RetrogeneDB ID: retro_btau_604

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 15:55922348..55922854(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2G1
• Ensembl ID: ENSBTAG00000014433
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2 G1 [Source:RefSeq peptide;Acc:NP_001075927]

Sequence

>retro_btau_604
ATGACTGAGCTGCAGTTGGTACTGCTATAGCGAAGACATCTGGCAGAACTCAACAAAAATCCAGTGGAAGGCTTTTCAGA
AGGTTTAATAGAGACAATGATCTTTACCAATGGGAAGTTCTTATTATTGCTCTTCCAGATACACTTTACGAAGGTGGTGT
TTTTAGAGCTCGTCTCACTTTCCCAAAAGATTATCCCCTTTGGCCTCCTAAAATGAAATTCATTACTGAAATCCAGCATC
CAAATGTTGATAAACATGGTGATGTATGCTTTTCTATTCTTCACAAATCTGGGGAAGATAAATATGGTTATGAAAAGCCA
GAGGAATGCTAGTTGCCTATTCACACAGTGGAAATCATCATGATTAGTGTCATGTCTATGCTGGCAGACCCCAATGGAGA
CTCCCCTGCTAATGTTGATGCTGCAAAAGAATGGAGGGAAGACAGAAACGGAGAAGTCAAGAGGACAGTTGCCCTCTGTG
TAAGAAGAAGCCAAGAGCCTGCTTTT

Alignment

ORF - retro_btau_604 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.12 %
• Parental protein coverage: 99.41 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTELQSALLLRRQLAELNKNPVEGFSAGLID-DNDLYRWEVLIIGPPDTLYEGGVFKAHLTFPKDYPLRP
          MTELQ..LL.RR.LAELNKNPVEGFS.GLI..DNDLY.WEVLII..PDTLYEGGVF.A.LTFPKDYPL.P
Retrocopy MTELQLVLL*RRHLAELNKNPVEGFSEGLIE<DNDLYQWEVLIIALPDTLYEGGVFRARLTFPKDYPLWP

Parental  PKMKFITEIWHPNVDKNGDVCISILHEPGEDKYGYEKPEERWLPIHTVETIMISVISMLADPNGDSPANV
          PKMKFITEI.HPNVDK.GDVC.SILH..GEDKYGYEKPEE..LPIHTVE.IMISV.SMLADPNGDSPANV
Retrocopy PKMKFITEIQHPNVDKHGDVCFSILHKSGEDKYGYEKPEEC*LPIHTVEIIMISVMSMLADPNGDSPANV

Parental  DAAKEWREDRNGEFKRKVARCVRKSQETAF
          DAAKEWREDRNGE.KR.VA.CVR.SQE.AF
Retrocopy DAAKEWREDRNGEVKRTVALCVRRSQEPAF

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
ERP005899_liver	0.00 RPM	65.10 RPM
ERP005899_muscle	0.00 RPM	35.79 RPM
SRP017611_brain	0.00 RPM	46.73 RPM
SRP017611_kidney	0.00 RPM	53.76 RPM
SRP017611_liver	0.00 RPM	35.79 RPM
SRP030211_testis	0.05 RPM	31.09 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_604 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_604 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_604 has 0 orthologous retrocopies within eutheria 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,