RetrogeneDB ID: retro_chof_51

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_56136:6473..7430(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000012816
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000007691
• Aliases: None
• Description: None

Sequence

>retro_chof_51
ATGGCTCTTCCGCTCATCATAAAATGGGGTGGACAGGAATATTCGGTGACTACACTTTCAGAAGATGATACTGTACTAGA
TCTTAAACAGTTTCTCAAGACCCTTACAGGAGTGCTGCCAGAACGTCAAAAGTTACTTGGACTCAAAGTTAAAGGCAAAC
CTGCAGAAAATGATGTTAAGCTTGGAGCTCTCAAACTGAAAACAAATACTAAAATCATGATGATGGGAACTCGTGAGGAG
AGCTTGGAAGATGTCTTAGGTCCACCACCTGACAATGATGATGTTGTCAACGATTTTGATATTGAAGATGAAGTAGTTGA
AGTAGAAAATAGGGAAGAAAACCTCCTGAAAATTTCTCGCAGAGTTAAAGAGTACAAAGTGGAAATTTTGAATCCTCCCA
GGGAAGGGAAAAAGCTTTTGGTTTTAGATGTTGATTATACATTATTTGACCATAGGTCTTGTGCAGAGACTGGTGTAGAA
TTAATGAGGCCATATCTTCATGAATTCCTAACATCTGCATATGAGGATTATGACATTGTTATATGGTCTGCAACAAATAT
GAAGTGGATTGAAGCTAAAATGAAAGAGCTGGGAGTGAGCACAAATGCAAACTATAAGATTACCTTCATGTTGGACAGTG
CTGCTATGATAACAGTGCATACTCCAAGGAGAGGATTAATAGACGTAAAACCTCTTGGTGTTATATGGGGAAAGTTTTCG
GAGTTTTACAGCAAAAAAAATACCATTATGTTTGATGACATAGGAAGAAATTTTCTAATGAACCCACAGAATGGACTAAA
GATAAGGCCTTTTATGAAAGCTCACCTAAATCGAGATAAAGACAAAGAACTTTTAAAATTAACTCAGTACCTCAAGGAAA
TAGCAAAATTAGATGACTTCCTGGAGCTAAATCACAAATATTGGGAAAGGTATCTCTCAAAGAAACAAGGACAGTAG

Alignment

ORF - retro_chof_51 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.95 %
• Parental protein coverage: 61.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALPLIIKWGGQEYSVTTLSEDDTVLDLKQFLKTVTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNT
          MALPLIIKWGGQEYSVTTLSEDDTVLDLKQFLKT.TGVLPERQKLLGLKVKGKPAENDVKLGALKLK.NT
Retrocopy MALPLIIKWGGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKTNT

Parental  KIMMMGTREESLEDVLVPPPDNDDVVNDFDIEDEVVEVKNREENLLKISRRVKEYKVEILNPPREGKKLL
          KIMMMGTREESLEDVL.PPPDNDDVVNDFDIEDEVVEV.NREENLLKISRRVKEYKVEILNPPREGKKLL
Retrocopy KIMMMGTREESLEDVLGPPPDNDDVVNDFDIEDEVVEVENREENLLKISRRVKEYKVEILNPPREGKKLL

Parental  VLDVDYTLFDHRSCAETGVELMRPYLHEFLTSAYEDYDIVIWSATNMKWIEAKMK
          VLDVDYTLFDHRSCAETGVELMRPYLHEFLTSAYEDYDIVIWSATNMKWIEAKMK
Retrocopy VLDVDYTLFDHRSCAETGVELMRPYLHEFLTSAYEDYDIVIWSATNMKWIEAKMK

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_51 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007691	1 retrocopy	retro_chof_51 ,
Echinops telfairi	ENSETEG00000000170	1 retrocopy	retro_etel_1142,
Microcebus murinus	ENSMICG00000010060	2 retrocopies	retro_mmur_1083, retro_mmur_1319,
Myotis lucifugus	ENSMLUG00000006359	1 retrocopy	retro_mluc_1367,
Monodelphis domestica	ENSMODG00000008063	2 retrocopies	retro_mdom_1251, retro_mdom_1351,
Mustela putorius furo	ENSMPUG00000013396	1 retrocopy	retro_mputfur_1098,
Mus musculus	ENSMUSG00000041231	1 retrocopy	retro_mmus_762,
Oryctolagus cuniculus	ENSOCUG00000002224	1 retrocopy	retro_ocun_1036,
Tupaia belangeri	ENSTBEG00000008983	1 retrocopy	retro_tbel_41,
Tursiops truncatus	ENSTTRG00000005876	1 retrocopy	retro_ttru_761,