RetrogeneDB ID: retro_cint_2

Retrocopy location

• Organism: Vase tunicate (Ciona intestinalis)
• Coordinates: HT000075.1:477648..478827(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCING00000023628
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCING00000005258
• Aliases: None
• Description: None

Sequence

>retro_cint_2
TTGAACATCATGAAAATCGCTGCGGTATTTCTCTTGTTTGTTATTGCATGCCAAGCTGGTCATGTGATTCAACTGAAAAA
AATGAAGACCGTACGTCAGGACATGCGTGAAAAAAACACCGATTTGTCACTTCTTATGCCTCCAAAATACCTGAAATTCA
TGGCCGCAAACGCTGCCCCAGAACCACTTACAAATTACCTAGACGCTCAATATTACGGCAAAATTTATATCGGAACACCT
CCACAGCCCTTTACTGTTGTTTTTGATACAGGGTCTTCTAATCTATGGGTACCTTCTGTACATTGCGCTATAACAGATAT
CGCATGTCTTATCCATAACAAGTACAAAGCTAGTGAATCTTCCAGTTACAAATCAAACGGCACTAGTTTTGCTATACAGT
ATGGGAGTGGCAGTCTTTCTGGTTATGTCAGTAGTGATATAGTTAGCATTGCTGGCGTAAAAAGCAAAAACCAATTATTT
GCTGAAGCTACAAAAGAACCTGGTCTTACTTTCGTTGCCGCGAAATTTGACGGCATTCTTGGTATGGGCTACCCTGAGAT
TTCTGTAAACGGTATAACACCAGTGTTCAACCAAATGTTTAAGCAAGAGGCTTTGGCTCATAACCAGTTCTCGTTCTATT
TAAACCGGGACGCCAATGCTAGTTCTGGAGGGGAACTGTATCTTGGCGGTGTAGATACTAAAAAATTTACTGGCAGTTTC
AGCTACCATCCTGTTACTGTAAAAGGCTACTGGCAAATTAGTATGGACAGTGTGAGCGTAGGCAGCTCTACAAGTGCATG
CGTTTCTGGCTGCAAAGCTATCGTAGATAGCGGTACTTCACTTTTAGCTGGGCCCACTGATGAAATTGAAAAAATTAACA
AGCTTATTGGTGCAACCAAATTTCTAAACGGCGAATATATAGTTCAATGCAATAAAATGGCGACCATGCCCGATATTACA
TTCTCTTTAAGCGGTGTTAAATATATCTTGAAGCCAAACGATTATGTTATGAAAGAATCTACTGCTGGTGAAAGCATATG
CATCTCTGGTTTTATGGGTTTGGACGTTCCTCCCCCTAGAGGACCCCTCTGGATTCTCGGCGATATTTTCATGGGAAAAT
TCTACACTACGTTTGATTTTGCTAATAACAGAGTGGGATTCGCACAGTTGGCAAAATAA

Alignment

ORF - retro_cint_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.17 %
• Parental protein coverage: 89.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PSKYTQHWARQTSNEPLTNYMDAQYFGEISIGTPEQTFTVIFDTGSSNLWVPSASCPSTNYACMTHNKYN
          P.KY....A.....EPLTNY.DAQY.G.I.IGTP.Q.FTV.FDTGSSNLWVPS..C..T..AC..HNKY.
Retrocopy PPKYLKFMAANAAPEPLTNYLDAQYYGKIYIGTPPQPFTVVFDTGSSNLWVPSVHCAITDIACLIHNKYK

Parental  SAASSTYVADGEEFRIQYGTGSMVGYDSVDTVKIAGVPSTSQTFAEALEEPGITFVAAKFDGILGMGYPN
          ...SS.Y...G..F.IQYG.GS..GY.S.D.V.IAGV.S..Q.FAEA..EPG.TFVAAKFDGILGMGYP.
Retrocopy ASESSSYKSNGTSFAIQYGSGSLSGYVSSDIVSIAGVKSKNQLFAEATKEPGLTFVAAKFDGILGMGYPE

