RetrogeneDB ID: retro_tnig_1

Retrocopy location

• Organism: Tetraodon (Tetraodon nigroviridis)
• Coordinates: 8:9917869..9919252(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTNIG00000013299
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: KCNS1
• Ensembl ID: ENSTNIG00000005219
• Aliases: None
• Description: potassium voltage-gated channel, delayed-rectifier, subfamily S, member 1 [Source:HGNC Symbol;Acc:6300]

Sequence

>retro_tnig_1
CAGTTTTTGGGGAAACTGCACGGCGGAGCCTCCATGGATGACAGCGCCGCCATCCGCATCAACGTGGGCGGCTTCAAGAA
GCGCCTCCAGTCAGATACGCTCTCCCGGTTCCCGGAGACGAGGCTTGCGCGTCTGCTCCACTGTCGGTCCAAAGAGTCCA
TATTGGAGCTTTGCGACGACTACGACGACGCGGAGAAAGAGTTTTACTTCGACAGGAACCCCGCACTCTTCCCGTACGTG
CTAAACTTTTACCACACCGGGCGGCTGCACGTCATGGCTGAACTTTGCATCTTCTCCTTCAGCCAGGAGATCGAGTACTG
GGGCATCAACGAGTTCTTCTTAGACTCGTGTTGCAGCAGCACTTATCACTGCAGAAAAATGGACCAGGACAGGGAGGACT
GGGACGACAAAAGCGAGGAAGGGAGCACTACTTCCTCCTTCGACGAGCTCCTGGAATTTTACAGCGATGCTTCCAAGTTT
GACAAGCAGCTGCTCGGGAGCGTCAGGAGGCGCATCTGGTTGATGCTGGATAACCCCGGCTACTCGGTGGCCAGCCGCAT
CATCAGCGTCCTCTCCATCCTGGTGGTGCTGGGCTCCATCGCCACAATGTGCATGAACAGCATGAGCGAGTTCAGCTTGG
TGGACAGTGAGGGCCATCCCACGGAAGACCCCCGCTTCGAGATCGTGGAGCACTTCGGCATCGGCTGGTTCACCCTGGAG
CTGCTCGCCAGGTTCGCGGTGGCGCCCGATCTCCTGCACTTCTTCGAGCACCCGTTGAACGTGATAGACCTGGTGTCCAT
TCTTCCGTTTTACCTGACTCTCCTGATAAACCTGGTGGTGGAGAGCAGCCCGGCTCTGGCCAACCTGGGCCGCGTCGCAC
AAGTGCTGAGACTGATGAGGATTTTCCGTATTCTGAAGCTGGCGCGTCACTCCACCGGGCTGCGCTCCCTGGGGGCCACG
CTCCGAAACAGTTACAAAGAAGTAGGTCTGCTGCTACTCTACCTAGCAGTAGGCGTGTCCTTTTTCTCCGTCATAGCCTA
CACGGTGGAGAAGGAAGACAACGAGGACCTCACCACCATCCCGGCGTGCTGGTGGTGGGCCACAGTCAGCATGACCACCG
TCGGTTACGGAGATGTGGTGCCCGTGTCCATCGTGGGCAAGCTGACTGCCTCGGCGTGCATCCTGGCAGGTATTTTAGTC
GTCGTGCTTCCCATCACGCTCATTTTCAACAAGTTCTCCCTCTTCTACAAGAGACAGAAGCAGCTGGAGATCGCCATGAG
GAGCTGCGATTTTAACGAGGGCATCAAGGAGGTGCCCTCGGTCAACCTGAGGAACTATTACGCACACAAAGTCAAATCCC
TCATGGCCAGTTTGTCAAACATG

Alignment

ORF - retro_tnig_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.85 %
• Parental protein coverage: 95.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEALVHVNVGGLRRSLCCSTLEKFPDTRLGRLLACRSQEDILQVCDDYDVQQREFYFDRHPGLFRHVLHF
          ..A....NVGG....L...TL..FP.TRL.RLL.CRS.E.IL..CDDYD....EFYFDR.P.LF..VL.F
Retrocopy DSAAIRINVGGFKKRLQSDTLSRFPETRLARLLHCRSKESILELCDDYDDAEKEFYFDRNPALFPYVLNF

Parental  YQTGKLHVTEELCVFSFSQEIEYWGINEFFLDGCCSYRYHDRKLERARRRSWDEESDASSLDTCVDEISD
          Y.TG.LHV..ELC.FSFSQEIEYWGINEFFLD.CCS..YH.RK....R...WD..S...S.....DE...
Retrocopy YHTGRLHVMAELCIFSFSQEIEYWGINEFFLDSCCSSTYHCRKMDQDRE-DWDDKSEEGSTTSSFDELLE

Parental  LNRDMQHFQDVSYGNVRRCLWLTLENPGYSIPSKLFSLLSISVVLTSIAITCINSIPEYQSLDPDGRPLE
          ...D...F.....G.VRR..WL.L.NPGYS..S...S.LSI.VVL.SIA..C.NS..E....D..G.P.E
Retrocopy FYSDASKFDKQLLGSVRRRIWLMLDNPGYSVASRIISVLSILVVLGSIATMCMNSMSEFSLVDSEGHPTE

Parental  DATTRALEGFCSCWFTLEVVTRLLLAPNRKRFFHHPLNIIDMASVVPIYITLTFDLTVGSESELGDLGRL
          D......E.F...WFTLE...R...AP....FF.HPLN.ID..S..P.Y.TL...L.V.S...L..LGR.
Retrocopy DPRFEIVEHFGIGWFTLELLARFAVAPDLLHFFEHPLNVIDLVSILPFYLTLLINLVVESSPALANLGRV

Parental  VQVFRLMRIFRVLKLARHSTGLRSLGATLRHSYREVGILLLYLAVGVSVFSGFAYTAEYEEDVGLDTIPA
          .QV.RLMRIFR.LKLARHSTGLRSLGATLR.SY.EVG.LLLYLAVGVS.FS..AYT.E.E....L.TIPA
Retrocopy AQVLRLMRIFRILKLARHSTGLRSLGATLRNSYKEVGLLLLYLAVGVSFFSVIAYTVEKEDNEDLTTIPA

Parental  CWWWGTVSMTTVGYGDVVPVTVAGKLAASGCILGGTLVVALPITIIFNKFSHFYRRQKALE
          CWWW.TVSMTTVGYGDVVPV...GKL.AS.CIL.G.LVV.LPIT.IFNKFS.FY.RQK.LE
Retrocopy CWWWATVSMTTVGYGDVVPVSIVGKLTASACILAGILVVVLPITLIFNKFSLFYKRQKQLE

Legend:

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

Expression

RNA-Seq

Tetraodon nigroviridis was not studied using RNA-Seq expression data.

ChIP-Seq

Tetraodon nigroviridis was not studied using ChIP-Seq data.

EST

Tetraodon nigroviridis was not studied using EST data.

TSS

Tetraodon nigroviridis was not studied using FANTOM5 data.

Lab

retro_tnig_1 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tnig_1 has 1 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Gasterosteus aculeatus	retro_gacu_10

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 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 ,
Tetraodon nigroviridis	ENSTNIG00000011060	1 retrocopy	retro_tnig_23,