RetrogeneDB ID: retro_chof_14

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_132126:3789..4347(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000001323
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000012555
• Aliases: None
• Description: None

Sequence

>retro_chof_14
ATGGAGCCCACACAAGACTATCCGCTGTTCGGAGGCACCTTTTCCGCCATGCTCCCCCTGGGGACCCTTGAGGTAAGCGA
CCTCCGACCGGTCCCGGACAATCAAGAAGTTTTCTGCCATCGCGCGACGGACCAGAGCTTGATCATGGAACTTCTGGAGC
TGCAGGCCCACGTGCAGGGCGAGGCGGCTGCGCGGTACCATTTTGAGGACGTTGGTGGGGTGCAGGGAGCTAGGGAGGTG
CAAGTGGAAGCTGTGCAGCCCCTCCCTGTGGAGAGCCTAGCCCTGAGGGGCTGCTGTCAAGAAGCCTGGGTCCTCTCTGG
CAAGCAAAAGGTGGCTAAAGAAAACCAGCCGGTAGCAAAGGACGTGACACTGCACCAGGCCTTGCTGCGGCTGCCCCGGT
ACCAGACTGATCTGCTCACCTTCAATCAGTCACACCCTGAGATCAGGTCATCTCTTGGCCCTGAAAATCTGTCACCCCCG
CCTTGGAGCATGGATGACTTTGAACTGCTGATGACCAGTCTGACCCTTCATGATCCCAACATCTTTGGTCCCCAGTAA

Alignment

ORF - retro_chof_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.72 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEPTRDYPLFGGAFSAMLPLETLDVSDLRPVPDNQEV-CHRATDPSLIVELLELQAHVQGEAAARYHFED
          MEPT.DYPLFGG.FSAMLPL.TL.VSDLRPVPDNQEV.CHRATD.SLI.ELLELQAHVQGEAAARYHFED
Retrocopy MEPTQDYPLFGGTFSAMLPLGTLEVSDLRPVPDNQEVFCHRATDQSLIMELLELQAHVQGEAAARYHFED

Parental  VGGVQGAREVQVEAVQPLPVESLALRGCCQEAWVLSGKQKVAKENQQVAKDVTMHQALVRLPQYQTDVLL
          VGGVQGAREVQVEAVQPLPVESLALRGCCQEAWVLSGKQKVAKENQ.VAKDVT.HQAL.RLP.YQTD.LL
Retrocopy VGGVQGAREVQVEAVQPLPVESLALRGCCQEAWVLSGKQKVAKENQPVAKDVTLHQALLRLPRYQTD-LL

Parental  TFNQS
          TFNQS
Retrocopy TFNQS

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_14 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012555	1 retrocopy	retro_chof_14 ,
Dasypus novemcinctus	ENSDNOG00000018164	1 retrocopy	retro_dnov_2261,
Dipodomys ordii	ENSDORG00000007147	2 retrocopies	retro_dord_325, retro_dord_346,
Macropus eugenii	ENSMEUG00000006399	2 retrocopies	retro_meug_1091, retro_meug_220,
Mus musculus	ENSMUSG00000032892	2 retrocopies	retro_mmus_175, retro_mmus_2983,
Rattus norvegicus	ENSRNOG00000004980	4 retrocopies	retro_rnor_1148, retro_rnor_2982, retro_rnor_2983, retro_rnor_759,