RetrogeneDB ID: retro_cint_5

Retrocopy location

• Organism: Vase tunicate (Ciona intestinalis)
• Coordinates: 14:2207730..2208813(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCING00000002259
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCING00000021861
• Aliases: None
• Description: None

Sequence

>retro_cint_5
ATGTCTGTTCAGGAAAACTTGAGCGCTGTCCTTTATAGAAAGCGCGAGGAATACCCTCAATGTGATATTGTCTTGGAAAA
TCGAAGCATTGTTGAGCCAAAAGAAAATGAAGTACTGCTTCAAATGCATTCTGTTGGCATTTGTGGGTCAGATGTTTCTT
ACTGGGTGAAAGGACGGATAGGTGACTTTATTGTGAATGACCCGATGGTAATTGGCCATGAGGCTGCAGGCAGGGTCGTT
AGGTGTGGAAAAAATGTCACTCATCTTAAACCTGGAGATAGGGTGGCCATTGAGCCAGGGTACCCTCTTCATAATGATGA
CTTTTTCAAGAAAGGTCGGTACAACTTAAGTGAAGTTTTCTTCTGTGCCACCCCGCCAGATGATGGTAACTTGTCGCGGT
TTTACACCCACAATGCTGATTTCTGCTACAAACTCCCTGATAATGTGTCATATGAAGAAGGTGCTCTAATAGAACCACTT
TCAGTTGGCATTCATGCGTGTCGACGGGCAGAGATCACTCTTGGTCATAATGTGTTTATTTGTGGAGCTGGTCCAATTGG
CCTTGTGTCTCTCCTGGTTGCCAAGGCCATGGGAGCATCAAAAATCGTAATATCCGATTTATTTCCAAAGCGTTTGGAAA
TGGCTAAACAACTAGGTGCAGATGAAGTGATTAAAGTGAATATCGGCGATGACGCTAAAACGGTCGCGTCTAAAGTAGAG
TGTTTACTCGGAGCTATGCCAGACCGTACAATAGAGTGCACAGGGGCGGAATCGGCGATCCAGACCGGAATCTACGCAAC
TAAGTCTGGCGGCTGCTTGTTGCTTGTGGGCTTAGGTCCAGCGATGGTAAATGTGCCAATTGTGAACGCGGCGGTTCGTG
AAGTCGACATACGCGGCGTGTTTAGATATTGCAATACGTACCCGACAGCAATTCAAATGCTGGCTTCACGCCAAGTCGAC
GTAACGCCGCTTGTCACACATCGATTTAAGTTGGAAGAAGTACAAAAAGCGTTTGAGGTGACAAGAGCTGGTGAGGGGAT
AAAAGTCATGTTAAAGTGTGACCCCAATGACCAAGGCATATAA

Alignment

ORF - retro_cint_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.39 %
• Parental protein coverage: 55.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IELAKWKLPELKNNDVLLSISAVGICGSDLKYWAYGKCGRFNLEGKPMVIGHEAAGVVVQVGSSVKSLQV
          I.L......E.K.N.VLL....VGICGSD..YW..G..G.F.....PMVIGHEAAG.VV..G..V..L..
Retrocopy IVLENRSIVEPKENEVLLQMHSVGICGSDVSYWVKGRIGDF-IVNDPMVIGHEAAGRVVRCGKNVTHLKP

Parental  GDRVAIEPGVSCKTCSHCKSGRYNLCPEMRFCATPPVHGNLCQYFVHDADFCFKLPPNVSDEEGAMIEPL
          GDRVAIEPG.........K.GRYNL..E..FCATPP..GNL.....H.ADFC.KLP.NVS.EEGA.IEPL
Retrocopy GDRVAIEPGYPLHNDDFFKKGRYNLS-EVFFCATPPDDGNLSRFYTHNADFCYKLPDNVSYEEGALIEPL

Parental  SVAVHTCRRACVTSGHHVLIFGCGPIGILCGLVAKHYGATQVTIVDIDQDRLEVAKKLGAADVV
          SV..H.CRRA..T.GH.V.I.G.GPIG....LVAK..GA....I.D....RLE.AK.LGA..V.
Retrocopy SVGIHACRRAEITLGHNVFICGAGPIGLVSLLVAKAMGASKIVISDLFPKRLEMAKQLGADEVI

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_5 retrocopy.

TSS

Ciona intestinalis was not studied using FANTOM5 data.

Lab

retro_cint_5 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 5 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000025496	1 retrocopy	retro_btau_1805,
Ciona intestinalis	ENSCING00000021861	1 retrocopy	retro_cint_5 ,
Mustela putorius furo	ENSMPUG00000010850	1 retrocopy	retro_mputfur_201,
Mus musculus	ENSMUSG00000027227	2 retrocopies	retro_mmus_2795, retro_mmus_505,
Rattus norvegicus	ENSRNOG00000017291	7 retrocopies	retro_rnor_1272, retro_rnor_1813, retro_rnor_2021, retro_rnor_2022, retro_rnor_2023, retro_rnor_2024, retro_rnor_2857,