RetrogeneDB ID: retro_onil_25

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831174.1:3883909..3884485(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSONIG00000020582
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RHOG
• Ensembl ID: ENSONIG00000007414
• Aliases: None
• Description: None

Sequence

>retro_onil_25
ATGCAGACCATAAAGTGTGTGGTGGTGGGTGACGGGGCAGTGGGTAAAACCTGCCTGCTCATCTCTTATACAACCAATGC
CTTTCCTGAAGAGTACATTCCCACAGTGTTTGACAACTACAGCGCTCAGATGAGTGTGGATGGCCGCACTGTCAGCCTCA
ACCTGTGGGACACGGCAGGCCAAGAGGAGTATGACCGCTTGCGCACTCTGTCCTATCCCCAAACCAATGTGTTCATTATA
TGCTTTTCCATTGGCAGCCCCTCCTCACACGCCAATGTCAGGCACAAGTGGCACCCTGAGGTGTCTCACCACTGCCCAAA
TGTGCCCATCCTGCTGGTAGGCACCAAGAAGGACCTAAGAAGTGATGCAGAAACGGTGAAGAAGTTAAAGGAGCAGGGCC
TGGTCCCTACAACCCAGCAGCAGGGCAATGCCCTGGCCAAGCAGATTGGGGCTGTTAAATACATGGAGTGTTCTGCACTG
CTGCAGGATGGCGTCAAGGAGGTGTTTTCTGAAGCTGTGAGGGCAGTGTTGTATCCAGTCACGAAAAAGAAAAAAGAAAA
GTGTGTGCTTTTGTAA

Alignment

ORF - retro_onil_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.01 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQTIKCVVVGDGAVGKTCLLISYTTGAFPKEYIPTVFDNYSSQLTVDGRIISLNLWDTAGQEEYDRLRTL
          MQTIKCVVVGDGAVGKTCLLISYTT.AFP.EYIPTVFDNYS.Q..VDGR..SLNLWDTAGQEEYDRLRTL
Retrocopy MQTIKCVVVGDGAVGKTCLLISYTTNAFPEEYIPTVFDNYSAQMSVDGRTVSLNLWDTAGQEEYDRLRTL

Parental  SYPQTNVFVICFSISSPASYENVKHKWHPEVSHHCPGVPILLVGTKSDLRNDAEIQRKLKEQNQAPVTHQ
          SYPQTNVF.ICFSI.SP.S..NV.HKWHPEVSHHCP.VPILLVGTK.DLR.DAE...KLKEQ...P.T.Q
Retrocopy SYPQTNVFIICFSIGSPSSHANVRHKWHPEVSHHCPNVPILLVGTKKDLRSDAETVKKLKEQGLVPTTQQ

Parental  QGAALARQIQAIRYMECSALNQEGIKEVFTEAVRAYLNPQPTVTKKPCVLL
          QG.ALA.QI.A..YMECSAL.Q.G.KEVF.EAVRA.L.P.....K..CVLL
Retrocopy QGNALAKQIGAVKYMECSALLQDGVKEVFSEAVRAVLYPVTKKKKEKCVLL

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_25 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_25 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oreochromis niloticus	ENSONIG00000007414	1 retrocopy	retro_onil_25 ,
Oreochromis niloticus	ENSONIG00000017151	1 retrocopy	retro_onil_34,
Tetraodon nigroviridis	ENSTNIG00000006325	1 retrocopy	retro_tnig_14,