RetrogeneDB ID: retro_trub_12

Retrocopy location

• Organism: Fugu rubripes (Takifugu rubripes)
• Coordinates: scaffold_261:132535..133105(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTRUG00000013066
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RAC3
• Ensembl ID: ENSTRUG00000004543
• Aliases: None
• Description: None

Sequence

>retro_trub_12
ATGTCTATTAAGTGTGTCCTTGTTGGGGACAACGCTGTGGGAAAGACGGCACTGCTGGTACGCTTCACCTCAGAGACCTT
CCCGGAGTCCTACAGGCCCACGGTGTTTGATAATACAGGGGTGGAGGTGTACATGGATGGTGTCCACATCAGCCTGGGAC
TGTGGGACACAGCGGGCAATGACACCTTTCAACAGATCCGACCCAGATCCTACCAGCAGGCGGACATCGTTCTCATCTGT
TACTCTGTGGCTAACCCGAACTCACTGGCCAATGTCCACAAAAAGTGGCTCCCTGAGGTTCGGGAGCACCTGCCCAATGT
TCCTGTTCTGGTTGTGGCCACACAAACGGACCTGCGGGAAATGGGGGCCTATCGGGGCAACTGCACCACATCAGCGGAGG
GGGCACAAATGGCTCGTGAAATTAAAGCCAAAGGCTACGTGGAATGTTCTGCCTTTAGCAACCGCGGCGTCCAGCAGGTG
TTTGAGTACGCCGTGCGAATTGTTGTCAACCAGGCCAAAAAACAGGCCCGACGGCGGATGTTCCGCATAAACCAGTGCAA
AGTCTTTTGA

Alignment

ORF - retro_trub_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.78 %
• Parental protein coverage: 61.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSY
          .IKCV.VGD.AVGKT.LL...T...FP..Y.PTVFDN....V..DG....LGLWDTAG.......RP.SY
Retrocopy SIKCVLVGDNAVGKTALLVRFTSETFPESYRPTVFDNTGVEVYMDGVHISLGLWDTAGNDTFQQIRPRSY

Parental  PQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRD
          .Q.D..LIC.S...P.S..NV..KW.PEVR.H.PN.P...V.T..DLR.
Retrocopy QQADIVLICYSVANPNSLANVHKKWLPEVREHLPNVPVLVVATQTDLRE

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_12 retrocopy.

TSS

Takifugu rubripes was not studied using FANTOM5 data.

Lab

retro_trub_12 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_trub_12 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000012902	3 retrocopies	retro_etel_1565, retro_etel_1645, retro_etel_42,
Oreochromis niloticus	ENSONIG00000017151	1 retrocopy	retro_onil_34,
Tupaia belangeri	ENSTBEG00000007272	4 retrocopies	retro_tbel_1796, retro_tbel_2564, retro_tbel_4296, retro_tbel_9,
Takifugu rubripes	ENSTRUG00000004543	1 retrocopy	retro_trub_12 ,
Takifugu rubripes	ENSTRUG00000016201	1 retrocopy	retro_trub_15,