Parental  IAVNGMKPVFNQMFEQGAVDQNLFAFYLNRDPEAADGGEITLGGVNPARYVGDFNYHDVTRQGYWQIKMD
          I.VNG..PVFNQMF.Q.A...N.F.FYLNRD..A..GGE..LGGV......G.F.YH.VT..GYWQI.MD
Retrocopy ISVNGITPVFNQMFKQEALAHNQFSFYLNRDANASSGGELYLGGVDTKKFTGSFSYHPVTVKGYWQISMD

Parental  GLSIADTAKTTACNGGCQVIVDSGTSLITGPSADTDAINQAIGAIKFVQGEYLVICRRIPEMPDITFVLD
          ..S......T.AC..GC..IVDSGTSL..GP......IN..IGA.KF..GEY.V.C.....MPDITF.L.
Retrocopy SVSVG--SSTSACVSGCKAIVDSGTSLLAGPTDEIEKINKLIGATKFLNGEYIVQCNKMATMPDITFSLS

Parental  GIEYVLTPQDYVIQKQMTADGQTQCLSAFMGMDIPEPTGPLWILGDAFMGKFYTSFDFGTNQVGFAKLA
          G..Y.L.P.DYV..K..TA.G...C.S.FMG.D.P.P.GPLWILGD.FMGKFYT.FDF..N.VGFA.LA
Retrocopy GVKYILKPNDYVM-KESTA-GESICISGFMGLDVPPPRGPLWILGDIFMGKFYTTFDFANNRVGFAQLA

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

39 EST(s) were mapped to retro_cint_2 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AV675328	477610	478253	97.9	631	11	619
AV977296	477624	478240	98.8	608	8	600
AV981425	477604	478248	98.7	634	9	624
BW039129	477612	478250	100	638	0	638
BW054407	477632	478275	98.2	631	12	619
BW216633	477617	478236	98.8	611	8	603
BW216796	477646	478246	98.9	593	7	586
BW241809	477618	478267	98.4	637	11	626
BW252417	477617	478249	98.3	621	11	610
BW265294	477618	478237	98.8	611	8	603
BW281279	477617	478241	98.6	615	9	606
BW285933	477617	478267	98.2	638	12	626
BW291628	477618	478268	98.4	639	11	628
BW309675	477618	478250	98.3	621	11	610
BW340649	477617	478268	98.4	640	11	629
BW344520	477608	478251	98.7	634	9	625
BW345447	477605	478256	98.5	641	10	631
BW345884	477608	478250	98.3	631	11	620
BW348812	477617	478271	98.4	643	11	632
BW348982	477640	478271	98.8	623	8	615
BW354963	477605	478254	99	642	7	635
BW359468	477611	478251	98.3	629	11	618
BW362598	477622	478231	99.1	603	6	597
BW363437	477617	478271	99.1	648	6	642
BW364871	477608	478242	98.9	627	7	620
BW367888	477617	478231	99.1	608	6	602
BW368576	477625	478244	98.6	613	6	606
BW368644	477623	478272	99.1	643	6	637
BW370882	477608	478251	99	636	7	629
BW371750	477625	478249	98.4	614	10	604
FF803813	477611	478246	98.6	626	9	617
FF848770	477609	478243	98.9	627	7	620
FF972383	477624	478260	98.2	624	12	612
FF990195	477777	478332	98.2	547	7	539
FK161916	477611	478245	98.6	625	9	616
FK172771	477606	478252	98.7	637	9	628
FK181955	477608	478254	97.7	634	12	621
FK198630	477605	478253	98.2	636	12	624
FK219721	477608	478254	98.2	634	12	622

TSS

Ciona intestinalis was not studied using FANTOM5 data.

Lab

retro_cint_2 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010157	1 retrocopy	retro_cfam_520,
Ciona intestinalis	ENSCING00000005258	1 retrocopy	retro_cint_2 ,
Ciona savignyi	ENSCSAVG00000008457	1 retrocopy	retro_csav_8,