RetrogeneDB ID: retro_chof_384

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_102299:3346..3884(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1orf52
• Ensembl ID: ENSCHOG00000012863
• Aliases: None
• Description: chromosome 1 open reading frame 52 [Source:HGNC Symbol;Acc:24871]

Sequence

>retro_chof_384
ATGGCAGCAGACGAAAAGGACCCTCTGAGCTATCTTGCAGTTTACAGGAGTAGCAGCTCAGGCTCCTCGGACGAGAAACA
CAACAGCAAGCAGGAAGAGATGAGTCGCAGGGCCTCAGATCCGGTGAAGCCAACGGGCAGCAGTGGAAATGATGGAAAAG
CAGCTGCCGGGACCCAACGAGCTGTTCCAGAGCGTGACTCGCCTGGCCTTTCTCTACAATCCCTTGAACAAGCAGACAAA
CAGGGAGAGGCATGTCATCAAGGCGCCCAAGGCACCTCCAAAGGAATTCAAAATATGGAAGTCAAACTATGAACCACCTC
CTGAGACCTACACTACCGAGAAGAAACCATGGCCCCCAGAGCTGGATATGGCAATAAAGTGGTCAAACATATATGAGGAC
AATGGTGATCATGCCCCATAGAATGCTAAGAAAGCTAGGTTTCTACCGGAAGGGGAGGAGACAGTGAAATCAGATGATGA
AAAAGATGAACATACTTCTAAAAAGTTGAAAGTGGAACCAGGAGAACCAGCAAAGAAG

Alignment

ORF - retro_chof_384 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.89 %
• Parental protein coverage: 98.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAADEKDPLSYFAAYGSSSSGSSDEEDNSEPEEMGRRTSDPVKPTGSSVN-MAKRLPGPDELFRSVTRPA
          MAADEKDPLSY.A.Y.SSSSGSSDE..NS..EEM.RR.SDPVKPTGSS.N.M.K.LPGP.ELF.SVTR.A
Retrocopy MAADEKDPLSYLAVYRSSSSGSSDEKHNSKQEEMSRRASDPVKPTGSSGN>MEKQLPGPNELFQSVTRLA

Parental  YLY-PLNKQXXXXXXXXXXXXXPPKEFKIWKSNYVPPPETYTTEKKPPPPELDMAIKWSNIYEDNGDDAP
          .LY.PLNKQ.............PPKEFKIWKSNY.PPPETYTTEKKP.PPELDMAIKWSNIYEDNGD.AP
Retrocopy FLYNPLNKQTNRERHVIKAPKAPPKEFKIWKSNYEPPPETYTTEKKPWPPELDMAIKWSNIYEDNGDHAP

Parental  QNAKKARLLPEGEETVESDDEKDEHTSKKRKVEPGEPAKK
          .NAKKAR.LPEGEETV.SDDEKDEHTSKK.KVEPGEPAKK
Retrocopy *NAKKARFLPEGEETVKSDDEKDEHTSKKLKVEPGEPAKK

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_384 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012863	1 retrocopy	retro_chof_384 ,
Oryctolagus cuniculus	ENSOCUG00000002803	2 retrocopies	retro_ocun_1489, retro_ocun_1892,