RetrogeneDB ID: retro_trub_1

Retrocopy location

• Organism: Fugu rubripes (Takifugu rubripes)
• Coordinates: scaffold_119:135184..136327(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTRUG00000007184
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: KCNJ8
• Ensembl ID: ENSTRUG00000009953
• Aliases: None
• Description: None

Sequence

>retro_trub_1
ATGTTGTCCAGGAAAGGGCTCATTCCTGAGGAATATCTGCTGACACGATTGGCCGAGGATGTCCTGCAGCCCAAGTTTAA
GGCGAAACAGGGGAAGGCTCGGTTCGTGGCCAAGAACGGCGCCTGCAATGTGGCGCACACGAACATCCGAGAGCAGGGCC
GGTTCCTCCAGGACGTCTTCACTACTCTGGTGGATTTAAAATGGCTCCACACGCTCATCATCTTCACCATGTCGTTTCTG
TGCAGTTGGCTCCTCTTCGGGATGATCTGGTGGCTCGTCGCCTTCGCGCACGGCGACTTGTTCCAAACAGGAGACGAGTT
CGTCCCGTGCGTCACGGAGGTTCACTCGTTCTCCTCCGCGTTCCTTTTCTCTATAGAGGTGCAGGTGACGATCGGCTTCG
GCGGACGGATGATCACGGAGGAATGCGTGTCCGCCATCGTCATCCTGATCGTCCAGAACATCGTCGGTCTGGTGATCAAC
GCCATCATGCTCGGGTGCATCTTCATGAAAACCGCGCAGGCCAACCGGCGCGCGGAGACGCTGATTTTCAGTAAACACGC
GGTCATCTCGGTCCGCAACAACAAGCTCTGCTTCATGATCCGCCTCGGCGACCTGAGGAAAAGCATGGTCATTAGCGCCT
CCGTGCGGATGCAAGTGGTCAGGAGAACCACCACCGAGGAGGGCGAGGTGGTGCCCCTGGACCAGATCGATATCCATATG
GACAACCCGGTGGGCACCAACGGGATCTTCCTGGTGTCCCCGCTCATCATATGTCACGTGATCGACAAGGAAAGCCCCCT
GTACGACCTGTCCGCGACCGATCTGCAGCACGAAGACATCGAGGTGATCGTGGTGCTGGAGGGGGTGGTGGAGACCACTG
GCATCACCATGCAGGCCAGGACCTCCTACGTGGCGGAGGAGATCTTATGGGGTCAGCGCTTCGTGCCCACGGTGTCCGAG
GAGGAGGGCATGTACGCGGTGGATTACTCCAAGTTCGGCAACACCATGAGGGTTCCGACCCCCTTCTGCAGCGCCAAGAA
ACTGGACGAGGCAGGCGGCATCGCCCGACTGAAGCTGGACGAGGGCGTCACCTTGCGGCCGTATGTGAGAAAGCGGCGAA
GCAACACGGTCCGCAGGTCCCGG

Alignment

ORF - retro_trub_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.17 %
• Parental protein coverage: 63.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CVTDVKSFTSAFLFSIEVQVTIGFGGRMITEECPAAIAFLITQNIIGLIINAVMLGCIFMKTAQSNRRAE
          CVT.V.SF.SAFLFSIEVQVTIGFGGRMITEEC..AI..LI.QNI.GL.INA.MLGCIFMKTAQ.NRRAE
Retrocopy CVTEVHSFSSAFLFSIEVQVTIGFGGRMITEECVSAIVILIVQNIVGLVINAIMLGCIFMKTAQANRRAE

Parental  TLIFSRHAVIAVRNNRLCFMVRIGDLRKSMIIGATVRLQVVRKTTTPEGEVIPIHQIDIQTESALNSNSL
          TLIFS.HAVI.VRNN.LCFM.R.GDLRKSM.I.A.VR.QVVR.TTT.EGEV.P..QIDI........N..
Retrocopy TLIFSKHAVISVRNNKLCFMIRLGDLRKSMVISASVRMQVVRRTTTEEGEVVPLDQIDIHMDNPVGTNGI

Parental  FLLAPLIICHIIDRTSPLYDLSAMELQCSDLEVIVILEGVVETTGITTQARTSYISEEIQWGHRFVPIVT
          FL..PLIICH.ID..SPLYDLSA..LQ..D.EVIV.LEGVVETTGIT.QARTSY..EEI.WG.RFVP.V.
Retrocopy FLVSPLIICHVIDKESPLYDLSATDLQHEDIEVIVVLEGVVETTGITMQARTSYVAEEILWGQRFVPTVS

Parental  EEEGVYSVDYSKFGNTVKIATPLCSARELDEKPSILIQSLQKSELSHQNSLRKRNS
          EEEG.Y.VDYSKFGNT....TP.CSA..LDE...I....L...........RKR.S
Retrocopy EEEGMYAVDYSKFGNTMRVPTPFCSAKKLDEAGGIARLKLDEG-VTLRPYVRKRRS

Legend:

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

Expression

RNA-Seq

Takifugu rubripes was not studied using RNA-Seq expression data.

ChIP-Seq

Takifugu rubripes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_trub_1 retrocopy.

TSS

Takifugu rubripes was not studied using FANTOM5 data.

Lab

retro_trub_1 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_trub_1 has 2 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Gasterosteus aculeatus	retro_gacu_7
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,