RetrogeneDB ID: retro_csav_12

Retrocopy location

• Organism: Pacific transparent sea squirt (Ciona savignyi)
• Coordinates: reftig_77:18989..20087(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCSAVG00000003142
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCSAVG00000005955
• Aliases: None
• Description: None

Sequence

>retro_csav_12
AAGCATAAAATGGCTGGCCCTTTAAACAACATGGCTGATAGGGAATTTAATCATTACGAGTTAAACAAGACTGATTGGGA
GGTGCCATCTAAATATGAAGATTTGGTTCCCATCGGTTGCGGGGCTTATGGTTCGGTGTGTTCGACTCTTAACTCCCAAC
TAAAAATGCGAATGGCGGTGAAGAAATTGGCACGGCCGTTCCAGTCGGTCACCCATGCGAAGCGCACGTACAGAGAACTG
AGATTGCTCAAGCACATGCACCATGAAAACGTGATTGGATTGCTCGACGTCTTCACCCCTGCTTCCTCGATTGAAAACTT
TACCGACATGTACCTAGTCACTCATCTTATGGGTGCGGATTTGAACCAGATCATTAAATCGCAGAAACTCACTGACGACC
ACGTGCAGTTTTTGATTTACCAGATCCTAAGAGGCCTAAAGTACATTCACTCTGCCGGCATTATTCACAGAGATTTAAAG
CCAAGTAATATCGCTGTCAACGAAGATTGCGAGTTAAAAATCCTCGATTTCGGCCTTGCGCGCTTAACAGATGATCAAAT
GACCGGTTACGTGGCGACCAGATGGTACAGAGCACCGGAGATCATGCTAAACTGGATGCATTATAACCAGACTGTTGATA
TCTGGTCTGTGGGTTGTATCATGGCGGAACTTCTAACAGGACAGACTCTTTTCCCAGGCTCCGACCACATTGATCAGTTA
AAATCCATCATGACCTTATGCGGAACGCCGAGAGATGACTTGCTTGAGAAAATCATCTCACAGTCAGCGCGGAACTTCAT
TAAAAACCTCCCCATCATTCCAAAGAAGGAATTCATCAACGTATTTGTTGGCGCGAATCCGAAAGCAGTCGATTTACTAG
AGCGCATGCTCGTGCTCGACACTGACTGCCGGTTAACAGCAAGCGAGGCGTTGCAACATCCATATTTGGAGAAATTCCAC
GACCCAGAAGATGAACCTACAGCCCCTCTGTACGACAAGACGTACGAAGACGCCGAGATTTCGATAGACGAGTGGAAGCA
ACTGGCTTACGACGAAATAGTCAACTTTAAATTTTCACCGGACCTTATAACAGATTAC

Alignment

ORF - retro_csav_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.95 %
• Parental protein coverage: 71.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ANAEFYTLQVSDSVFTVLKRYQSLKPIGSGAQGMVCAAHDTVLGQNVAIKKLSRPFQNPTHAKRAYRELV
          A..EF...........V...Y..L.PIG.GA.G.VC......L....A.KKL.RPFQ..THAKR.YREL.
Retrocopy ADREFNHYELNKTDWEVPSKYEDLVPIGCGAYGSVCSTLNSQLKMRMAVKKLARPFQSVTHAKRTYRELR

Parental  LMRAVNHKNIIGLLNVFSPQSTYEEFSHVYLVMELMDASLCQVIQ-MDLDHERLSYLLYQLLCGIKHLHS
          L.....H.N.IGLL.VF.P.S..E.F...YLV..LM.A.L.Q.I....L.......L.YQ.L.G.K..HS
Retrocopy LLKHMHHENVIGLLDVFTPASSIENFTDMYLVTHLMGADLNQIIKSQKLTDDHVQFLIYQILRGLKYIHS

Parental  AGIIHRDLKPSNIVVRSDCTLKILDFGLARTAGGSFMMTPYVVTRYYRAPEVILG-MGYQEVVDIWSVGC
          AGIIHRDLKPSNI.V..DC.LKILDFGLAR.......MT.YV.TR.YRAPE..L..M.Y...VDIWSVGC
Retrocopy AGIIHRDLKPSNIAVNEDCELKILDFGLARLTDD--QMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGC

Parental  IFGEMIRGQVLFPGTDHIDQWNKITEQLGTPSQDFINK-LQPTVRNYVLNRPM
          I..E...GQ.LFPG.DHIDQ...I....GTP..D...K......RN...N.P.
Retrocopy IMAELLTGQTLFPGSDHIDQLKSIMTLCGTPRDDLLEKIISQSARNFIKNLPI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ciona savignyi was not studied using RNA-Seq expression data.

ChIP-Seq

Ciona savignyi was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_csav_12 retrocopy.

TSS

Ciona savignyi was not studied using FANTOM5 data.

Lab

retro_csav_12 was not experimentally validated.

Homology

Retrocopy orthology:

Ciona savignyi 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.

---

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,