RetrogeneDB ID: retro_trub_38

Retrocopy location

• Organism: Fugu rubripes (Takifugu rubripes)
• Coordinates: scaffold_386:189288..189996(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTRUG00000006565
• Aliases: None
• Description: None

Sequence

>retro_trub_38
GTTAACCTCGCGATTCCTCCAGATAACTCAGAGTTGAGGAGAGAAGTGCTTGAAGTCCATGCCACTGTTGTCAGCCACCA
TGATCCAACTAATGTTTTGCTGAACTACTTTTCCACCTGGTATAAGCTCAGAAGAGCTGTTGCATGGTTCCTAAAGCTGA
AGAGTTTGCTCACCCAATGCGCTCTCAAAAGAAAGGGGACCTTAAAGGCAGTCATGACTGGCCCCATGACACTCTCTGTT
CAAGACCTGGAAGAGGCAGAAGAAGCCATTGTGAAGTTCTGCCAAAATCAAGCACTTTTGCAGGAGATGGCAAGTCTGCG
CAATGGAAGGAATGTCAGCCGGAAAAGCTCCCTCTTCAAACTGGATCCATTCCTTGACCATGGCATATTAAGAATTGGTG
GTCGCCTGAGCAGGATGGCTATGCCAAAGGAGCAGAAACATCCAGCTATCTTGCCTAAGAGGCATTTCGTCTCAGAGCTC
CTGCTTCGGCACATTCATCAGCAGGTTGGGCATTGTGGCAGAAATCACATTTTGGCAAGCTTAAGGCAAAAATATTGGAT
TCCTTGTGCAAATTCCTTTGCAAGGGAAATTGTGAACAATTGTGTCCCCTGCAGGCGAAACTATGCACATGCAGGTGAAC
AAAAGCTGTCCGATCTGCCAATTGATCGTTTGACTCCTGACCTCCCTCCATTCTCATACGTCGGAGTG

Alignment

ORF - retro_trub_38 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.93 %
• Parental protein coverage: 57.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKMAAPPLAVSSQFNKGMSVLSLTKECHHDPTNVLLNYFSTWYKLRRAVAWFLKLKSLLTQCTLKKKGTL
          ...A.PP....S...........T...HHDPTNVLLNYFSTWYKLRRAVAWFLKLKSLLTQC.LK.KGTL
Retrocopy VNLAIPP--DNSELRREVLEVHATVVSHHDPTNVLLNYFSTWYKLRRAVAWFLKLKSLLTQCALKRKGTL

Parental  KAVTAGPMTLSVQDLEEAEEAIVKFCQNQGFSQEMASLRNGRNVSRKSSIFKLDPFLD--ILRVGGRLSR
          KAV..GPMTLSVQDLEEAEEAIVKFCQNQ...QEMASLRNGRNVSRKSS.FKLDPFLD..ILR.GGRLSR
Retrocopy KAVMTGPMTLSVQDLEEAEEAIVKFCQNQALLQEMASLRNGRNVSRKSSLFKLDPFLDHGILRIGGRLSR

Parental  MAMPEKQKHPAILPKRHFISELLLRHIHQQVGHCGRNHILASLRQKY---CANSFAREIVNNCVPCRRNY
          MAMP..QKHPAILPKRHF.SELLLRHIHQQVGHCGRNHILASLRQKY...CANSFAREIVNNCVPCRRNY
Retrocopy MAMPKEQKHPAILPKRHFVSELLLRHIHQQVGHCGRNHILASLRQKYWIPCANSFAREIVNNCVPCRRNY

Parental  ARASEQKMSDLPIDHLTPDLPPFSYVGV
          A.A.EQK.SDLPID.LTPDLPPFSYVGV
Retrocopy AHAGEQKLSDLPIDRLTPDLPPFSYVGV

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_38 retrocopy.

TSS

Takifugu rubripes was not studied using FANTOM5 data.

Lab

retro_trub_38 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_trub_38 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Takifugu rubripes	ENSTRUG00000006565	1 retrocopy	retro_trub_38 ,