RetrogeneDB ID: retro_trub_42

Retrocopy location

• Organism: Fugu rubripes (Takifugu rubripes)
• Coordinates: scaffold_6052:4857..5736(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTRUG00000002327
• Aliases: None
• Description: None

Sequence

>retro_trub_42
ATGTTTTTGCTCTTTGCAACCGTCATCTGCCTTCCCACCACCATGATTCCAGAGGTTCTCGGTGGTAATGTTTTGGTTTT
TCCACACGGAGGAAGCCACTGGGTGAACATGAGGGTCCTGATTGAGGAGCTGCACTCCAGAGGACACAATGTGACGGTGG
TCCGGGCTGCAGACAGCTGGTACATCAGCCAAACGTCCCCACATTACAAGAGCATCACACTCGATGTCGCCGTCGGGGCA
AACGACACATTTTTCCATCACTTTGTTACTGAAGTTGTCAAGATCAAACGTCACCAAGGCAACGCTTGGTCCCGTTTTGG
ATTAGACAGCGAGTTAAAAAACAACTTCTATGAATTGCACAGGAAAATATGTGAAGCGATTGTGCACATGTTTGAGAATG
AAGACTTGATGGAATCCTTCCAAGATTCCAAGTTTGACATAGTTCTGACAGATCCTGCCAACGGAGGAGGGGTCCTTCTG
GCTCACCGCCTCGGGTTGCCGTTGGTGTTCAACGCTCGGTGGACCGTCCACGGCGAGGCCCACTTTGCTGTCGCACCCTC
TCCCCTCTCTTACGTCCCACTTCCACCTTCAGAATTATCTGACAAGATGAATTTCATTGAGAGGGTCAAGAACTTGCTTT
TTTACATCATGAGGATGCATCTCTACAAGCAGGTTGTGGGGCCACATTATTCTGCGGTGGTCAGCCGTTACTTTGACCAA
GACACGGACTACTTCTCCCTGTTTCAAGCTGCTGACCTGTGGCTGATGAGAGTGGACTTTGCATTTGAGTTTCCCCGTCC
CACCATGCCTAATGTTGTCTATATGGGAGGGTTCCAGTGTAAACCTGCCAAGCCTTTACCTGAACACCTGGAAGAGTTT

Alignment

ORF - retro_trub_42 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.78 %
• Parental protein coverage: 55.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFLLFATIICLPTSMIPEVLGSNVLVFPHEGSHWVNMRVLIEELHSRGHNVTVVRAADSWYISQTSPHYK
          MFLLFAT.ICLPT.MIPEVLG.NVLVFPH.GSHWVNMRVLIEELHSRGHNVTVVRAADSWYISQTSPHYK
Retrocopy MFLLFATVICLPTTMIPEVLGGNVLVFPHGGSHWVNMRVLIEELHSRGHNVTVVRAADSWYISQTSPHYK

Parental  SITLDVAVGANDTFFHHFVTEVVKIKRHQGNAWYRFGLDSELKNNFYELHRKICEAIVHMFENEDLMESF
          SITLDVAVGANDTFFHHFVTEVVKIKRHQGNAW.RFGLDSELKNNFYELHRKICEAIVHMFENEDLMESF
Retrocopy SITLDVAVGANDTFFHHFVTEVVKIKRHQGNAWSRFGLDSELKNNFYELHRKICEAIVHMFENEDLMESF

Parental  QDSKFDIVLTDPANGGGVLLAHRLGLPLVFNARWTVHGEAHFAVAPSPLSYVPLPPSELSDKMNFIERVK
          QDSKFDIVLTDPANGGGVLLAHRLGLPLVFNARWTVHGEAHFAVAPSPLSYVPLPPSELSDKMNFIERVK
Retrocopy QDSKFDIVLTDPANGGGVLLAHRLGLPLVFNARWTVHGEAHFAVAPSPLSYVPLPPSELSDKMNFIERVK

Parental  NLLFYIMRISTTRKVDSEKSSLFSSQRIDPGTDYISLFQAADLWLMRVDFVFEYPRPTMPNVVYMGGFQC
          NLLFYIMR......V.....S...S...D..TDY.SLFQAADLWLMRVDF.FE.PRPTMPNVVYMGGFQC
Retrocopy NLLFYIMRMHLYKQVVGPHYSAVVSRYFDQDTDYFSLFQAADLWLMRVDFAFEFPRPTMPNVVYMGGFQC

Parental  KPAKPLPEHLEEF
          KPAKPLPEHLEEF
Retrocopy KPAKPLPEHLEEF

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_42 retrocopy.

TSS

Takifugu rubripes was not studied using FANTOM5 data.

Lab

retro_trub_42 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_trub_42 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	ENSTRUG00000002327	1 retrocopy	retro_trub_42 ,