RetrogeneDB ID: retro_csav_34

Retrocopy location

• Organism: Pacific transparent sea squirt (Ciona savignyi)
• Coordinates: reftig_77:454990..456121(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCSAVG00000004560
• Aliases: None
• Description: None

Sequence

>retro_csav_34
ATGTCAAGCAAGTCAAAACTAGACGAAAAGGTTCATGTTGCAGTGCGATGCAGACCCATGACAGCTAGTGAGAGGACCAG
CAATATAAGAAGGGCCGTGGACTGTAACTCAAAATCCCGCGAAATCAGTGTCGCCACCCATTCAAACGGCATATCATCCG
TGAATACATCAAAATCATATCATTTTGACAAGGTGTTTGGCCCAAAAGCTGAACAAATCGATGTCTACAAGAGCGTTGTG
TCAGCTCAGCTCGATGATGTTTTGGCTGGCTATAACTGCACTGTTCTTGCGTATGGACAGACGGGCACAGGTAAAACCTA
CACCATGGAAGGAGAAAGAAGCCCTAGTAAGGATTACACATGGGACAATGACCCACGTGCCGGAATTATTCCTCGTGCTC
TCAGTCAACTCTTTGATGAGTTGAATAAGAGTGGTGCAGAATACAGTGTGAGGGTTTCACTGCTAGAAATCTACAACGAA
GAGATCCACGACCTTCTTTCCCCCCTAGCCGAGCAGATTAAAATGAAAATTTATGAAGACCACCAAAAGAAAGGACATAG
TAAAGTTGTTGTGTCCGGACTTACTGATATTGTCATACGAAACAAGTCCGATATTTACGATATCTTGCAAAAGGGAGCTA
TAAAACGAAAAACGGCGGCCACTGATCTAAATGAATTCTCCAGCAGATCGCACAGCATCTGCACTGCCATCATCCACACC
AAGGACATCACACATAACAACATGGAAGAAGAAGAATTTGTTAAAATTGGGAAACTAAATCTGGTGGACCTGGCAGGAAG
CGAGAACATCGGTCGGTCAGGGGCGGTGGAGAAGAGAGCACGGGAGGCGGGAAACATCAACACCAGCTTGTTGGCATTAG
GAAGATGTATCACTGCGTTGGTGGAGAAGGCCCCACATGTCCCCTACAGAGAGAGCAAACTCACCCGACTCCTCCAAGAC
TCGCTCGGTGGAAACACGAAGACGTCGATCATCGCAACCATCTCCCCCGGCAGCGACAATGTGGAGGAAACACTCAGCAC
ACTTGACTATGCGTACCGAGCCAAGAACATCAACAACAAACCACGCGTCAACCAGAAGCTAACCAAGCGTGCTCTTATTA
AGGAATATGAC

Alignment

ORF - retro_csav_34 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.46 %
• Parental protein coverage: 98.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASKSKLDEKVHVAVRCRPMTASERTSNIRRVVDCNSKSREISVTTHSNGMGLSSANTSKSYHFDKVFGP
          M.SKSKLDEKVHVAVRCRPMTASERTSNIRR.VDCNSKSREISV.THSNG...SS.NTSKSYHFDKVFGP
Retrocopy MSSKSKLDEKVHVAVRCRPMTASERTSNIRRAVDCNSKSREISVATHSNG--ISSVNTSKSYHFDKVFGP

Parental  KAEQIDVYKSVVSAQLDDVLAGYNCTVLAYGQTGTGKTYTMEGERSPSEDYTWDNDPRAGIIPRALSQLF
          KAEQIDVYKSVVSAQLDDVLAGYNCTVLAYGQTGTGKTYTMEGERSPS.DYTWDNDPRAGIIPRALSQLF
Retrocopy KAEQIDVYKSVVSAQLDDVLAGYNCTVLAYGQTGTGKTYTMEGERSPSKDYTWDNDPRAGIIPRALSQLF

Parental  DELDKSGAEYSVRVSLLEIYNEEIHDLLSPLAEPIKMKIYEDNQKKG--KVVVSGLTEIVIRNKSDIYDI
          DEL.KSGAEYSVRVSLLEIYNEEIHDLLSPLAE.IKMKIYED.QKKG..KVVVSGLT.IVIRNKSDIYDI
Retrocopy DELNKSGAEYSVRVSLLEIYNEEIHDLLSPLAEQIKMKIYEDHQKKGHSKVVVSGLTDIVIRNKSDIYDI

Parental  LQKGAIKRKTAATDLNEFSSRSHSIFTATIHTKDITQNNMEEEELVKIGKLNLVDLAGSENIGRSGAVEK
          LQKGAIKRKTAATDLNEFSSRSHSI.TA.IHTKDIT.NNMEEEE.VKIGKLNLVDLAGSENIGRSGAVEK
Retrocopy LQKGAIKRKTAATDLNEFSSRSHSICTAIIHTKDITHNNMEEEEFVKIGKLNLVDLAGSENIGRSGAVEK

Parental  RAREAGNINTSLLALGRCITALVEKAPHVPYRESKLTRLLQDSLGGNTKTSIIATISPGSDNVEETLSTL
          RAREAGNINTSLLALGRCITALVEKAPHVPYRESKLTRLLQDSLGGNTKTSIIATISPGSDNVEETLSTL
Retrocopy RAREAGNINTSLLALGRCITALVEKAPHVPYRESKLTRLLQDSLGGNTKTSIIATISPGSDNVEETLSTL

Parental  DYACRAKNINNKPRVNQKLTKRALIKVSD
          DYA.RAKNINNKPRVNQKLTKRALIK..D
Retrocopy DYAYRAKNINNKPRVNQKLTKRALIKEYD

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_34 retrocopy.

TSS

Ciona savignyi was not studied using FANTOM5 data.

Lab

retro_csav_34 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona savignyi	ENSCSAVG00000004560	1 retrocopy	retro_csav_34 ,
Otolemur garnettii	ENSOGAG00000015192	1 retrocopy	retro_ogar_519,