RetrogeneDB ID: retro_onil_34

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831245.1:1866512..1867100(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSONIG00000021413
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RAC3
• Ensembl ID: ENSONIG00000017151
• Aliases: None
• Description: ras-related C3 botulinum toxin substrate 3 (rho family, small GTP binding protein Rac3) [Source:HGNC Symbol;Acc:9803]

Sequence

>retro_onil_34
ATGAATGGCTTTCCGGAAATGTCGATTAAGTGCGTCCTAGTCGGGGACAGCGCAGTCGGAAAGACGGCGCTTCTGGTCCG
CTTCACCTCAGAGACTTTCCCTGACACCTATAAGCCCACAGTGTTTGACAACACAGGGGTGGAGGTGTACATGGACGGTA
TCCAGATCAGCCTGGGGCTGTGGGACACGGCTGGCAATGACAGCTTCAAACAGATCCGACCAAGATCATACCAGCAGGCC
GATGTCGTCCTAATCTGCTTCTCTGTGGCTAACCCCCACTCTCTCGCCAGTGTCCAGAACAAGTGGATCAATGAGGTTCG
ACAACACTTGCCAAGGGTACCGGTGCTGGTTGTGGCAACACAGACAGACTTGAGGGAAATGGGTGGGCACCGGGGCACAT
GCATCACACCAACAGAGGGTAAACATGTGGCTCAAGATGTTAGGGCTAAAGGCTATTTGGAGTGCTCCTCCTTAAGCAAC
CGCGGTGTGCAGCAGGTGTTTGAGTACGCTGTGCGGACGGTTGTTAACCAGGCCAAGAAACAGGCCAGAAGACGCATGTT
CAGCATGAACCAGTGTAAGGTCTTTTGA

Alignment

ORF - retro_onil_34 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.94 %
• Parental protein coverage: 61.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSY
          .IKCV.VGD.AVGKT.LL...T...FP..Y.PTVFDN....V..DG....LGLWDTAG.......RP.SY
Retrocopy SIKCVLVGDSAVGKTALLVRFTSETFPDTYKPTVFDNTGVEVYMDGIQISLGLWDTAGNDSFKQIRPRSY

Parental  PQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRD
          .Q.DV.LICFS...P.S...V..KW..EVR.H.P..P...V.T..DLR.
Retrocopy QQADVVLICFSVANPHSLASVQNKWINEVRQHLPRVPVLVVATQTDLRE

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_34 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_34 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 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000012902	3 retrocopies	retro_etel_1565, retro_etel_1645, retro_etel_42,
Oreochromis niloticus	ENSONIG00000007414	1 retrocopy	retro_onil_25,
Oreochromis niloticus	ENSONIG00000017151	1 retrocopy	retro_onil_34 ,
Tupaia belangeri	ENSTBEG00000007272	4 retrocopies	retro_tbel_1796, retro_tbel_2564, retro_tbel_4296, retro_tbel_9,
Takifugu rubripes	ENSTRUG00000004543	1 retrocopy	retro_trub_12,
Takifugu rubripes	ENSTRUG00000016201	1 retrocopy	retro_trub_15,