RetrogeneDB ID: retro_chof_2181

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_56425:8957..9365(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2G1
• Ensembl ID: ENSCHOG00000011801
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2G 1 [Source:HGNC Symbol;Acc:12482]

Sequence

>retro_chof_2181
GGTGCTGTGAGAAGAGCTGGACCGAACGGACCCGAACAGGCAACGAGGAGCCGCTATCGCGCCCCAGCCCGGCCTTCCTT
GATTTCCGCTCTCCGGTCTTGGGGTCCTGGGTTCCTCAGCACACCCAGCTCCAGTCGCCCCCGGAGCCTCCCTCCAGTCC
TTCGGAAGTCCCTGCGCTAGCCCGGGCCCTTGGCGGGGAGGATGACGGAGCTGCAGTCGGCACTGCTGCTGCGAAGACAG
CTGGCAGAACTCAACAAAAATCCAGTGGAAAGCTTTTCAGCAGGTTTAATAGATGACAATGATCTCTACCGATGGGAAGT
CCTTATTATTGGTCCTCCAGATACTCTTTATGAAGGTGGTGTTTTTAAGGCTCATCTTACTTTCACAAAAGAGGATCCCC
TCCAGCCT

Alignment

ORF - retro_chof_2181 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.23 %
• Parental protein coverage: 57.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GAVRRAGPNGPEPATRSRYR-PS-PAFFDFGASVL-GPGFLSTPSSSRPQSLLPVLRKSRHQPGPLAGRM
          GAVRRAGPNGPE.ATRSRYR.P..PAF.DF...VL.GPGFLSTPSSSRP.SL.PVLRKS...PGPLAGRM
Retrocopy GAVRRAGPNGPEQATRSRYRAPA<PAFLDFRSPVL>GPGFLSTPSSSRPRSLPPVLRKSLR*PGPLAGRM

Parental  TELQSALLLRRQLAELNKNPVEGFSAGLIDDNDLYRWEVLIIGPPDTLYEGGVFKAHLTFPKDYPLRP
          TELQSALLLRRQLAELNKNPVE.FSAGLIDDNDLYRWEVLIIGPPDTLYEGGVFKAHLTF.K..PL.P
Retrocopy TELQSALLLRRQLAELNKNPVESFSAGLIDDNDLYRWEVLIIGPPDTLYEGGVFKAHLTFTKEDPLQP

Legend:

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

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_2181 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,