RetrogeneDB ID: retro_trub_37

Retrocopy location

• Organism: Fugu rubripes (Takifugu rubripes)
• Coordinates: scaffold_3206:2015..3812(-)
• Located in intron of: ENSTRUG00000001663

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTRUG00000008276
• Aliases: None
• Description: None

Sequence

>retro_trub_37
CTTGCTACGATGGCGGACAGAACAATTGGACGTCCACTGCTGCTGTTTATTTCGATTCTCTCTCTCAAATCCGTCATTGG
GCAAGTGAGCTACTCGGTACCAGAGGAAATGCCGAAAGGCTCTTTTATTGGTGATATTGCTCAAGATCTGGGTTTGGATC
CGAAAAGGCTGAAATCGGGAAAGGCGCGCATCTATACGGGAGACAATGCGGAGTACATCGAGCTGAATAAAGAGAAAGGG
ATCCTGCTCATCAAAGACAGAATAGACAGAGAGGCCATCTGTGCCCAGACATCGCCCTGTTCGTTGCATTTCCAGGTAAT
TTTAGAGAATCCGATGGAGTTTTACAGCATCACTGTCGAGGTTACGGACATCAACGACAACGCCCCGACTTTTAATAGTG
GTGAGATGAAATTCAGAATTAGCGAATCTGCTGTTACAGGAGCTGTTTTCTCGTTGCAGCCAGCAATAGATCTGGATGTC
GGTATTAATGGATTACAAAATTATCGGTTGCATCCAGCCGACAACTTCGCTTTGAAGCTACAAAACCAAGCAGACGGAAG
CAAGATGGTAGAAATGGTTTTACAGAAGCCATTAGACAGAGAGACGAAAGATCATTTGACTCTGGTTCTGACTGCAGTAG
ACGGTGGTGAGCCGCAGCTCTCCGGGACCGTGCAGATAGATATAAACGTACTAGATGCTAACGATAACGCTCCTGTTTTT
ACACAAAAAATCTACAAATCAACAATAAAAGAAAATTCGCTTCCTGGAACGAAAATAATAACTGTTCGTGCCTCCGATTT
GGATGAAGGATCATACGGTAAAATTTCTTATAGTATACAAAATATTCTCGACACTGTATCAGATTTATTTAATGTTGACA
GAGAGACAGGGCAGGTTACATTAGTCGGAAATACAGACTTTGAAAAAAAACGACAGTATCAAGTACATGCCAGAGCCAGT
GATGAGGGAGGTTTAACTGATTCTTGTAAAATTATTGTTGAAATAACAGACACAAATGACAATGCTCCTGTTATAAATGT
AATGTCAAAGTCCAGTGCAATAACTGAAGACATTCAGCCTGGCACTGTTGTGACAATGATAAACATCCAAGATCCAGACT
CGGGGGAGAATGGAAATGTTCACTGTTATATTAAAGAAAGCATTCCATTCACAATTTCTTCAACATCCACTAACTTTTTC
AGTTTAACGACAGACAGTGAGCTGGACAGGGAGAGAGAATCCGAGTATAACATCACAGTGAGCTGCTCTGATGAGGGAGT
GCCCTCCCTCTCCAGCAGCGTCACTCTCACCTTACAGATCTCTGATGTCAATGACAACCCTCCTGTCTTTGAGAGGAGCT
CATATGAGGCCTACATTGTAGAGAACAACACACCAGGTCTCTCTATATTCACAGTCAAAGCCAGAGACGCTGACTGGAAC
CAGAACGCTCGTGTTTCCTACATCCTGGAGGACTCCTCTGTTAACGGAGTTCCAGTCTCCTCATATGTGTCCGTTAGTGC
TGATAGTGGAGTCGTTCATGCAGTGCGCTCTTTTGACTACGAGCAGATCAAAGACTTTCACTTCCTGGTCAAAGCTCAGG
ATGGAGGTTCTCCTCCACTCAGCAGCAACGTGAGCGTGAAAATCCTGATCCAGGACCAGAACGATAACCCCCCTCAGGTT
CTGTACCCGGTCCAGACTGGAGGCTCTATGGTGGCTGAAATGGTGCCTCGTTCAGCAGATGTGGGCTACCTGGTGACTAA
AGTGGTGGCTGTTGATGTGGACTCTGGACAGAATGCC

