RetrogeneDB ID: retro_chof_1606

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_33704:1929..2419(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C2orf68
• Ensembl ID: ENSCHOG00000004242
• Aliases: None
• Description: chromosome 2 open reading frame 68 [Source:HGNC Symbol;Acc:34353]

Sequence

>retro_chof_1606
ATGGAGGTGGTGCCAGACCTCAGGCCAGGATTCTGCTGCAAGCCTGGCGGGCAGCTGGACATGAGCCACAGCTTCACGCA
CCATATCCAGCAGAACAAGCTCAGCTGGGACGACGACGAGAAGGAAGAAGGTAAAGCAGGCGGCCAAGGAGAAGGTGGGA
AGGTGGCACACGCCTGCGCTGACACGCCACGAAAGCCCAACCTGCAAGTACCTGCTGTGACTCTGCGAGGACTCTACTGT
CCGAGCAACTCAGTCTACAGAAGTCCAGCAAAAGCAGCAGTAGTGGTGGCTTCAAGCTGGAGGCTTCCGGGTATCAGCTC
TTCTTCTTAGAATCGGGGCCAACAGCGGAGAGGTCACATCAGTTATCATGTATCAGGATGATCATCCAGAAATGGTGAGT
GAGGAGGTGTCAGCCCACACGCCTCTGGATCCACCCATGCGAGAGGCCCTCAAGTTGTGCATCCAAGAGGAGACTGCAAA
GCACCAGAGC

Alignment

ORF - retro_chof_1606 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.79 %
• Parental protein coverage: 98.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MEVVPDLRPGFCCKPGGQLDMSHSFTHHIQQNKLSWD-DDE-KKVKQAAKEKVGRWHTPALTPRK-PNLQ
          MEVVPDLRPGFCCKPGGQLDMSHSFTHHIQQNKLSWD.D...KKVKQAAKEKVGRWHTPALT....P...
Retrocopy MEVVPDLRPGFCCKPGGQLDMSHSFTHHIQQNKLSWDDDEK>KKVKQAAKEKVGRWHTPALTRHESPTCK

Parental  YLL-LCDDST-RPSNPDY-EESGESSSSGGSELEPSGHQLFCLE-YEADSGEVTSVIVYQDDDPERVIEE
          YLL.LC.DST..PSN..Y...S..SSSSGG..LE.SG.QLF.LE...A.SGEVTSVI.YQDD.PE.V.EE
Retrocopy YLL*LCEDST<CPSNSVY<QKSSKSSSSGGFKLEASGYQLFFLE<IGANSGEVTSVIMYQDDHPEMVSEE

Parental  VSAHTPLDPPMREALKLRIREEIAKRQS
          VSAHTPLDPPMREALKL.I.EE.AK.QS
Retrocopy VSAHTPLDPPMREALKLCIQEETAKHQS

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_1606 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004242	1 retrocopy	retro_chof_1606 ,
Otolemur garnettii	ENSOGAG00000033817	1 retrocopy	retro_ogar_1736,