RetrogeneDB ID: retro_cint_13

Retrocopy location

• Organism: Vase tunicate (Ciona intestinalis)
• Coordinates: 9:1601143..1602604(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCING00000021397
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCING00000002368
• Aliases: None
• Description: None

Sequence

>retro_cint_13
TTAAAAATCGAACTATGTTTTATCATGTTTACTTTGTTCTCTGTCTGCTACGCAAGTGAATCTTTATTCCCTGAAGGACA
TCTCAAACCTTTTGGCTTCCACCGACCCCCCACTGTCCTCTTGGACGAATTTACGCTCGAAAATGCTCCTAAACCGGCAG
AGTTTTACGAAAATTACTTCAAAGCGATGAAGCCTGCAATTTTTCGTGGCGGTTTAGTGAATACTGATGTATTTAAGCAC
TGGACAAACGATTATCTGAAGGAACATTACGGAGACTTAGAAATGAGAGTTTTAAGATTGGATGAAAAAAAGCATGATGG
TATGTTAGCACCGTTGGGGGAGAAATATTATGGCCGGGATACGATACGACATTTTGTAGATCACTTCCAAAGCGAGGAAT
CCAACAGTTACATGGTGTCTGAGCTACCAGCTCAAATGTACAAAGAATTTCCTGTCCTGCCTTCGATTGGGGCGTGCGGA
GAATTCACGAGAAACTTTATTGAAATTAACATTTGGTGGAATAAAGGTGGAAGCTCAAGCTTGCTTCACGAGGATTCGTA
CAACCAACTCAACTGTCAACTGATTGGTAGCAAGCAATGGAAGCTAGCAGAGCCACAATACACGAAATGGGTGTATGAAC
AAGATGAATACGGTAAGGCCGCCGACGGTGGAGCTTCTTTGTTCGATCCAATGGCTGTTGATTTGATTAAATATCCGGAT
ATTGTGAAAGTTCCATGGACAAATGTGACCCTGCACGCTGGGGATTGTATATTTTTTCCAAAGAGGTATTATCATCAAGT
AAACTCGTTGGGCAATAACAGTTTATCAGTTGTTATACAATTTGGTGTTGATAATGACAAAGAGAATAGCGTGGACCAGA
GTTTTGAAGATAATACTTTAGATGTTTCAGATTGTCTTGAAAGTACGGATTACAAGACACCAAGACTGCTTAACGAATTC
GATGTAATGTGGAAATGGTATGGGGAAGGGTATATGAACTTTGGGCAAACGAGTTTTGTACATGCCAGAGAAAATTTACT
AATGGAGTTAAACAAATGTGATGGGAAGTGCAACTTTAAGGAGTTTCAAACGATTTGTGAACATCGTGCGAATTGGTGGT
GCAACTCTACTCGTGTGTTTAACTCGCTGGACACAAATAAAGACGGATTGATTACAACGGACGAAGGAAATACAGCAACC
TGGGATCAACTGCGAGTCTATGTTAAAGAAATTTCGGATTTTGAATCCATTAATTCAGTTTTTCTTGAGGCGACTCTAAT
ACCTCGAACAAATGTGGAACATTTCCTTCACATGGCACTTGGCAAAGCCGAGAACTTGAAAAGAGAAACATGGTTAAAAG
TGTACCAGAGGTTAAGAGGAACTTCTTTTATGGGAGACAGAATCTTCACGCGTCTTGTGGGTTCGAGTGAGATTAATGAA
GTCAGAAGCGAAAGCATTACG

Alignment

ORF - retro_cint_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.25 %
• Parental protein coverage: 56.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LRLIFLFVVVFNCIKAQD---PVGHLKPLGEQTPPTVPIDEFTIDNAPRPYDFYENYVKPSKAAIFRGAM
          ..L.F.....F....A.....P.GHLKP.G...PPTV..DEFT..NAP.P..FYENY.K..K.AIFRG..
Retrocopy IELCFIMFTLFSVCYASESLFPEGHLKPFGFHRPPTVLLDEFTLENAPKPAEFYENYFKAMKPAIFRGGL

Parental  LDTSGFKLWTDEYIKENYGTMEV---RTEGKKEKNSKIPVGVKYLGRDTISHFVDNYHLPNTSMYMVSEL
          ..T..FK.WT..Y.KE.YG..E....R...KK......P.G.KY.GRDTI.HFVD.........YMVSEL
Retrocopy VNTDVFKHWTNDYLKEHYGDLEMRVLRLDEKKHDGMLAPLGEKYYGRDTIRHFVDHFQSEESNSYMVSEL

Parental  PEVMFKEVGVLPSLGACGEMGRRFVEIDIWWNGGGGRSVIHKDAFNQLNCLYRGTKSWKLYEYKYEKWIH
          P..M.KE..VLPS.GACGE..R.F.EI.IWWN.GG..S..H.D..NQLNC...G.K.WKL.E..Y.KW..
Retrocopy PAQMYKEFPVLPSIGACGEFTRNFIEINIWWNKGGSSSLLHEDSYNQLNCQLIGSKQWKLAEPQYTKWVY

Parental  KHWEPENEV-GGFSEVDVDAVDLYKHPNIAKIPWSNITINAGDCLFLPKSYYHQVHSNGEQNLAVSILF
          ...E......GG.S..D..AVDL.K.P.I.K.PW.N.T..AGDC.F.PK.YYHQV.S.G...L.V.I.F
Retrocopy EQDEYGKAADGGASLFDPMAVDLIKYPDIVKVPWTNVTLHAGDCIFFPKRYYHQVNSLGNNSLSVVIQF

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_13 retrocopy.

TSS

Ciona intestinalis was not studied using FANTOM5 data.

Lab

retro_cint_13 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000002368	2 retrocopies	retro_cint_13 , retro_cint_17,