RetrogeneDB ID: retro_onil_7

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831244.1:1287416..1288856(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSONIG00000020489
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: KCNS1
• Ensembl ID: ENSONIG00000005340
• Aliases: None
• Description: None

Sequence

>retro_onil_7
ATGACAGGTCAGGTCCTGGGGGAACCGTGCGGCGGGGCTCACACGGATGAAAACGCCGCCATCCGCATCAACGTGGGCGG
CTTCAAGAAACGTCTCCAGTCGGACACTCTCTCCCGGTTTCCCGAGACCAGGCTCGCGCGTCTGCTCCACTGCCAGTCCA
AAGAGTCCATCCTGGAACTGTGCGATGACTACGACGACACGGAGAAAGAGTTTTACTTCGACAGGAACCCAGCGCTCTTT
CCCTACGTGTTGAATTTTTACAACACGGGGCGGCTCCACGTCATGGCCGAGCTCTGCATCTTCTCTTTCAGCCAGGAGAT
CGAGTACTGGGGCATTAACGAGTTCTTCATCGACTCCTGCTGCAGCAGCTCCTACCACTGTAGGAAAATGGACCAGGACC
GGGAGGACTGGGATGACCGCAGCGATGAAGGAAGCACCACTTCATCTTTTGACGAGCTGTTGGAGTTTTACAACGACGCC
TCCAAGTTTGATAAGCAGCTGCTCGGGAGCGCACGGAGGCGCATCTGGTTGATGCTGGATAACCCCGGCTACTCCGTGGC
CAGCCGCATCATCAGCATCCTCTCCATCCTGGTGGTGCTCGGCTCCATAGCCACTATGTGCATGAACAGTATGAGTGACT
TCAGCCTGCTGGACAGCGAAGGCCAGCCCACAGAGGACCCACGTTTCGAAACTGTGGAGCACTTTGGTATCGGCTGGTTC
ACTCTGGAGCTGGTGGCCAGGTTCGTTGTGGCGCCAGATCTGCTGCACTTCTTCGATCATCCGTTAAATGTGATAGACCT
GGTGTCCATACTTCCGTTTTACCTGACACTTCTTATAAACCTGGTGGTGGAGAGCAGCCCCGCACTGGCAAACCTAGGAC
GCGTTGCGCAAGTGCTGCGGCTGATGAGAATTTTCCGCATTCTGAAACTGGCCCGTCATTCCACGGGGCTGCGCTCCCTG
GGAGCCACACTCAGGAACAGCTACAAAGAAGTGGGACTTTTGCTCCTCTACTTGGCAGTCGGAGTGTCGTTTTTCTCCGT
TATGGCCTATACGGTGGAGAAAGAGGATAACGAGGATCTCACCACCATTCCGGCATGCTGGTGGTGGGCCACTGTCAGCA
TGACCACCGTGGGATACGGTGATGTTGTGCCGGTGTCTATTGCCGGCAAACTGACCGCCTCTGCGTGCATCCTGGCCGGG
ATCTTAGTAGTTGTGCTTCCGATTACGCTCATTTTCAACAAATTCTCCCTCTTCTACAAGAGACAGAAACAGCTGGAGAT
CGCAATGAGAAGCTGCGACTTCGACGAGGGGATAAAAGAGGTGCCCTCCGTCAACCTGAGGAATTATTACGCACACAAAG
TCAAATCCCTCATGGCGAGCTTGTCAAACATGAGCCGGAGTTCACCTAGTGAACAGAGTTTAAACGAATCAATACACTGA

Alignment

ORF - retro_onil_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.05 %
• Parental protein coverage: 83.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AHQDSDEGLVHVNVGGLKRSLCSSTLKKFPDTRLGKLLACDSEEAILQVCDDYDVQEKEFYFDRNPGLFP
          AH.D........NVGG.K..L.S.TL..FP.TRL..LL.C.S.E.IL..CDDYD..EKEFYFDRNP.LFP
Retrocopy AHTD-ENAAIRINVGGFKKRLQSDTLSRFPETRLARLLHCQSKESILELCDDYDDTEKEFYFDRNPALFP

Parental  YVLHFYQTGKLHIMEELCVFSFSQEIEYWGINEFFLDSCCSYRYHDRKLESSRHRSWDDESDASSVDTSV
          YVL.FY.TG.LH.M.ELC.FSFSQEIEYWGINEFF.DSCCS..YH.RK....R...WDD.SD..S...S.
Retrocopy YVLNFYNTGRLHVMAELCIFSFSQEIEYWGINEFFIDSCCSSSYHCRKMDQDRE-DWDDRSDEGSTTSSF

Parental  DEISDLNKDMQHFQEVRYGNIRKCLWLTLENPGYSIPSKLFSLLSIGVVLTSIATMCINSMPEYQTFDSD
          DE......D...F.....G..R...WL.L.NPGYS..S...S.LSI.VVL.SIATMC.NSM......DS.
Retrocopy DELLEFYNDASKFDKQLLGSARRRIWLMLDNPGYSVASRIISILSILVVLGSIATMCMNSMSDFSLLDSE

Parental  GKLIEEPTMQALEVFCSCWFTFEVVTRLLLAPNRKKFFHHPLNIIDMVSVVPIYVTLVFDVTVGSESELG
          G...E.P.....E.F...WFT.E.V.R...AP....FF.HPLN.ID.VS..P.Y.TL.....V.S...L.
Retrocopy GQPTEDPRFETVEHFGIGWFTLELVARFVVAPDLLHFFDHPLNVIDLVSILPFYLTLLINLVVESSPALA

Parental  DLGRLIQVFRLMRIFRVLKLARHSTGLRSLGATLRHSYREVGILLLYLAVGVSVFSGIAYTAEYEEDVGL
          .LGR..QV.RLMRIFR.LKLARHSTGLRSLGATLR.SY.EVG.LLLYLAVGVS.FS..AYT.E.E....L
Retrocopy NLGRVAQVLRLMRIFRILKLARHSTGLRSLGATLRNSYKEVGLLLLYLAVGVSFFSVMAYTVEKEDNEDL

Parental  DTIPACWWWGTVSMTTVGYGDVVPVTVVGKLAASGCILGGTLVVALPITIIFNKFSHFYRRQKALEASVR
          .TIPACWWW.TVSMTTVGYGDVVPV...GKL.AS.CIL.G.LVV.LPIT.IFNKFS.FY.RQK.LE...R
Retrocopy TTIPACWWWATVSMTTVGYGDVVPVSIAGKLTASACILAGILVVVLPITLIFNKFSLFYKRQKQLEIAMR

Parental  N
          .
Retrocopy S

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_7 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_7 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000008198	1 retrocopy	retro_apla_7,
Gasterosteus aculeatus	ENSGACG00000000019	1 retrocopy	retro_gacu_10,
Oreochromis niloticus	ENSONIG00000005340	2 retrocopies	retro_onil_31, retro_onil_7 ,
Tetraodon nigroviridis	ENSTNIG00000005219	1 retrocopy	retro_tnig_1,