RetrogeneDB ID: retro_onil_48

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831259.1:1429294..1429687(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF5
• Ensembl ID: ENSONIG00000013523
• Aliases: None
• Description: None

Sequence

>retro_onil_48
CGGCAGCGGGATCGAGCCACCTTCGAGTGCAACATTTGCTTGGACACTGCCAGGGACGCCGTCATCAGTCTGTGCGGACA
CCTGTTCTGCTGGCCCTGTCTTCATCAGTGGTTGGAGACACGGCCCAGCCGACAGCAGTGTCCCGTGTGCAAGGCAGGCA
TCAGCAGAGAGAAAGTAATCCCGCTATACGGCAGAGGGAGCTCCAGCCAGGAGGACCCCAGGTTGAAAACTCCACCCCGG
CCTCAGGGGCAGAGAACAGAACCCGAGAGCAGAGGCGGGATGTTCCGCGGTTTCGGGGACACCGGCTTCCACATGTCTTT
CGGCATCGGCGTGTTCCCCTTCGGCTTCTTCACAACAGTCTTCAATGCCAACGACCCCTTCCACAGAGCAGAT

Alignment

ORF - retro_onil_48 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.47 %
• Parental protein coverage: 65.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RERDRATFECNICLDTARDAVISLCGHLFCWPCLHQWLETRPSRQQCPVCKAGISREKVIPLYGRGSSSQ
          R.RDRATFECNICLDTARDAVISLCGHLFCWPCLHQWLETRPSRQQCPVCKAGISREKVIPLYGRGSSSQ
Retrocopy RQRDRATFECNICLDTARDAVISLCGHLFCWPCLHQWLETRPSRQQCPVCKAGISREKVIPLYGRGSSSQ

Parental  EDPRLKTPPRPQGQRTEPESRGGMFRGFGDTGFHMSFGIGAFPFGFFTTVFNANDPFHRAD
          EDPRLKTPPRPQGQRTEPESRGGMFRGFGDTGFHMSFGIG.FPFGFFTTVFNANDPFHRAD
Retrocopy EDPRLKTPPRPQGQRTEPESRGGMFRGFGDTGFHMSFGIGVFPFGFFTTVFNANDPFHRAD

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_48 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_48 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000016417	1 retrocopy	retro_ocun_1241,
Otolemur garnettii	ENSOGAG00000031466	1 retrocopy	retro_ogar_1951,
Oreochromis niloticus	ENSONIG00000013523	1 retrocopy	retro_onil_48 ,
Ochotona princeps	ENSOPRG00000004366	2 retrocopies	retro_opri_166, retro_opri_667,
Pan troglodytes	ENSPTRG00000018010	1 retrocopy	retro_ptro_2740,
Ictidomys tridecemlineatus	ENSSTOG00000024478	1 retrocopy	retro_itri_480,
Tupaia belangeri	ENSTBEG00000016320	1 retrocopy	retro_tbel_2183,