RetrogeneDB ID: retro_trub_4

Retrocopy location

• Organism: Fugu rubripes (Takifugu rubripes)
• Coordinates: scaffold_1:501163..501664(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTRUG00000011134
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ube2g1a (2 of 2)
• Ensembl ID: ENSTRUG00000005995
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2G 1a (UBC7 homolog, yeast) [Source:ZFIN;Acc:ZDB-GENE-030131-6065]

Sequence

>retro_trub_4
ATGACAGAACCCCGCTCAGCGCTGTTACTAAGGAAACAGCTTGCAGAACTAAACAAAAGTCCAGTGGATGGATTTTCGGC
AGGCTTGATCCAGGACAACGATCTCTATAGATGGGAAGTAATCATCATTGGGTCTGCGGACACATTCTACGAAGGCGGCG
TGTTCAAAGCTCATCTGACATTTCCCAAAGATTATCCGCTCAGGCCACCTAAAATGAAATTCATCACAGATATATGGCAC
CCTAATATCGACAAGAACGGAGATGTTTGTATTTCTATTTTGCACGAGCCTGGGGAAGACAAGTATGGCTATGAGAAGCC
AGAAGAGCGTTGGCTCCCCATCCACACAGTAGAAACCATCATGATCAGCGTCATCTCAATGCTGGCAGACCCAAATACCG
AATCGCCTGCAAATGTGGATGCTGCCAAAGAGTGGAAGGAAGACAGAGATGAGTTCAAAAGGAAAGTTGCTCGTTGTGTA
CGGAAAAGCCAAGATGACTGA

Alignment

ORF - retro_trub_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.81 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTEPRSALLLRRQLTELNKSPVDGFSAGLIRDNDLYRWEVMIIGPPDTLYEGGVFKAHLTFPKDYPLRPP
          MTEPRSALLLR.QL.ELNKSPVDGFSAGLI.DNDLYRWEV.IIG..DT.YEGGVFKAHLTFPKDYPLRPP
Retrocopy MTEPRSALLLRKQLAELNKSPVDGFSAGLIQDNDLYRWEVIIIGSADTFYEGGVFKAHLTFPKDYPLRPP

Parental  KMKFITDIWHPNVDKNGDVCISILHEPGEDKYGYEKPEERWLPIHTVETIMISVISMLADPNSDSPANVD
          KMKFITDIWHPN.DKNGDVCISILHEPGEDKYGYEKPEERWLPIHTVETIMISVISMLADPN..SPANVD
Retrocopy KMKFITDIWHPNIDKNGDVCISILHEPGEDKYGYEKPEERWLPIHTVETIMISVISMLADPNTESPANVD

Parental  AAKEWREDRDGEFKRKVARCVRKSQDD
          AAKEW.EDRD.EFKRKVARCVRKSQDD
Retrocopy AAKEWKEDRD-EFKRKVARCVRKSQDD

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_4 retrocopy.

TSS

Takifugu rubripes was not studied using FANTOM5 data.

Lab

retro_trub_4 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_trub_4 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014433	1 retrocopy	retro_btau_604,
Choloepus hoffmanni	ENSCHOG00000011801	1 retrocopy	retro_chof_2181,
Ciona savignyi	ENSCSAVG00000009498	1 retrocopy	retro_csav_4,
Macropus eugenii	ENSMEUG00000009769	3 retrocopies	retro_meug_360, retro_meug_473, retro_meug_647,
Myotis lucifugus	ENSMLUG00000002118	1 retrocopy	retro_mluc_104,
Oryctolagus cuniculus	ENSOCUG00000000248	1 retrocopy	retro_ocun_152,
Otolemur garnettii	ENSOGAG00000008795	1 retrocopy	retro_ogar_2554,
Rattus norvegicus	ENSRNOG00000010041	3 retrocopies	retro_rnor_2496, retro_rnor_317, retro_rnor_970,
Sarcophilus harrisii	ENSSHAG00000002399	1 retrocopy	retro_shar_75,
Tupaia belangeri	ENSTBEG00000006117	1 retrocopy	retro_tbel_2852,
Tetraodon nigroviridis	ENSTNIG00000008566	1 retrocopy	retro_tnig_11,
Takifugu rubripes	ENSTRUG00000005995	1 retrocopy	retro_trub_4 ,
Tursiops truncatus	ENSTTRG00000000595	1 retrocopy	retro_ttru_1578,
Drosophila melanogaster	FBgn0058045	1 retrocopy	retro_dmel_6,