RetrogeneDB ID: retro_csav_14

Retrocopy location

• Organism: Pacific transparent sea squirt (Ciona savignyi)
• Coordinates: reftig_0:2507888..2508308(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCSAVG00000008955
• Aliases: None
• Description: None

Sequence

>retro_csav_14
ATTCTTACAATGAGAGACACCGAGGATATATGGTTTAAGAGTTTTAAGAAACAAATAACTCAAAATACTACCTTTAAGAA
CATATTACAAACTTGTTTGTCAGTTTTAGGATTTAAACTTTTTTTATTTGGTCAAAGAATAGTTCAAGCTGGATTTGGTT
ATAAACTTGGTTTTCGAAATGATATGAATGAAATGCTATTCAAAATGCATTATCGTCGCCATAACACACATGTAATACAG
AATACCCCAAAAGCTCAGCTGTTGGTTTTCAATCTAAAAGATGGATGGGGGCCACTGTGTGAATTCCTAGAACTACCTGA
ACCTGATACTGCATTTCCACACAGAAATAAAAACGCAGGAATTACTGAGGAATACTTGAATACACATCCTGTTTTCCTGA
GAATGCAGCGTGAATCTAAA

Alignment

ORF - retro_csav_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.11 %
• Parental protein coverage: 54.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VFTMRESEEKWWESMKNQQAENSSQLVNIM--FLSPTGRRLFRYGSAIVKAVIGQDVNPTSKTLNEMLFK
          ..TMR..E..W..S.K.Q...N.....NI....LS..G..LF..G..IV.A..G..........NEMLFK
Retrocopy ILTMRDTEDIWFKSFKKQITQNTT-FKNILQTCLSVLGFKLFLFGQRIVQAGFGYKLG-FRNDMNEMLFK

Parental  MAYRRHNAHVLQNAPKDQLLVFNFKDGWDPLCQFLGVPVPKIPFPHKNKNASITTEILKTNKTALRMQQE
          M.YRRHN.HV.QN.PK.QLLVFN.KDGW.PLC.FL..P.P...FPH.NKNA.IT.E.L.T....LRMQ.E
Retrocopy MHYRRHNTHVIQNTPKAQLLVFNLKDGWGPLCEFLELPEPDTAFPHRNKNAGITEEYLNTHPVFLRMQRE

Parental  FK
          .K
Retrocopy SK

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_14 retrocopy.

TSS

Ciona savignyi was not studied using FANTOM5 data.

Lab

retro_csav_14 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ciona savignyi	ENSCSAVG00000008955	1 retrocopy	retro_csav_14 ,