RetrogeneDB ID: retro_onil_44

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831219.1:1943703..1944627(-)
• Located in intron of: ENSONIG00000003729

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_44
CAAATTAGTGAGAATCTGAAACTGGCCCGTGAATATGCCTTGCTGGGAAACTACAGCTCAGCCAGTGTTCTCTATCATGG
GCTGCTTGAACAAATCAAAAAATATGCGTACACGGTGCGAGACAGCAGTTTCCAGCAGAGGTGGCAGCAGCTGTGGCAGG
AAATCATCGAAGAGAATCAACAAGTTCAGGACATAATGTCAACTCTGGGGAACTTTCAGTTGGACACGGCTCCTGTTAAA
CCCAGTAACCACGATGATTTTGAAATGAGACCTTTGCATGTGGAACAGAGACACTCTCCCTGTCCTGTCAGACGTCCTAC
CAACCCCCATAAAGACAGCAAACCTGCAAACAACCGCCTGAGCGTGGCTGTGAAGGCCCAGCAGAGACACCTGCCCCAAG
GGGCCAACGGCAACAGAGGCAGACCTTCCAAGGGCAAAGAAAAGAAGGAACCAAAGGAGGCGGCTGGCAAAGCAAAGGAT
GATAAGAATAAATCAGATGTCCAGGAGAAAGAAGCATAGAGGTTTGATGGGGCAGGATATGATAAAGACCTCGTGGAAGC
TCTGGAGGGGGATATTATATCTCAAAATCCAAATATTAAATGGGATGACATCGCAGACTTGGAAGATGCAAAAAAACTGC
TGAAAGAAGCAGTTGTGTTGCCGATGTGGATGCCAGCGTTTTTTAAAGGAATTAGACGACCCTGGAAGGGTGCGCTTATG
GTGGGACCTCCTGGCACGGGGAAAACACTTCTGGCTAAAGCAGTCACTACCGAATGTAGAACCACGTTCTTCAATGTTTC
CTCATCAACTCTGACCTCTAAGTACAGAGGAGAGTCTGAGAAACTAGTTCGCCTTCTCTTTGAAATGGCACGTTTTTATG
CTCCCACCACAATCTTCATTGATGAAATTGACTCAATGTGCAGC

Alignment

ORF - retro_onil_44 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.08 %
• Parental protein coverage: 63.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EISENLKLAREYALLGNYSSASVLYHGLLEQIKKYVYTVRDSSFQQRWQQLWQEIIEENQQVQDIMSTLG
          .ISENLKLAREYALLGNYSSASVLYHGLLEQIKKY.YTVRDSSFQQRWQQLWQEIIEENQQVQDIMSTLG
Retrocopy QISENLKLAREYALLGNYSSASVLYHGLLEQIKKYAYTVRDSSFQQRWQQLWQEIIEENQQVQDIMSTLG

Parental  NFQLDTAPVKPSNHDDFEMRPLHVEQRHSPCPVRRPTNPYKDSKPANNRLSVAVKAQQRHLPRGANGDRG
          NFQLDTAPVKPSNHDDFEMRPLHVEQRHSPCPVRRPTNP.KDSKPANNRLSVAVKAQQRHLP.GANG.RG
Retrocopy NFQLDTAPVKPSNHDDFEMRPLHVEQRHSPCPVRRPTNPHKDSKPANNRLSVAVKAQQRHLPQGANGNRG

Parental  RPSKGKEKKEPKEAAGKAKDDKNKSDVQEKEAKRFDGAGYDKDLVEALERDIISQNPNIKWDDIADLEDA
          RPSKGKEKKEPKEAAGKAKDDKNKSDVQEKEA.RFDGAGYDKDLVEALE.DIISQNPNIKWDDIADLEDA
Retrocopy RPSKGKEKKEPKEAAGKAKDDKNKSDVQEKEA*RFDGAGYDKDLVEALEGDIISQNPNIKWDDIADLEDA

Parental  KKLLKEAVVLPMWMPAFFKGIRRPWKGVLMVGPPGTGKTLLAKAVATECRTTFFNVSSSTLTSKYRGESE
          KKLLKEAVVLPMWMPAFFKGIRRPWKG.LMVGPPGTGKTLLAKAV.TECRTTFFNVSSSTLTSKYRGESE
Retrocopy KKLLKEAVVLPMWMPAFFKGIRRPWKGALMVGPPGTGKTLLAKAVTTECRTTFFNVSSSTLTSKYRGESE

Parental  KLVRLLFEMARFYAPTTIFIDEIDSMCS
          KLVRLLFEMARFYAPTTIFIDEIDSMCS
Retrocopy KLVRLLFEMARFYAPTTIFIDEIDSMCS

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_44 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_44 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 ,