RetrogeneDB ID: retro_gacu_7

Retrocopy location

• Organism: Stickleback (Gasterosteus aculeatus)
• Coordinates: groupXIX:13049737..13050790(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGACG00000011042
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: kcnj8
• Ensembl ID: ENSGACG00000001115
• Aliases: None
• Description: potassium inwardly-rectifying channel, subfamily J, member 8 [Source:ZFIN;Acc:ZDB-GENE-060308-1]

Sequence

>retro_gacu_7
ATGTTGTCCAGGAAAGGACTCATTCCAGAGGATTATTTACTCACACGTCTGGCCGAGGATGTCCTGCAGCCGAAGTGTTT
TAAGGTCAAACCGGGGAAAGCACGGTTCGTCACCAAGAACGGCACCTGCAACGTAGCGCACACCAACATCAGAGAACAAG
GTCGATTCCTGCTGGACGTCTTCACCACTCTGGTGGATTTAAAATGGCTCCACACGCTCATCATTTTCACCATGTCCTAC
CTGTGCAGTTGGCTCCTTTTCGGGATGATCTGGTGGCTCATCGCGTTTGCGCACGGCGACTTGGACCAGAAGGGAGACGA
CTTTGTCCCGTGCGTAACGGACATTCACTCCTTCTCCTCCGCTTTCCTCTTCTCAATAGAGGTCCAGGTGACCATCGGCT
TCGGCGGCCGGATGGTCACAGAGGAGTGCGTCTCCGCCATCGTCGTCCTCATCGTGCAGAACATCGTCGGACTGCTCATC
AACGCCATCATGCTCGGGTGCATCTTCATGAAAACCGCGCAGGCCAATCGGCGCGCGGAGACGCTCATTTTCAGCAAGCA
CGCAGTCATCTCCGTCCGCAACAACAAGCTGTGCTTCATGATCCGCATCGGCGACCTGAGGAAGAGCATGATCATCAGCG
CCACCGTGCGGCTGCAGGTGGTCAGGAGAAGCTCCACGGAGGAGGGCGAGGTTCTGCCTCTGGACCAGATCGACATCCAC
ATGGATAACCCGGTGGGCACCAACGGCGTCTTCCTGGTGTCCCCCCTCATCATCTGCCACGTGATCGACAAGGACAGCCC
CCTGTACGAGCTGTCCGCTGGTGACCTGCAGTACGACGACATCGAAGTGATCGCGGTGCTGGAAGGGGTGGTGGAGACCA
CGGGCATCACCACCCAGGCCAGGACCTCATACGTGTCGGAGGAGATCCTGTGGGGGCAGCGCTTCGTGCCGACCGTCTCC
GCGGAGGACGGCATGTACGCCGTGGACTACTCTAAGTTCGGGAACACCACGAAGGTCCCCACGCCGTGCTGCAGCGCCAA
AAAACTGGACGAG

Alignment

ORF - retro_gacu_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.89 %
• Parental protein coverage: 85.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLARKSIIPEEFGLPGLASRMPRKPVFRDRVNKARFIAKNGSCNLAHKNIREQGRFLQDVFTTLVDLKWR
          ML.RK..IPE...L..LA........F.....KARF..KNG.CN.AH.NIREQGRFL.DVFTTLVDLKW.
Retrocopy MLSRKGLIPEDYLLTRLAEDVLQPKCFKVKPGKARFVTKNGTCNVAHTNIREQGRFLLDVFTTLVDLKWL

Parental  FTLVIFTTTFVSSWLLFAMSWWLVAFAHGDLDSARWQNKTYCVTDVKSFTSAFLFSIEVQVTIGFGGRMI
          .TL.IFT.....SWLLF.M.WWL.AFAHGDLD.........CVTD..SF.SAFLFSIEVQVTIGFGGRM.
Retrocopy HTLIIFTMSYLCSWLLFGMIWWLIAFAHGDLDQ-KGDDFVPCVTDIHSFSSAFLFSIEVQVTIGFGGRMV

Parental  TEHCPTAITVLIMQNIIGLIINAVMLGCIFMKTAQSNRRAETLIFSRHAVIAVRNNCLCFMIRIGDLRKS
          TE.C..AI.VLI.QNI.GL.INA.MLGCIFMKTAQ.NRRAETLIFS.HAVI.VRNN.LCFMIRIGDLRKS
Retrocopy TEECVSAIVVLIVQNIVGLLINAIMLGCIFMKTAQANRRAETLIFSKHAVISVRNNKLCFMIRIGDLRKS

Parental  MIIGATVRLQVVRKTTTPEGEVIPIHQIDVATETAVASNSLFLLAPLIICHVIDKNSPLYDLSAMELQCS
          MII.ATVRLQVVR...T.EGEV.P..QID......V..N..FL..PLIICHVIDK.SPLY.LSA..LQ..
Retrocopy MIISATVRLQVVRRSSTEEGEVLPLDQIDIHMDNPVGTNGVFLVSPLIICHVIDKDSPLYELSAGDLQYD

Parental  DLEVIVILEGVVETTGITTQARTSYISEEIQWGHRFVPIVTEEEGVYSVDYSKFGNTIKVTTPRCSAREL
          D.EVI..LEGVVETTGITTQARTSY.SEEI.WG.RFVP.V..E.G.Y.VDYSKFGNT.KV.TP.CSA..L
Retrocopy DIEVIAVLEGVVETTGITTQARTSYVSEEILWGQRFVPTVSAEDGMYAVDYSKFGNTTKVPTPCCSAKKL

Parental  DE
          DE
Retrocopy DE

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_7 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_gacu_7 has 2 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Takifugu rubripes	retro_trub_1
Tetraodon nigroviridis	retro_tnig_7

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Gasterosteus aculeatus	ENSGACG00000001115	1 retrocopy	retro_gacu_7 ,
Tetraodon nigroviridis	ENSTNIG00000006480	1 retrocopy	retro_tnig_7,
Takifugu rubripes	ENSTRUG00000009953	1 retrocopy	retro_trub_1,
Xiphophorus maculatus	ENSXMAG00000017494	1 retrocopy	retro_xmac_24,