RetrogeneDB ID: retro_gacu_10

Retrocopy location

• Organism: Stickleback (Gasterosteus aculeatus)
• Coordinates: groupXX:894986..896426(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGACG00000003519
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: KCNS1
• Ensembl ID: ENSGACG00000000019
• Aliases: None
• Description: potassium voltage-gated channel, delayed-rectifier, subfamily S, member 1 [Source:HGNC Symbol;Acc:6300]

Sequence

>retro_gacu_10
ATGACGGGTCAGGCCCTGGGTGAGCTGCGCGGCGGGACTCGCGCGCATGATAACGCCGCCATCCACATCAACGTGGGCGG
CTTCAAGAAGCGCCTCCTGTCCCACACCCTCTCCCGGTTCCCCGAGACGAGGCTCGCACGCCTGCTCCACTGCCAGTCCA
AAGAGTCCATCCTGGAGCTGTGCGACGATTACGACGACACGGAGAAGGAGTTCTACTTCGACAGGAACCCGGCGCTCTTC
CCCTACGTGTTGAATTTCTACAACACAGGCCGGCTGCACGTCATGGCCGAGCTGTGCATCTTCTCTTTCAGCCAGGAGAT
CGAGTACTGGGGCATCAACGAGTTCTTCATCGATTCGTGCTGCAGCAGCGCTTACCACTGCCGGAAAATGGACCAGGACC
GGGAGGACTGGGACGACAGGAGCGACGAAGGGAGCACCACGTCGTCTTTCGACGAGCTGTTGGAGTTTTACAGTGACGCC
ACGAAGTTTGACAAGCAGCCACTCGGGAGCGCGCGGAGGCGCGTGTGGTTGATGCTGGACAACCCCGGCTACTCCGTGGC
CAGCCGCATCATTAGCATCCTCTCCATCCTCGTCGTGCTCGGCTCCATCGCGACCATGTGCCTGAACAGCATGAGCGAGT
TCTGCCTGTTGGACGACGAAGGGCTGCCCGCGGAAGACCCCCGTTTCGAGACCATGGAGCACTTCGGCATCGGCTGGTTC
ACTCTCGAGCTGGTCGCCCGGTTCACGGTGGCGCCGGACCTGCCGCATTTCTTCGAGCACCCGTTGAACCTGATCGACCT
GGTGTCCATCCTCCCGTTTTACCTGACGCTCCTCGTCAACCTAGTGGTGGAGAGCAGCCCGACGCTGGCCAATCTGGGAC
GCGTCGCGCAAGTGCTGAGGCTGATGAGGATTTTCCGCATCCTGAAGCTGGCGCGTCACTCCACGGGACTGCGCTCGCTG
GGGGCCACCCTCAGGAACAGTTATAAGGAGGTGGGCCTGTTGCTCCTCTACCTGGCCGTCGGGGTGTCATTTTTCTCCGT
CATGGCCTACACGGTGGAGAAAGAGGACAGCGACGATCTCTCCACAATCCCGGCGTGCTGGTGGTGGGCCACCGTCAGCA
TGACCACCGTTGGATACGGGGACGTGGTGCCGGTGTCCATAGCTGGCAAGCTTACCGCCTCGGCGTGCATCTTGGCCGGG
ATCCTTGTTGTCGTGCTTCCAATCACGCTCATTTTCAACAAATTCTCTCTCTTCTACAAGAGACAGAAGCAGCTGGAGGC
TGCGATGAGGAGCTGCGACTTCGACGAGGGGATCAAGGAGGTGCCCCCGGTCAACCTGAGGAACTATTATGCGCATAAAG
TCAAATCCCTCATGGCGAGCTTGTCTAACATGAGCCGGAGCTCACCAAGCGAGCACAGCCTGAACGAATCAATACACTGA

Alignment

ORF - retro_gacu_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.27 %
• Parental protein coverage: 86.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VHINVGGLKRSLCRSTLRRFPNTRLGKLLSCDSEEDILQVCDDYDVQQKEFYFDRNPGLFTYVLHFYQTG
          .HINVGG.K..L...TL.RFP.TRL..LL.C.S.E.IL..CDDYD...KEFYFDRNP.LF.YVL.FY.TG
Retrocopy IHINVGGFKKRLLSHTLSRFPETRLARLLHCQSKESILELCDDYDDTEKEFYFDRNPALFPYVLNFYNTG

Parental  KLHIMEELCVFSFSQEIEYWGINEFFLDSCCSYRYHDRKLEGSRHHTWDEDSEVSSVDTSVDEISDLNRD
          .LH.M.ELC.FSFSQEIEYWGINEFF.DSCCS..YH.RK....R...WD..S...S...S.DE......D
Retrocopy RLHVMAELCIFSFSQEIEYWGINEFFIDSCCSSAYHCRKMDQDRED-WDDRSDEGSTTSSFDELLEFYSD

Parental  MLHFQEVRHGNVRKCLWLTLENPGYSLPSKLFSLVSIGVVLASIASMCISSIPEYQTFDDEGKLMEDPSM
          ...F.....G..R...WL.L.NPGYS..S...S..SI.VVL.SIA.MC..S..E....DDEG...EDP..
Retrocopy ATKFDKQPLGSARRRVWLMLDNPGYSVASRIISILSILVVLGSIATMCLNSMSEFCLLDDEGLPAEDPRF

Parental  QALEVFCTCWFTFEVVTRLLLAPNKRKFLHHPLNIIDLVSVAPVYVTLLFDTTVGSESQLGVLGRLVQVF
          ...E.F...WFT.E.V.R...AP....F..HPLN.IDLVS..P.Y.TLL....V.S...L..LGR..QV.
Retrocopy ETMEHFGIGWFTLELVARFTVAPDLPHFFEHPLNLIDLVSILPFYLTLLVNLVVESSPTLANLGRVAQVL

Parental  RLMRIFRVLKLARHSTGLRSLGATLRYSYREVGILLLYLAVGVSVFSGIAYTAEYEEGVGLDTIPACWWW
          RLMRIFR.LKLARHSTGLRSLGATLR.SY.EVG.LLLYLAVGVS.FS..AYT.E.E....L.TIPACWWW
Retrocopy RLMRIFRILKLARHSTGLRSLGATLRNSYKEVGLLLLYLAVGVSFFSVMAYTVEKEDSDDLSTIPACWWW

Parental  G-VSMTTVGYGDVVP
          ..VSMTTVGYGDVVP
Retrocopy ATVSMTTVGYGDVVP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Gasterosteus aculeatus was not studied using RNA-Seq expression data.

ChIP-Seq

Gasterosteus aculeatus was not studied using ChIP-Seq data.

EST

Gasterosteus aculeatus was not studied using EST data.

TSS

Gasterosteus aculeatus was not studied using FANTOM5 data.

Lab

retro_gacu_10 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_gacu_10 has 1 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Tetraodon nigroviridis	retro_tnig_1

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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,