RetrogeneDB ID: retro_cint_16

Retrocopy location

• Organism: Vase tunicate (Ciona intestinalis)
• Coordinates: 11:3954037..3954763(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCING00000023055
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCING00000006307
• Aliases: None
• Description: None

Sequence

>retro_cint_16
ATTGCTGCGAAGCTCCGTGGCCCTGGATCTGGTCGGTACAAGCTACCTTCCACGTGCGGATTCAAGGGTCATGATTTCAC
TCAGCATATGAAGCCTGCCTATTCTTTTGGAAAGAGGCTCGGGAATTCTTTTATCAGCAGTAATAAGTGTAGCCCTGGGC
CTGTATATTATATCGAACCACGCTACACCAGACACGGTAAAGATGGAACGCCACATTACTCGATTCTTGGTCGGCCGCTA
AACCCAAACACCTTCAAGACCCCGGGACCCGGAAAATACCAGAACGAAAAGGTGCACCCACAAGGAGAAATACACGCGCC
GAAATATTCAATGGGATCACGCACTCGCTACCGTCAATGCGACTCCTACCCCTCACCTAACAACTACGGCCTACCAAGTT
TACTCGGAAGCAAAGTCATCAATAAAGTGTCCAGCGCAAGTTACTCTATGACGGGACGGTCTCTTACTGGTAGTTTTGAC
GAAGACCTCGCCAAGACCCCTGGCTCGGCTCGATACAGCATCGTAGATCCGAACATTTATAGAAAGCGTGCGCCCTGCTA
CTCTATGCTGGCAAGGCGATACATGCCAGGCGACAAAACAACGAAACCGGGCCCTGGTGCCCACCATCCGGAGATGGTGG
TCATTAATCGACCCAGAGCACCACAATATTCAACCGGAATCCGACACTCAGAGTACATAACGCCTTTTGTTAACGAAAGC
ACCGAT

Alignment

ORF - retro_cint_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.09 %
• Parental protein coverage: 99.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IAARERGPGPGRYALPTSVGFKGHDFTKHMKPSYSFGQRLDNSMFSKD-VSPGPKYHVNPRFTRSGPEGE
          IAA..RGPG.GRY.LP...GFKGHDFT.HMKP.YSFG.RL.NS..S....SPGP.Y...PR.TR.G..G.
Retrocopy IAAKLRGPGSGRYKLPSTCGFKGHDFTQHMKPAYSFGKRLGNSFISSNKCSPGPVYYIEPRYTRHGKDGT

Parental  PKYSMLARQPDPNVFRPPGPGTYDNHRVFPQGERAAPAYSMGGRTRYRKRDCHPAANAYTLPQLVGPKII
          P.YS.L.R...PN.F..PGPG.Y.N..V.PQGE..AP.YSMG.RTRYR..D..P..N.Y.LP.L.G.K.I
Retrocopy PHYSILGRPLNPNTFKTPGPGKYQNEKVHPQGEIHAPKYSMGSRTRYRQCDSYPSPNNYGLPSLLGSKVI

Parental  NKSAHPAYSMTGRSNIHGFDEDLARTPGPAKYNVTTPNAYRNKQPLYSMLGRNIMPGDNTRKPGPGAHSP
          NK.....YSMTGRS....FDEDLA.TPG.A.Y....PN.YR...P.YSML.R..MPGD.T.KPGPGAH.P
Retrocopy NKVSSASYSMTGRSLTGSFDEDLAKTPGSARYSIVDPNIYRKRAPCYSMLARRYMPGDKTTKPGPGAHHP

Parental  EKVYINKRKAPVVSMGIRHSEFVCPLIIDVTD
          E.V.IN...AP..S.GIRHSE...P.....TD
Retrocopy EMVVINRPRAPQYSTGIRHSEYITPFVNESTD

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_16 retrocopy.

TSS

Ciona intestinalis was not studied using FANTOM5 data.

Lab

retro_cint_16 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000006307	1 retrocopy	retro_cint_16 ,