RetrogeneDB ID: retro_csav_30

Retrocopy location

• Organism: Pacific transparent sea squirt (Ciona savignyi)
• Coordinates: reftig_55:1111912..1113083(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCSAVG00000001437
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_csav_30
GAAAAGAATTCGAAATGTGAAATATGTGGAAAATGTTTTCAAAATCGTGATGTTTTGATGGTTCATTTAAGAACACATAC
TGGAGAACGACCTTACACATGTGATATATGCAAGAAATCCTTTAAGCAAAAGGCACACTTAGATACCCACACAAAATTTC
ATTTTAATAATCGAGAGTTTAAATGTGGGCTCTGTGAAAAATCGTACAATATAAAATCCAATCTAAATAAACATATGAAG
ACTCATGCTGGAGAGAGAGCGTTTTCGTGTGATGTGTGTGAAAAAACATTTGTTCATGCCACCGGATTGAATCTCCACAA
GAAACTTCACACTGCTGAAAGGCCATACAAATGCAGTTTGTGCGAAAAATCTTTTACAAGAAGTCATCATTTGCAAATAC
ATCACATGACTCACACTGGTCAGATGCCTTATAAATGTGATGTGTGTGAGAAAACCTTCCGACAAAGTAGCAATATGAGG
TCGCACAAAGCAACTCACAACAAAGAAAAAACAATAAAATGTGACATTTGTGAAAATATGTTTGCTACACAAATACATCT
GAATAAACATCGAAAAATTCATTTTGAACGGAATAAAGTCAAATGCAATGTATGTGAAAAGTCATTCAGCTCTGCTCTTG
CCTTGAAAATACACCAACGTTCACACAGTGGTGATAGGCCGTACAAATGTGAAGTTTGTGATCGAAGCTTTCGTGACGGT
TCACACCTCAAAAAACATAAAACAATTCATACTGGAGAGAAACCTCACAAATGTGATGTTTGTGGAAAGTCATTTAGAAT
GATAGGAGATTTAAAAGCACATCAACTGACCCACAGCAAAGAAAGGCTGTACAAATGTGATGTCTGTGAAAAGTCGTTCC
GTCAGAAACCTGGTTTAAATTCGCACCGAAAAATCCATGATGGTGTAAAACCGTACAAGGTGTGAAACATGTGGAAAATT
ATTTCGTACAAGTTCAGAGATGAAGAAACACGAAAGGATTCACACCGACGAGAAACCGTTTACATGTACCATTTGCGAAC
GTAGCTTTCTTCACTCTAACTCCCTAAAACAACATGAACGAATTCACACCGGAGAGAAACCTTACAAATGTAACATTTGC
GAGAGAATGTTTAATTGTCAAAGCAACATGACAAAACATCAAGCAAGGCAT

Alignment

ORF - retro_csav_30 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.23 %
• Parental protein coverage: 57.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ERPYKCSFCEKSFTRSHHLKIHHMTHTGQMPYKCDVCEKTFRQSSNMRTHKATHNKEKTIKCDVCGNMFA
          E...KC..C.K.F.....L..H..THTG..PY.CD.C.K.F.Q.....TH...H......KC..C.....
Retrocopy EKNSKCEICGKCFQNRDVLMVHLRTHTGERPYTCDICKKSFKQKAHLDTHTKFHFNNREFKCGLCEKSYN

Parental  TQMHLNKHQKIHSERKRPFSCDVCEKTFVYATGLNLHKKLHTAERPYKCSFCEKSFTRSHHLKIHHMTHT
          ....LNKH.K.H....R.FSCDVCEKTFV.ATGLNLHKKLHTAERPYKCS.CEKSFTRSHHL.IHHMTHT
Retrocopy IKSNLNKHMKTHAG-ERAFSCDVCEKTFVHATGLNLHKKLHTAERPYKCSLCEKSFTRSHHLQIHHMTHT

Parental  GQMPYKCDVCEKTFRQSSNMRTHKATHNKEKTIKCDVCENMFATQMHLNKHRKIHSERSKFKCNVCEKSY
          GQMPYKCDVCEKTFRQSSNMR.HKATHNKEKTIKCD.CENMFATQ.HLNKHRKIH.ER.K.KCNVCEKS.
Retrocopy GQMPYKCDVCEKTFRQSSNMRSHKATHNKEKTIKCDICENMFATQIHLNKHRKIHFERNKVKCNVCEKSF

Parental  NSALALKIHQRSHSDERPYKCEVCDRSFRDGSVLKKHKTIHTGEKPHKCDVCEKSFRSAGYLKAHQLIHG
          .SALALKIHQRSHS..RPYKCEVCDRSFRDGS.LKKHKTIHTGEKPHKCDVC.KSFR..G.LKAHQL.H.
Retrocopy SSALALKIHQRSHSGDRPYKCEVCDRSFRDGSHLKKHKTIHTGEKPHKCDVCGKSFRMIGDLKAHQLTHS

Parental  EDRLYKCDVCEKSFRQRPGLNSHRKIHEGEKPFK-CETCGKLFGTSSQMKKHEKIHTDEKPFTCTICERS
          ..RLYKCDVCEKSFRQ.PGLNSHRKIH.G.KP.K.CETCGKLF.TSS.MKKHE.IHTDEKPFTCTICERS
Retrocopy KERLYKCDVCEKSFRQKPGLNSHRKIHDGVKPYK>CETCGKLFRTSSEMKKHERIHTDEKPFTCTICERS

Parental  FLLSKCLKQHERIHTGEKPYKCDICQRMFSLKCKLNIHMKTH
          FL.S..LKQHERIHTGEKPYKC.IC.RMF........H...H
Retrocopy FLHSNSLKQHERIHTGEKPYKCNICERMFNCQSNMTKHQARH

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_30 retrocopy.

TSS

Ciona savignyi was not studied using FANTOM5 data.

Lab

retro_csav_30 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,