RetrogeneDB ID: retro_cint_4

Retrocopy location

• Organism: Vase tunicate (Ciona intestinalis)
• Coordinates: HT000098.1:755595..757140(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCING00000008044
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCING00000004383
• Aliases: None
• Description: None

Sequence

>retro_cint_4
AATATGGATTTTCCTATTGTTGGAGTAAGTAGAGTTGATGCCAGCTCTAACGTATTTGATGGCATTATATTAGTTACGGA
TAAAATAGAAAGCATTGGCTCTGAGTTTAACTTCATTAAAGATGCTCTCCTGAAGTTGAAAAGCATTGATGATTCTGTTG
GAAAGGATGTGGCAATAGGTACAATTGATGGGCCCATGAAACGAGTTATATTTTCTCCTACTGGCCCCCTCGATCGTGAT
TATGATGACGTGAGAAGATTTGGTGATGCAGCAGGAAAGGGAGTGGAAAGGGCTTTGAGCGCTGGGTGCAAAAAACCTTT
ACTGGTTACCATAAAGGATAAAAGGTACAAGCAATGTAGTTTTGCCTCAGCAATGGGCGCGTTGCAGAAGCTTTATGTAC
CTTTAGAAATTCGAGAAGCCTTGCCAGAAAAAAAGCAAAAAGTAGAAAAGTTTGGTCTTTGGAGCAAAGAAAATGTGGAA
TATCTTGTTCAAATGACCAGTGCGTTTGAAAAAGGAAAAATAGTTTCACGGGATATTGGAGCATCAGATCCGGAAAGAAT
GGCACCACCTAAAGTGGCTGAATATGTGTTGGAAGCATTTAGAGATACATGTGTTAAAGTTACTGTTGAATCTGATTTAA
AAGTAATTGAGAAGAATTATCCATGTTTGGCTGCTGTGAATAGATGTGCAAGTGTGATTGACAGACATGGGGCAAGAGTT
GTGCGGTTGTTTTATGAGGGGGAGGGTCCAATTACCAACACTGTGTTTCTGGTTGGAAAGGGTGTTACATATGACACAGG
TGGAGCAGATGTGAAGGCTGGTGGTAACATGGCGGGCATGCACAGAGACAAATGTGGAGCTGCAACTGTGGCAGGGATTC
TTAAGATATTTGCAGAGTTGAAACCAAAGCATTTGAAAGTGTGTGGTACCATGTCTATGGTAAGAAATAGTATTGGGGCA
AATTGTTACGTTGCAGACGAGATCATTACGTCCCGTGCTGGAGTCAGACTGCGGATAGGAAACACTGATGCTGAAGGAAG
AATGGCAATGGCTGATTGCTTGTGTGAAGCTAAAGAGGAAGCATTGGCAGCGATAAATCCACAGTTATACACTCTTGCTA
CTCTCACTGGTCATGCAATCTTGGCTGTTGGGCCAAACTACACTCTAGTCATGGACAATGGTCCAGCAAAAGAAGCAAAC
AACAGCATTATGATTCAAATCAAAGGTCATGTGCTGGGTGATCCATGCGAAATGTCAACTATAAGAAGAGAAGATTATGA
GTTCCATACTGGAAAGTCAGAGTATGAGGATGTGTTGCAAGCTGGTAACAAACCTTCAACACAAACTCCAAGAGGTCATC
AAGGTCCGGCAGCGTTCCTTATCATGGCATCTGGGCTTGACAAACATGGGTTGGATTCCAACAAGCAGCTCAAGTACACA
CACGTTGACAATGCAGCAGCTGTATTTCCTTTCCCAGGTATACCCGAAGCCAAGGCAACAACAATGTTGGCTGCAAGGTA
CATCATGGAAAATCCGCACCATAAT

Alignment

ORF - retro_cint_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.56 %
• Parental protein coverage: 95.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FDGVILVCEKLDDLKDSLSFLKKPLEDLKQIDDSVGKSVTVAALDGGLKRVIFAPTGPLNRDYDDVRRFA
          FDG.ILV..K.........F.K..L..LK.IDDSVGK.V.....DG..KRVIF.PTGPL.RDYDDVRRF.
Retrocopy FDGIILVTDKIESIGSEFNFIKDALLKLKSIDDSVGKDVAIGTIDGPMKRVIFSPTGPLDRDYDDVRRFG

