RetrogeneDB ID: retro_onil_42

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831204.1:2489221..2490145(-)
• Located in intron of: ENSONIG00000012653

Retrocopy information

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

Parental gene information

• Parental gene symbol: KATNA1
• Ensembl ID: ENSONIG00000011405
• Aliases: None
• Description: None

Sequence

>retro_onil_42
AGACACTCTCCCTGTCCTGTCAGACGTCCTACCAACCCCGATAAAGACAGCAAACCTGCAAACAACCGCCTGAGCATGGC
TGTGAAGGCCCAGCAGAGACACCTGCCCCGAGGGGCCAACGGCGACAGAGGCAGACCTTCCAAGGGCAAAGAAAAGAAGG
AACCAAAGGAGGCTGCTGGCAAAGCAAAGGATGATAAGAATAAATCAGATGTCCAGGAGAAAGAAGCAAAGAGGTTTGAT
GGGGCAGGATATGATAAAGACCTCATGGAAGCTCTGGAGAGGGATATTATATCTCAAAATCCAAATATTAAATGGGATGA
CATCACAGACTTGGAAGATGCAAAAAAACTGCTGAAAGAAGCAGTTGTGTTGCCGACGTGGATGCCAGCGTTTTTTAAAG
GAATTAGACGACCCTGGAAGGGTGTGCTTATGGTGGGACCTCCTGGCACGGGGAAAACACTTCTGGCTAAAGCAGTCGCT
ACCGAATGTAGAACCACGTTCTTCAATGTTTCCTCATCAACTCTGACCTCTAAGTACAGAGGAGAGTCTGAGAAACTAGT
TCGCCTTCTCTTTGAAATGGCACGTTTTTATGCTCCCACCACGATCTTCATTGATGAAATTGACTCAATGTTCAGCCGCA
GAGGAACCTCAGAGGAACATGAAGCTAGCAGGAGAGTAAAGGCAGAGCTACTTGTGCAAATGGATGCTGTTGGTGGAGCA
TCAGAGAACGACGACCCATCAAAGATGGTAATGGTCCTGGCTGCAACCAACTTTCCATGGGACATTGACGAGGCTCTGAG
GAGGCGCCTGGAGAAGCGGATCTACATTCCTCTTCCTTCAACTAAGGGGCAAGTGGAGCTGCTCAAGATTAACCTCAGGG
AGCTGGAGCTGGCCAGCGACGTGGACTTGGACAAGATCGCCGAG

Alignment

ORF - retro_onil_42 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.4 %
• Parental protein coverage: 63.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RHSPCPVRRPTNPYKDSKPANNRLSVAVKAQQRHLPRGANGDRGRPSKGKEKKEPKEAAGKAKDDKNKSD
          RHSPCPVRRPTNP.KDSKPANNRLS.AVKAQQRHLPRGANGDRGRPSKGKEKKEPKEAAGKAKDDKNKSD
Retrocopy RHSPCPVRRPTNPDKDSKPANNRLSMAVKAQQRHLPRGANGDRGRPSKGKEKKEPKEAAGKAKDDKNKSD

Parental  VQEKEAKRFDGAGYDKDLVEALERDIISQNPNIKWDDIADLEDAKKLLKEAVVLPMWMPAFFKGIRRPWK
          VQEKEAKRFDGAGYDKDL.EALERDIISQNPNIKWDDI.DLEDAKKLLKEAVVLP.WMPAFFKGIRRPWK
Retrocopy VQEKEAKRFDGAGYDKDLMEALERDIISQNPNIKWDDITDLEDAKKLLKEAVVLPTWMPAFFKGIRRPWK

Parental  GVLMVGPPGTGKTLLAKAVATECRTTFFNVSSSTLTSKYRGESEKLVRLLFEMARFYAPTTIFIDEIDSM
          GVLMVGPPGTGKTLLAKAVATECRTTFFNVSSSTLTSKYRGESEKLVRLLFEMARFYAPTTIFIDEIDSM
Retrocopy GVLMVGPPGTGKTLLAKAVATECRTTFFNVSSSTLTSKYRGESEKLVRLLFEMARFYAPTTIFIDEIDSM

Parental  CSRRGTSEEHEASRRVKAELLVQMDGVGGASENDDPSKMVMVLAATNFPWDIDEALRRRLEKRIYIPLPS
          .SRRGTSEEHEASRRVKAELLVQMD.VGGASENDDPSKMVMVLAATNFPWDIDEALRRRLEKRIYIPLPS
Retrocopy FSRRGTSEEHEASRRVKAELLVQMDAVGGASENDDPSKMVMVLAATNFPWDIDEALRRRLEKRIYIPLPS

Parental  TKGRVELLKINLRELELASDVDLDKIAE
          TKG.VELLKINLRELELASDVDLDKIAE
Retrocopy TKGQVELLKINLRELELASDVDLDKIAE

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_42 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_42 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	ENSONIG00000011405	2 retrocopies	retro_onil_42 , retro_onil_44,