RetrogeneDB ID: retro_cint_17

Retrocopy location

• Organism: Vase tunicate (Ciona intestinalis)
• Coordinates: 14:4240543..4241986(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCING00000007314
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_cint_17
ATGAATATCCTTCGGCTTTTCCTGCTCGGGGTTTTGCTGAGTTGTGTCTTAGCTGTTACGGCAGACACCCCTGTAGGGCA
TCTACAAGTATTAGGCTCGCATCGGCCACCGAGTATTGACATTGACGAGTTTACGTTGGACAACGCTCCGAAGCCCGAAG
CTTTCTACCGAGATTATGTTAGAAATGGTAAAGCTGCTATATTCCGAGGCGCAGTACTCGGTTCGAAAGGATTTAATCTC
TGGACCGATGAATACATCAGAGAAAACTATGGCGAACTCGAGGCTCGGATCGAAGGAAAGAAAGAAAAAGGCGGCGGAAT
ACCCGTGGGTGAAACATACATCGGGCGAGATACACTAAGACATTTCGTTGACACGTACCATAACTCTAGCAGCTACATGG
TGTCGGAGCTACCCCAGCAGATGTTTAAAGAGGTTGGAATCATTCCGTCAGTGGGCGCTTGTGGGTTGATGGCTAAAAGG
TTCGTCGAGATTGATATTTGGTGGAACGGAGGAGGAGGAAAGAGCATCATACACAAAGATGCTTTCAATCAAATCAACTG
TTTATTCCGCGGCACCAAACAGTGGAAGCTGTTCGAGTATAAATATGAGAAGTGGATTTATAAACATGTAGAAAGAGAGG
ATGCTATTGGAGGTTTTTCTGACGTTAATGTTGATGCAGTAGATCTTATTAAACATAAAGACTTTGCGAAAATACCATGG
TCTAATATTACAATATACGCCGGTGATTGTTTGTATTTGCCCAAGAGTTATTACCACCAAGTTTACTCTGAAGGAACAAA
TAACCTCGCGGTGTCGATTCTCTTTAGTAGAATGGATGGTTTGGATGAGATAGATGTTTCAGATTGTAATGATAAGACAG
ACTATAAAGCGATAAAGCATTTGGATGAGTTTGACGTGATGTGGAAATGGAATGGCAGTGGTTACATGTCAATGGGGCGC
GGGGATTTAGTTTACGGCCACCAGCAGGACTTGATTGAGAATATCAACGACTTTGGTGAAGATCTTACTGTGGACATGTT
GTCTGAATCGCAAGGTCTCATAGCGGGGCAAGCACCTAAGGAGAAATTCCCGGACCTCGAAGCTAGGAATATTTCAAGAG
CTTTTGAGCTTCTGGACCTAAATGGGAATGGAAGATTAAGCGTTGAAGAAGTGGAGGGGGCAACATGGGACGCGCTGAGG
TATTATGGGCTACAGATTGAAGAGTACGAGCCTTCAAACTCGTACATATTCGAGTATTCTCTTATACCATATGAGAAAGT
CCGTTGGTTAGTGACTGAATGTTTCAAGAGGTATGAGAAGCTAACCAGAGCTAAGTGGGTTAAGTTGTATGTGAAAAACT
TGAAGGGTACGGAGCATTATGCCAACATTGTGTTCGATGGTTTGGCGGGTTCTGCTGACGTAGTTGTTGCTAGTGACGTC
ACA

Alignment

ORF - retro_cint_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.49 %
• Parental protein coverage: 72.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IFLFVVVFNCI---KAQDPVGHLKPLGEQTPPTVPIDEFTIDNAPRPYDFYENYVKPSKAAIFRGAMLDT
          .FL..V...C.....A..PVGHL..LG...PP...IDEFT.DNAP.P..FY..YV...KAAIFRGA.L..
Retrocopy LFLLGVLLSCVLAVTADTPVGHLQVLGSHRPPSIDIDEFTLDNAPKPEAFYRDYVRNGKAAIFRGAVLGS

Parental  SGFKLWTDEYIKENYGTMEVRTEGKKEKNSKIPVGVKYLGRDTISHFVDNYHLPNTSMYMVSELPEVMFK
          .GF.LWTDEYI.ENYG..E.R.EGKKEK...IPVG..Y.GRDT..HFVD.YH..N.S.YMVSELP..MFK
Retrocopy KGFNLWTDEYIRENYGELEARIEGKKEKGGGIPVGETYIGRDTLRHFVDTYH--NSSSYMVSELPQQMFK

Parental  EVGVLPSLGACGEMGRRFVEIDIWWNGGGGRSVIHKDAFNQLNCLYRGTKSWKLYEYKYEKWIHKHWEPE
          EVG..PS.GACG.M..RFVEIDIWWNGGGG.S.IHKDAFNQ.NCL.RGTK.WKL.EYKYEKWI.KH.E.E
Retrocopy EVGIIPSVGACGLMAKRFVEIDIWWNGGGGKSIIHKDAFNQINCLFRGTKQWKLFEYKYEKWIYKHVERE

Parental  NEVGGFSEVDVDAVDLYKHPNIAKIPWSNITINAGDCLFLPKSYYHQVHSNGEQNLAVSILFSRFDGIEH
          ...GGFS.V.VDAVDL.KH...AKIPWSNITI.AGDCL.LPKSYYHQV.S.G..NLAVSILFSR.DG...
Retrocopy DAIGGFSDVNVDAVDLIKHKDFAKIPWSNITIYAGDCLYLPKSYYHQVYSEGTNNLAVSILFSRMDGLDE

Parental  IDVSDCTDQTDYKIPRPLSEAGVMWKWCGTGMMSMGNGDFEGEYRPMLMRTIADLNEAGMDFTVDNIAEL
          IDVSDC.D.TDYK....L.E..VMWKW.G.G.MSMG.GD........L...I...N..G.D.TVD...E.
Retrocopy IDVSDCNDKTDYKAIKHLDEFDVMWKWNGSGYMSMGRGDLVYGHQQDLIENI---NDFGEDLTVDMLSES

Parental  SG
          .G
Retrocopy QG

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

6 EST(s) were mapped to retro_cint_17 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BM960146	4240530	4241046	98.7	507	7	500
BW047494	4240548	4241257	99.1	702	7	695
BW054465	4240734	4241350	98.9	609	7	602
BW099752	4240527	4240814	99	283	3	280
BW226943	4240526	4240842	99.1	313	3	310
FF881898	4240538	4241316	99.5	777	1	775

TSS

Ciona intestinalis was not studied using FANTOM5 data.

Lab

retro_cint_17 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 ,