RetrogeneDB ID: retro_onil_66

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831895.1:54195..55521(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSONIG00000013199
• Aliases: None
• Description: None

Sequence

>retro_onil_66
ATTGGTGTAGCAGTGGTTTTGATTTGTCCCGCAGAGGTTGTGGTTGGTGCCGCAGTTGTTGTGGTTGGTTCAGCAGTAGT
GGTGGTTGGGGCAGCTGTTGTTCTGGTTGGTGAAACAGTGGTTGTGGTACTTGCCACTGTTGTTGTAGTTGGTGCCACCG
TTGTTGTGGTTGGTGCCACAGTGGTTGTGGTTGGTGCCGTAGTGGTTGTGGATGGGACAGTTGATGTTGTTGTTGGTATA
GCATTGGTTGTGGTTAAGGCCGCTGTTCTTGTGACGGGAGCCACCGTTGTTGTTGTTGGTCCCGCAGTTGTTGTGGTTGG
GTCAGCTGTATTTTTAGTTGGAGCACCTGTTGTTGTTGTTAGTGCCACCGTTGTTTTGGTTGGTGTGGGAGCGGTTGTGG
ATGGGGCAGCTGTTGTTGTGGTTGGTGCCACCATGGTTGTGGTTGGTCCTGCAGTGGTTGTGGTCTGTGCCCCAGTGGTT
GTGGTTGGAGCAGTTGATGTTGTGGTTGGTGGCGCAGTGGTTGTTGTTGGTGCGGCAGTGGTTGTGCTGGGGCCAGCTGA
TCTTTTTGTTGTTGGAGCAGTGGTTTTGGTTTGTGCCGCAGAGGTTGTGGTTGATGCCGCAGTTATTGTGGTTTGGCCAG
CTGTAGTTGTAGTTGGAGCACCTGTTGTCCTTGTTGGTGCCACTGTTGTTGTGGTTGTTGGTGCAGCAGTTGTGGTTGGG
GCAGCTTTTGTTGTGGTTGTTGGAGAAGGCATTGTGTTTGGTGCCACTGTTGTCGTGGTTGGTGGCGCAGTTGTTGTGGT
TAGGGCAGTTGATGTTGTTGTTGGTAGACTAGTGGTTGTGGTTAAGGCCACTGTTGTTGTGGGTGTTGCTACAGTGGTTG
TGGTTGGTGCCACTGTTGTCGTGAATGTTTCTACAGTGGTTCTCATTGGTGAGACTGTTTTTGTGGTTGGTGGGGCAGCA
GTTGTGGTTGGGGAAGCTGTTGTTGTGGTTGGTGCCACTTATGTCGTGTTTGATATCGCAGCGGTGGTTGTGGATGGTGC
CACTGTTGTTGAGGTTTTTTACCACAGTCGTTGTTGTCGGTTCAGCATTAGCGGTGGTTGGGGCAGATGTTGTTTTGGTT
GGTGGAGCAGTGGTTGTGCTTGTGGTTGCCGCCACTGTTGTTGTGGTTGGTGTGGCAGTGGTTGTGGTTGCGGCAGTTGA
TGTTGTTAGTGGTGGTGAGTGGCTGTTTTTGTGATGGGAGCCACTGTTGTCGTTGGTGGTGCCGCAGGTGTTGTGGTTGG
GCCAGGTGTAGTCGTAGTTGGAGCACCTGTTGTCATTGTTGGTGCC

Alignment

ORF - retro_onil_66 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.25 %
• Parental protein coverage: 91.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VAAAVVVVGAVVVVVGAVVVVVGAVVVVVGATVVVVGAVVVVVWAAVVVVGAVVVVVGAAVVVVGAVVVV
          ...AVV......VVVGA.VVVVG..VVVVGA.VV.VG..VVVV.A.VVVVGA.VVVVGA.VVVVGAVVVV
Retrocopy IGVAVVLICPAEVVVGAAVVVVGSAVVVVGAAVVLVGETVVVVLATVVVVGATVVVVGATVVVVGAVVVV

Parental  VGAVVIVVAAAVVVVGAVVVVVGAVVVVVGAVVVVVGAIVFVVAAVVVVVVAVVVVVGAAVIVVGAVVVV
          .G.V..VV..A.VVV.A.V.V.GA.VVVVG..VVVVG..VF.V.A.VVVV.A.VV.VG....V.GA.VVV
Retrocopy DGTVDVVVGIALVVVKAAVLVTGATVVVVGPAVVVVGSAVFLVGAPVVVVSATVVLVGVGAVVDGAAVVV

Parental  VGAAVVVVGAVVVVVGAVVVVVWAAVVVVAAAVVVVGAVVVAVWVVVVVVGAVVVVVAAAVVVVGAVVVA
          VGA..VVVG..VVVV.A.VVVV.A..VVV..AVVVVGA.VV........V...VV.V.AA.VVV.A.V..
Retrocopy VGATMVVVGPAVVVVCAPVVVVGAVDVVVGGAVVVVGAAVVVLGPADLFVVGAVVLVCAAEVVVDAAVIV

Parental  VWAVVVVVGAVVVVVVGAAVVVVVGATVVVVVGEVVVVVVVGAVVVVVEATVVLVGAVVVVVAAVVVVVA
          VW..VVVVGA.V.V.VGA.VVVVVGA.VVV..G...VVVV....V....ATVV.VG..VVVV.AV.VVV.
Retrocopy VWPAVVVVGAPV-VLVGATVVVVVGAAVVV--GAAFVVVVGEGIVF--GATVVVVGGAVVVVRAVDVVVG

Parental  AAVVVVWAPVVVVGAVVVVVGAVVVVVGAAVVVVGAVVVVVRAVVVVVGEAVVVVGEAVVVVG-AIVVVV
          ..VVVV.A.VVV..A.VVVVGA.VVV....VV..G..V.VV....VVVGEAVVVVG...VV...A.VVV.
Retrocopy RLVVVVKATVVVGVATVVVVGATVVVNVSTVVLIGETVFVVGGAAVVVGEAVVVVGATYVVFDIAAVVVD

Parental  GATVVVV-AAVVVVVVPVVVVVGAAVVVVGTGVV--VVGAVVVVVGAAVVVVEAVVVVVGAA-VVVVAAA
          GATVV.V....VVVV.....VVGA.VV.VG..VV..VV.A.VVVVG.AVVVV.AV.VV.G...V.V....
Retrocopy GATVVEV>FTTVVVVGSALAVVGADVVLVGGAVVVLVVAATVVVVGVAVVVVAAVDVVSGGE<VAVFVMG

Parental  VVVV--GAVVVVVWAVVVVVGAAVVVVGA
          ..VV..GA..VVV...VVVVGA.VV.VGA
Retrocopy ATVVVGGAAGVVVGPGVVVVGAPVVIVGA

Legend:

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

Expression

RNA-Seq

Oreochromis niloticus was not studied using RNA-Seq expression data.

ChIP-Seq

Oreochromis niloticus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_onil_66 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_66 was not experimentally validated.

Homology

Retrocopy orthology:

Oreochromis niloticus 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oreochromis niloticus	ENSONIG00000013199	2 retrocopies	retro_onil_66 , retro_onil_67,