RetrogeneDB ID: retro_cint_31

Retrocopy location

• Organism: Vase tunicate (Ciona intestinalis)
• Coordinates: HT000155.1:56392..56881(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RHYSIN2/DELTEX3-C
• Ensembl ID: ENSCING00000003195
• Aliases: None
• Description: Rhysin2/Deltex3-c protein [Source:RefSeq peptide;Acc:NP_001071963]

Sequence

>retro_cint_31
TTGAATTGCAACCATAAGTTCCATGAAGCTTGCATTAATAGAGCGTTGGCTGTTAAACCTGTGTGCCCATGTTGTAACAC
ATGTGTGGGGAAGCCACAAGGAGTTGTATTGGAAGGGGCTACTATGATGCATATGATAGAAAAGACATCGTTGCCGGGGT
ACGAGGGTTGCAACACCATCTGTATCGTATACAACATTCCTGATGGTACACAAGGAGCACAACATCCACACCCAGGGAAG
ACATACCACGGCACAAACAGGGTGGCGTATCTCCCCGATAACGAGGACGGTCGCCATGTGTTGGGGTTATTGAGCCAAGC
ATTTGTTGCCGGGTTGGTGTTCGTTGTTGGTCGTTCGTTGACTACAGGGCTCGATGACTCCATCGTGTGGAATGATATCC
ATCATAAAACTCACCACACGGGGGCGCATGGCTACCCTGACGCTGGGTATCTACAGAGGGTGAAGGAAGACTTACGCGCC
AAAGGGATT

Alignment

ORF - retro_cint_31 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.29 %
• Parental protein coverage: 87.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKCKHKFHVHCIEQALKQKSFCPMCNTPVGAPCGNQPIGGRMTWSMNNRIHLPGYDNFGAIVIRYSFSGG
          L.C.HKFH..CI..AL..K..CP.CNT.VG.P.G....G..M...M.....LPGY.....I.I.Y....G
Retrocopy LNCNHKFHEACINRALAVKPVCPCCNTCVGKPQGVVLEGATMM-HMIEKTSLPGYEGCNTICIVYNIPDG

Parental  TQQHNHPHPGQRYSGTTRIAYLPDSHEGQEVLALLTRAFDARLIFTVGRSITSGRDNQITWNDIHHKTRT
          TQ...HPHPG..Y.GT.R.AYLPD...G..VL.LL..AF.A.L.F.VGRS.T.G.D..I.WNDIHHKT..
Retrocopy TQGAQHPHPGKTYHGTNRVAYLPDNEDGRHVLGLLSQAFVAGLVFVVGRSLTTGLDDSIVWNDIHHKTH-

Parental  HGGAHGYGYPDPEYLKRVKEDLRAKGI
          H.GAH..GYPD..YL.RVKEDLRAKGI
Retrocopy HTGAH--GYPDAGYLQRVKEDLRAKGI

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_31 retrocopy.

TSS

Ciona intestinalis was not studied using FANTOM5 data.

Lab

retro_cint_31 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	ENSCING00000003195	1 retrocopy	retro_cint_31 ,