Alignment

ORF - retro_trub_37 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.96 %
• Parental protein coverage: 61.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LTVLLNRTMRRQVFFFTMLFSLDSVLGQVSYSIPEEMPKGSVLGNIARDLGLDVKRLKSGKARIFTGDSA
          L.....RT..R....F....SL.SV.GQVSYS.PEEMPKGS..G.IA.DLGLD.KRLKSGKARI.TGD.A
Retrocopy LATMADRTIGRPLLLFISILSLKSVIGQVSYSVPEEMPKGSFIGDIAQDLGLDPKRLKSGKARIYTGDNA

Parental  EYIELNRDRGVLLVKDRIDRETLCKQTTPCALHLQIILENPMELFRITVEITDINDNSPVFKKEEMRFRI
          EYIELN...G.LL.KDRIDRE..C.QT.PC.LH.Q.ILENPME...ITVE.TDINDN.P.F...EM.FRI
Retrocopy EYIELNKEKGILLIKDRIDREAICAQTSPCSLHFQVILENPMEFYSITVEVTDINDNAPTFNSGEMKFRI

Parental  SESAVIGAKFVLERAMDLDVGVNGLQSYSLKPTDNFQLKLQDQQDGSKKVEMILQKNLDRETQEHLSLIL
          SESAV.GA.F.L..A.DLDVG.NGLQ.Y.L.P.DNF.LKLQ.Q.DGSK.VEM.LQK.LDRET..HL.L.L
Retrocopy SESAVTGAVFSLQPAIDLDVGINGLQNYRLHPADNFALKLQNQADGSKMVEMVLQKPLDRETKDHLTLVL

Parental  TAVDGGDPQLSGTMRVEISVLDANDNAPVFVQEVYKITIMENAPKGTVFTTVSAVDADEGSYGKVSYFIT
          TAVDGG.PQLSGT....I.VLDANDNAPVF.Q..YK.TI.EN...GT...TV.A.D.DEGSYGK.SY.I.
Retrocopy TAVDGGEPQLSGTVQIDINVLDANDNAPVFTQKIYKSTIKENSLPGTKIITVRASDLDEGSYGKISYSIQ

Parental  NTFDDAHAVFQVNEDSGEIILIGNIDYENAKNYHINIRASDDGGLTDSCKVIVEVMDVNDNKPTINIMSK
          N..D.....F.V....G...L.GN.D......Y....RASD.GGLTDSCK.IVE..D.NDN.P.IN.MSK
Retrocopy NILDTVSDLFNVDRETGQVTLVGNTDFXXXRQYQVHARASDEGGLTDSCKIIVEITDTNDNAPVINVMSK

Parental  SNIISEHSKLNTVVAMMNVQDPDSAENGRVHCFLNENMPLAIKSTSNNFYSLVTDSELDRERESEYNITV
          S..I.E.....TVV.M.N.QDPDS.ENG.VHC...E..P..I.STS.NF.SL.TDSELDRERESEYNITV
Retrocopy SSAITEDIQPGTVVTMINIQDPDSGENGNVHCYIKESIPFTISSTSTNFFSLTTDSELDRERESEYNITV

Parental  SCSDEGVPSLSSSVTLTLQISDVNDNPPVFERSSYEAYIVENNTPGLSIFTVKARDADWNQNARVSYILE
          SCSDEGVPSLSSSVTLTLQISDVNDNPPVFERSSYEAYIVENNTPGLSIFTVKARDADWNQNARVSYILE
Retrocopy SCSDEGVPSLSSSVTLTLQISDVNDNPPVFERSSYEAYIVENNTPGLSIFTVKARDADWNQNARVSYILE

Parental  DSSVNGVPVSSYVSVSADSGVVHAVRSFDYEQIKDFHFLVKAQDGGSPPLSSNVSVKILIQDQNDNPPQV
          DSSVNGVPVSSYVSVSADSGVVHAVRSFDYEQIKDFHFLVKAQDGGSPPLSSNVSVKILIQDQNDNPPQV
Retrocopy DSSVNGVPVSSYVSVSADSGVVHAVRSFDYEQIKDFHFLVKAQDGGSPPLSSNVSVKILIQDQNDNPPQV

Parental  LYPVQTGGSMVAEMVPRSADVGYLVTKVVAVDVDSGQNA
          LYPVQTGGSMVAEMVPRSADVGYLVTKVVAVDVDSGQNA
Retrocopy LYPVQTGGSMVAEMVPRSADVGYLVTKVVAVDVDSGQNA

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_37 retrocopy.

TSS

Takifugu rubripes was not studied using FANTOM5 data.

Lab

retro_trub_37 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_trub_37 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Takifugu rubripes	ENSTRUG00000008276	2 retrocopies	retro_trub_20, retro_trub_37 ,