Parental  DAAENGIKRAIKAGCQSPVLVTVKNDKFKYASFVAALGAMQALYVPLEIREAKPEKKNKLLKLGLWSGES
          DAA..G..RA..AGC..P.LVT.K....K..SF..A.GA.Q.LYVPLEIREA.PEKK.K..K.GLWS.E.
Retrocopy DAAGKGVERALSAGCKKPLLVTIKDKRYKQCSFASAMGALQKLYVPLEIREALPEKKQKVEKFGLWSKEN

Parental  SPYLIPTVDAFESGRSLVRDIQGSDPERMAPPRVADYVTANFANTNIKVEVVSDCDYIEKNYPCLGAVNR
          ..YL.....AFE.G....RDI..SDPERMAPP.VA.YV...F..T..KV.V.SD...IEKNYPCL.AVNR
Retrocopy VEYLVQMTSAFEKGKIVSRDIGASDPERMAPPKVAEYVLEAFRDTCVKVTVESDLKVIEKNYPCLAAVNR

Parental  AAKVVPRHNARVIKLFYEGSGPITDTLFLVGKGVTYDTGGADVKAGGIMAGMHRDKGGASAVAGFFQILE
          .A.V..RH.ARV..LFYEG.GPIT.T.FLVGKGVTYDTGGADVKAGG.MAGMHRDK.GA..VAG...I..
Retrocopy CASVIDRHGARVVRLFYEGEGPITNTVFLVGKGVTYDTGGADVKAGGNMAGMHRDKCGAATVAGILKIFA

Parental  KLKPAHLKVYGTMSMVRNSIGANGYVADEIITARSGKRVRVGNTDAEGRMAMADCLCEAKEMAKNEVNPH
          .LKP.HLKV.GTMSMVRNSIGAN.YVADEIIT.R.G.R.R.GNTDAEGRMAMADCLCEAKE.A....NP.
Retrocopy ELKPKHLKVCGTMSMVRNSIGANCYVADEIITSRAGVRLRIGNTDAEGRMAMADCLCEAKEEALAAINPQ

Parental  LYTIATLTGHAIIAMGPGYSIAMDNGPAREIQNSLKLRDAGDAVGDMFEISTIRREDYVFHTGKSEYEDI
          LYT.ATLTGHAI.A.GP.Y...MDNGPA.E..NS......G...GD..E.STIRREDY.FHTGKSEYED.
Retrocopy LYTLATLTGHAILAVGPNYTLVMDNGPAKEANNSIMIQIKGHVLGDPCEMSTIRREDYEFHTGKSEYEDV

Parental  LQCNNAPSSRTPRGHQSPSAFMIMTSGLDSHGLDSDHPLKYTHLDIAGSEGKFPGIPTGAPITGLYSRYF
          LQ..N.PS..TPRGHQ.P.AF.IM.SGLD.HGLDS...LKYTH.D.A.....FPGIP.....T.L..RY.
Retrocopy LQAGNKPSTQTPRGHQGPAAFLIMASGLDKHGLDSNKQLKYTHVDNAAAVFPFPGIPEAKATTMLAARYI

Parental  V
          .
Retrocopy M

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

11 EST(s) were mapped to retro_cint_4 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AV958099	756146	756693	99.5	544	2	540
AV961888	755608	756211	99.4	598	4	593
AV962286	755592	756231	99.4	635	4	631
BW294649	755943	756537	99.2	589	5	584
BW326991	755592	756297	98.9	696	8	688
FF703946	755592	756235	99	639	4	634
FF787221	756007	756569	96.1	540	22	518
FF884043	755832	756319	97.4	480	6	470
FK143327	755608	756231	99.4	618	4	614
FK181260	755593	756144	99.3	547	4	543
FK193869	755602	756057	98.9	449	5	443

TSS

Ciona intestinalis was not studied using FANTOM5 data.

Lab

retro_cint_4 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000004383	1 retrocopy	retro_cint_4 ,
Homo sapiens	ENSG00000002549	1 retrocopy	retro_hsap_3457,
Gorilla gorilla	ENSGGOG00000001110	1 retrocopy	retro_ggor_2333,
Nomascus leucogenys	ENSNLEG00000016606	1 retrocopy	retro_nleu_2711,
Pongo abelii	ENSPPYG00000014626	1 retrocopy	retro_pabe_2858,
Pan troglodytes	ENSPTRG00000015938	1 retrocopy	retro_ptro_2344,
Rattus norvegicus	ENSRNOG00000003289	1 retrocopy	retro_rnor_1332,
Tursiops truncatus	ENSTTRG00000006175	1 retrocopy	retro_ttru_1013,