RetrogeneDB ID: retro_trub_45

Retrocopy location

• Organism: Fugu rubripes (Takifugu rubripes)
• Coordinates: scaffold_750:29358..30171(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTRUG00000002008
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FZD4
• Ensembl ID: ENSTRUG00000006345
• Aliases: None
• Description: None

Sequence

>retro_trub_45
CCCGACAAGTTCCAGTTTGTGGAGAAGAGCCAGTCGTGCGCGCCGCGCTGTTCTGCCGCCGTGGACGTCTACTGGTCCAA
GCAGGACAAGGACTTTGCCTTCATTTGGATGACAGTGTGGTCCATTCTGTGCTTTATCTCCACCGCCTTCACCGTCCTCA
CCTTCTTCCTGGAGCCCCACCGCTTCCAGTACCCCGAACGGCCCATCATCTTCCTCTCAATGTGCTACAATGTCTACTCT
GTGGCTTTCATCATCCGCTCGGTGGCCGGCGCGGAGAACATTGCCTGCGACCGCGAGAACGGTGAGTTGTACATCATCCA
GGAGGGGTTGGAGTCAACGGGCTGCACCATCGTCTTCCTCATCCTGTATTACTTTGGCATGGCCTCTTCCATCTGGTGGG
TCATCCTCACTCTCACCTGGTTCTTGGCTGCTGGGAAGAAGTGGGGCCACGAGGCCATTGAAGCCCACAGCAACTATTTC
CATATGGCCGCCTGGGGCATTCCGGCACTGAAGACCATCGTCATCCTCACCATGAGAAAGGTGGCTGGAGATGAGCTGAC
AGGACTTTGCTACGTGGGCAGCATGGACGCCGGTGCGCTCACGGGCTTCGTTCTCACCCCTCTATCCTGCTACCTGATCA
TCGGGACCTCCTTCATCCTCACGGGCTTCGTGGCTCTTTTCCACATCCGAAAAGTGATGAAGACGGAGGGCACGAACACC
GAGAAGCTGGAGAAGCTGATGGTGAAAATAGGCATCTACTCCATCCTCTACACGGTGCCTGCCACCTGCGTCATTGTCTG
CTACTTCTACGAG

Alignment

ORF - retro_trub_45 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.56 %
• Parental protein coverage: 53.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PDQYIWLKQTESCTLQCGYDSGLY-RRGTKVFTDAWMAVWAVLCFLSTTLTVLTFVLDSQRFSYPERPII
          PD.........SC...C......Y.....K.F...WM.VW..LCF.ST..TVLTF.L...RF.YPERPII
Retrocopy PDKFQFVEKSQSCAPRCSAAVDVYWSKQDKDFAFIWMTVWSILCFISTAFTVLTFFLEPHRFQYPERPII

Parental  FLSMCCNLYSVAYLVRWTLGREHVSCDLEATAVPVLVQEGLKSTGCAIVFLLLYFFGMASSLWWVILTLT
          FLSMC.N.YSVA...R...G.E...CD.E........QEGL.STGC.IVFL.LY.FGMASS.WWVILTLT
Retrocopy FLSMCYNVYSVAFIIRSVAGAENIACDRENGEL-YIIQEGLESTGCTIVFLILYYFGMASSIWWVILTLT

Parental  WFLAAGLKWGHEAIEMHSSYFHIAAWAIPAVKTIVILIMRLVDADDLTGLCYVGNQQQEALIGFVVAPLA
          WFLAAG.KWGHEAIE.HS.YFH.AAW.IPA.KTIVIL.MR.V..D.LTGLCYVG.....AL.GFV..PL.
Retrocopy WFLAAGKKWGHEAIEAHSNYFHMAAWGIPALKTIVILTMRKVAGDELTGLCYVGSMDAGALTGFVLTPLS

Parental  TYLLLGTLFICAGLVALFRIRSNLQKDGAKTDKLERLMVKIGVFSVLYTVPASTVIGCYIYQ
          .YL..GT.FI..G.VALF.IR......G..T.KLE.LMVKIG..S.LYTVPA..VI.CY.Y.
Retrocopy CYLIIGTSFILTGFVALFHIRKVMKTEGTNTEKLEKLMVKIGIYSILYTVPATCVIVCYFYE

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_45 retrocopy.

TSS

Takifugu rubripes was not studied using FANTOM5 data.

Lab

retro_trub_45 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_trub_45 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Gadus morhua	ENSGMOG00000014266	1 retrocopy	retro_gmor_8,
Takifugu rubripes	ENSTRUG00000006345	2 retrocopies	retro_trub_27, retro_trub_45 ,