RetrogeneDB ID: retro_trub_2

Retrocopy location

• Organism: Fugu rubripes (Takifugu rubripes)
• Coordinates: scaffold_141:447188..447965(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTRUG00000010393
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: rab34a (1 of 2)
• Ensembl ID: ENSTRUG00000005937
• Aliases: None
• Description: RAB34, member RAS oncogene family a [Source:ZFIN;Acc:ZDB-GENE-041010-197]

Sequence

>retro_trub_2
ATGAACCTCCTTCCTCCCATCCAGAACGACCGCATCATCTCTCGGCTCCCCCAGTGTTTTAGGAGAGAGGCTGCGTTGCA
CAGAAGGGAGAACTTTAACGACAAGGTCAAGACGGCCTGTCAGGAGCAGCCTAGCGGACGCCTGGCTTATAAGATCTCTA
AAGTGATCGTGGTGGGCGACCTGGCTGTGGGCAAGACCTGTCTGATTAATAGGTTTTGCAAAGACGTCTTTGATAGAAAC
TATAATGCAACGTTGGGGGTGGACTTTGAGATAGAGAATTTCCAGGTGCTGGGTGTTCCCTTCACGCTCCAGCTATGGGA
CACCTCAGGACAAGAGAGGTACAAATGTATCGCTTCCTCGTACTACAGAGGAGCTCAGGTCGTGATCGTCGCCTTTGACG
TGAACGATATCGGCTCCTTTTCCCATGTGAGGCAGTGGCTGGAAGAGTCATTGGAGGACAACGACGTAGCAGCTATCCAG
CTGTTCCTCGTGGGCACGAAGAAAGACCTGAGCTCTCCCGCTCAGTACTCTCAGATGGAACGAGACGCTCTGAAGCTAGC
GCGGGAGATCGGCGCGGAGTACTGGGCCGTGTCGTCGCTGACAGGGGAGAACGTCAACGAGTTTTTCTCTCGGGTCGCCT
CACTGGGGTTCGAGAACAGCATCCTGGCCGAGTTGGAGGAAAAAGGGTCGGCCACGCAGATGGGCGAGGTCCCAATAAGC
AGCCACTTGCTGTACATCCCATCAAAGAAGGAGAAAAAGTGCAGCTGCTGCCAGTGA

Alignment

ORF - retro_trub_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.86 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSVLPPIRKDRVIARLPQCFRKEAALHTKEDFNNKVKTACQEQRTGTVGRFKISKVIVVGDLAVGKTCLI
          M..LPPI..DR.I.RLPQCFR.EAALH..E.FN.KVKTACQEQ..G.....KISKVIVVGDLAVGKTCLI
Retrocopy MNLLPPIQNDRIISRLPQCFRREAALHRRENFNDKVKTACQEQPSGRLA-YKISKVIVVGDLAVGKTCLI

Parental  NRFCKDVFDKNYKATIGVDFEMERFEVLGVPFSLQLWDTAGQERFKCIASTYYRGAQVVIIAFDVNDIGS
          NRFCKDVFD.NY.AT.GVDFE.E.F.VLGVPF.LQLWDT.GQER.KCIAS.YYRGAQVVI.AFDVNDIGS
Retrocopy NRFCKDVFDRNYNATLGVDFEIENFQVLGVPFTLQLWDTSGQERYKCIASSYYRGAQVVIVAFDVNDIGS

Parental  FSHVRQWLEDSLKENDPTAVQLFLVGTKKDLSSPAQYSQMEQEALKLAQELSAEYWAVSSLTGENVNEFF
          FSHVRQWLE.SL..ND..A.QLFLVGTKKDLSSPAQYSQME..ALKLA.E..AEYWAVSSLTGENVNEFF
Retrocopy FSHVRQWLEESLEDNDVAAIQLFLVGTKKDLSSPAQYSQMERDALKLAREIGAEYWAVSSLTGENVNEFF

Parental  FRVASLAFETSVLAELEKSGS-RQIGEVVRISSNSSNLNRSSKKKQSNCCQ
          .RVASL.FE.S.LAELE..GS..Q.GE.V.ISS..........KK.S.CCQ
Retrocopy SRVASLGFENSILAELEEKGSATQMGE-VPISSHLLYIPSKKEKKCS-CCQ

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_2 retrocopy.

TSS

Takifugu rubripes was not studied using FANTOM5 data.

Lab

retro_trub_2 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_trub_2 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	ENSTRUG00000005937	1 retrocopy	retro_trub_2 ,