RetrogeneDB ID: retro_cint_23

Retrocopy location

• Organism: Vase tunicate (Ciona intestinalis)
• Coordinates: 11:4823873..4824602(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCING00000019488
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: JNK
• Ensembl ID: ENSCING00000009313
• Aliases: None
• Description: c-jun N-terminal kinase [Source:RefSeq peptide;Acc:NP_001071750]

Sequence

>retro_cint_23
CTTCTAAAGTATGAGGACTTGATCCCCATAGGCTGCGGTGCTTATGGGAGTGTGTGTTCTACTTATAACTCTGAGCTTAA
AATGAGAATGGCCGTCAAAAAGTTGGCAAGACCGTTTCAATCTGTGACGCACGCTAAGCGAACATACAGGGAACTGAGGT
TACTGAAACACATGCATCATGAGAATGTTATCGGGCTGTTGGACGTCTTCACACCAGCTACTACATTGGAGGGATTCACG
GACATGTACCTCGTCACACACTTAATGGGTGCAGACCTTAACCAGATCATAAAATCACAGAAGTTGACAGACGACCACGT
CCAGTTTTTAATTTATCAAATCCTAAGGGGTTTGAAGTACATTCACTCTGCAGGGATCATACATCGAGATCTCAAACCAA
GCAATATAGCAGTGAACGAAGACTGTGAACTGAAAATTCTTGACTTTGGTCTGGCTAGACTCACAGATGACCAAATGACC
GGATACGTTGCAACGCGATGGTATAGAGCGCCTGAAATTATGTTAAACTGGATGCACTACAACCAGACTGTAGATCTATG
GTCTGTTGGTTGCATTATGGCCGAGCTGCTCACTGGAAAGACCCTATTCCCAGGCTCTGATCATATTGACCAGTTAAAGT
CAATAATGAATCTTTGCGGGACGCCGAGAGAGGATTTATTGGAGAAAATAATCTCGCAATCGGCGAGAAATTTCATCAAA
ACGCTTCCC

Alignment

ORF - retro_cint_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.24 %
• Parental protein coverage: 55.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKRYQSLKPIGSGAQGMVCAAHDTVLGQHVAIKKLSRPFQNPTHAKRAYRELVLMRAVNHKNIIGLLNVF
          L..Y..L.PIG.GA.G.VC......L....A.KKL.RPFQ..THAKR.YREL.L.....H.N.IGLL.VF
Retrocopy LLKYEDLIPIGCGAYGSVCSTYNSELKMRMAVKKLARPFQSVTHAKRTYRELRLLKHMHHENVIGLLDVF

Parental  SPQSSYEDFSHVYLVMELMDASLCQVIQ-MDLDHERLSYLLYQLLCGIKHLHSAGIIHRDLKPSNIVVRS
          .P....E.F...YLV..LM.A.L.Q.I....L.......L.YQ.L.G.K..HSAGIIHRDLKPSNI.V..
Retrocopy TPATTLEGFTDMYLVTHLMGADLNQIIKSQKLTDDHVQFLIYQILRGLKYIHSAGIIHRDLKPSNIAVNE

Parental  DCTLKILDFGLARTAGGSFMMTPYVVTRYYRAPEVILG-MGYQEVVDIWSVGCIFGEMIRGQVLFPGNDH
          DC.LKILDFGLAR.......MT.YV.TR.YRAPE..L..M.Y...VD.WSVGCI..E...G..LFPG.DH
Retrocopy DCELKILDFGLARLTDD--QMTGYVATRWYRAPEIMLNWMHYNQTVDLWSVGCIMAELLTGKTLFPGSDH

Parental  IDQWNKITEQLGTPSEDFINK-LQPTVRNYVLNRP
          IDQ...I....GTP.ED...K......RN.....P
Retrocopy IDQLKSIMNLCGTPREDLLEKIISQSARNFIKTLP

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_23 retrocopy.

TSS

Ciona intestinalis was not studied using FANTOM5 data.

Lab

retro_cint_23 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000009313	1 retrocopy	retro_cint_23 ,
Ciona savignyi	ENSCSAVG00000005955	1 retrocopy	retro_csav_12,
Dasypus novemcinctus	ENSDNOG00000008538	1 retrocopy	retro_dnov_2425,
Myotis lucifugus	ENSMLUG00000014533	1 retrocopy	retro_mluc_888,