSESGSLRCHQRVHTGEKPYKCDICE

Parental  RLFTTNSHLRDHQRLHSGQRPYKCNLCEKAFTRSSNLKIHQKFHTGEKPYKCDLCERAFSASSNLKSHNH
          R.F..N..LR.HQR.H.G..PYKC..C.K.F.....L..HQ..HTGEKPYKCD.CE..F..S.NLK...H
Retrocopy RTFSENGSLRSHQRVHTGEKPYKCDICDKSFVQQCHLRRHQRVHTGEKPYKCDICEKSFVQSGNLKT--H

Parental  ELIHTGEKPYQCNICGKSFAKNSFLKGHQKVHTGEKPHQCNICDRSFSTNGILTRHHKVHTGEKPYQCEI
          ...HTGEKPY.C.ICGKSF...S.L..HQ..HTGEK.H.CNIC...F..N..L.RH..VH.GEKPY.C.I
Retrocopy QRVHTGEKPYKCDICGKSFSDGSILRSHQRTHTGEKLHKCNICKKCFGENSKLRRHQRVHIGEKPYKCDI

Parental  CQKSFSTTTKLKYHQRVHTGEKP
          C..SF.....L..HQ..H.GEKP
Retrocopy CEISFVQSCNLRRHQGIH-GEKP

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_11 retrocopy.

TSS

Ciona intestinalis was not studied using FANTOM5 data.

Lab

retro_cint_11 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	ENSCING00000003072	1 retrocopy	retro_cint_11 ,
Ficedula albicollis	ENSFALG00000008344	1 retrocopy	retro_falb_4,