RetrogeneDB ID: retro_csav_31

Retrocopy location

• Organism: Pacific transparent sea squirt (Ciona savignyi)
• Coordinates: reftig_55:1114347..1115506(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCSAVG00000007589
• Aliases: None
• Description: None

Sequence

>retro_csav_31
AAATGTGAAGTATGTGGAAAATGTTTTCAAAATCGTGATGTTTTGATGGTTCATTTGAGAACTCATACTGGAGAACGACC
TTACACATGTGATATATGCAAGAAATCCTTCAAGCAAAAGATACACTTAGATACCCACACAAAATGTCATTTTAATAATC
CAGATTTTAAGTGTAGGCTCTGTGAAAAATCGTACAATATAAAATCCGATCTAAATATACATATGAAGACTCATGCTGGA
GAGAGAGCGTATTCGTGTGATGTGTGTGACAAAACATTTGTTCATGCCGCCGGATTGAATCTCCACAAGAAACTTCACAC
TACTGAAAGGCCATACAAATGCAGTTTGTGCGAAAAATCTTTTACAAGAAGTCATCATTTGCAAATACATCACTTGAGTC
ACACTGGTCAGATGCCTTATAAATGTGATGTGTGTGAGAAAACCTTCCGACAAAGTAGCAATATGAGGTCGCACAAAGCA
ACTCACAACAAAGAAAAAACAAAAAAATGTGACATTTGTGGAAATATGTTTGCTACACAAAAAAATTTAAATATTCATCG
AAAAATTCATTCTGAACGGAGTAAAGTCAAATGCAATGTATGTGAAAAGTCATACAGCTCTGCTGCAGCCTTGAAAATAC
ACCAACGTTCACACAGTGGTGAGAGACCGTACAAATGTGAAGTTTGTCATCGAAGCTTTCGTGACGGTTCAGATCTCAAA
AAACATAAAACAATTCATACTGGAGAGAAACCTCACAAATGTGATGTATGTGAGAAATCATTCAGATCGGCCTTTGATCT
AAAAGCACATCAACTGATCCACGGTGAAGAGAGGCTGTACAAATGTGATGTCTGTGAAAAGTCGTTCCGTCAGAAACCTG
GTTTAAATTCGCACCGTAAAATTCATGATGGTGTGAAACCATTCAAGTGTAAAACATGTTAAAAATTATTTCGTACAAGT
TCAGAGATGAAGAAACACGAAAGGATTCACACCAACGAGAAACCGTTTACATGCACCATTTGCGAACGCAGCTTTCTCCA
CTCTAATTCCCTAAAACAACATGAACGAATTCACACCGGGAGAGAAACCTTACAAATGTAACATTTGCGAGAGAATGTTT
AATTGTCAAAGCAACATGAGAAAACATCAAGCAAGGCAT

Alignment

ORF - retro_csav_31 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.16 %
• Parental protein coverage: 57.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KCSFCEKSFTRSHHLKIHHMTHTGQMPYKCDVCEKTFRQSSNMRTHKATHNKEKTIKCDVCGNMFATQMH
          KC..C.K.F.....L..H..THTG..PY.CD.C.K.F.Q.....TH...H......KC..C.........
Retrocopy KCEVCGKCFQNRDVLMVHLRTHTGERPYTCDICKKSFKQKIHLDTHTKCHFNNPDFKCRLCEKSYNIKSD

Parental  LNKHQKIHSERKRPFSCDVCEKTFVYATGLNLHKKLHTAERPYKCSFCEKSFTRSHHLKIHHMTHTGQMP
          LN.H.K.H....R..SCDVC.KTFV.A.GLNLHKKLHT.ERPYKCS.CEKSFTRSHHL.IHH..HTGQMP
Retrocopy LNIHMKTHAG-ERAYSCDVCDKTFVHAAGLNLHKKLHTTERPYKCSLCEKSFTRSHHLQIHHLSHTGQMP

Parental  YKCDVCEKTFRQSSNMRTHKATHNKEKTIKCDVCENMFATQMHLNKHRKIHSERSKFKCNVCEKSYNSAL
          YKCDVCEKTFRQSSNMR.HKATHNK.....CD.C.NMFATQ..LN.HRKIHSERSK.KCNVCEKSY.SA.
Retrocopy YKCDVCEKTFRQSSNMRSHKATHNKXXXXXCDICGNMFATQKNLNIHRKIHSERSKVKCNVCEKSYSSAA

Parental  ALKIHQRSHSDERPYKCEVCDRSFRDGSVLKKHKTIHTGEKPHKCDVCEKSFRSAGYLKAHQLIHGEDRL
          ALKIHQRSHS.ERPYKCEVC.RSFRDGS.LKKHKTIHTGEKPHKCDVCEKSFRSA..LKAHQLIHGE.RL
Retrocopy ALKIHQRSHSGERPYKCEVCHRSFRDGSDLKKHKTIHTGEKPHKCDVCEKSFRSAFDLKAHQLIHGEERL

Parental  YKCDVCEKSFRQRPGLNSHRKIHEGEKPFKCETCGKLFGTSSQMKKHEKIHTDEKPFTCTICERSFLLSK
          YKCDVCEKSFRQ.PGLNSHRKIH.G.KPFKC.TC.KLF.TSS.MKKHE.IHT.EKPFTCTICERSFL.S.
Retrocopy YKCDVCEKSFRQKPGLNSHRKIHDGVKPFKCKTC*KLFRTSSEMKKHERIHTNEKPFTCTICERSFLHSN

Parental  CLKQHERIHT-GEKPYKCDICQRMFSLKCKLNIHMKTH
          .LKQHERIHT.GEKPYKC.IC.RMF........H...H
Retrocopy SLKQHERIHT>GEKPYKCNICERMFNCQSNMRKHQARH

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_31 retrocopy.

TSS

Ciona savignyi was not studied using FANTOM5 data.

Lab

retro_csav_31 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.

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008838	1 retrocopy	retro_acar_51,
Anolis carolinensis	ENSACAG00000023302	2 retrocopies	retro_acar_3, retro_acar_34,
Anolis carolinensis	ENSACAG00000026389	2 retrocopies	retro_acar_13, retro_acar_4,
Anolis carolinensis	ENSACAG00000026721	1 retrocopy	retro_acar_23,
Anolis carolinensis	ENSACAG00000026996	1 retrocopy	retro_acar_22,
Anolis carolinensis	ENSACAG00000027062	1 retrocopy	retro_acar_29,
Ciona savignyi	ENSCSAVG00000007589	2 retrocopies	retro_csav_30, retro_csav_31 ,
Equus caballus	ENSECAG00000010608	1 retrocopy	retro_ecab_68,
Equus caballus	ENSECAG00000021667	1 retrocopy	retro_ecab_560,
Macaca mulatta	ENSMMUG00000013571	1 retrocopy	retro_mmul_248,