RetrogeneDB ID: retro_chof_902

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_165636:3361..3710(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2C
• Ensembl ID: ENSCHOG00000005054
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2C [Source:HGNC Symbol;Acc:15937]

Sequence

>retro_chof_902
ATAGCAGGTGACAAAGGAATTTCCACTTTCCCTGAATCAGACAACCTTTTCAAATGGATGGAGACCATCCATGGAATAGG
TTTCATGGTATATGAAGATCTGAGGTGTAAGGTGTCCCTGGAGTTCCCCAGTGGCTACCCATACAACCCACCCTAGGTAA
AGTTCCTTATAATCTGATACCACCCAACATGGACCCCCAGGGTAACATCTGCTTGGACATCCTGAAGGACAAGTGGTCCA
CCCTGTATGAAGTCAAAACGATCTTCTTCTCTATCTAGAGCCTGCTGGGAGAACTCAACATTTTAACTCTTTGAACACAC
ATGCTGCTAAGCTCTGGAAAAACCATACA

Alignment

ORF - retro_chof_902 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.11 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSGDKGISAFPESDNLFKWIGTIHGAAGTVYEDLRYKLSLEFPSGYPYNAPTVKFLTPCYH-PNVDTQGN
          ..GDKGIS.FPESDNLFKW..TIHG....VYEDLR.K.SLEFPSGYPYN.P.VKFL...YH.PN.D.QGN
Retrocopy IAGDKGISTFPESDNLFKWMETIHGIGFMVYEDLRCKVSLEFPSGYPYNPP*VKFLII*YH<PNMDPQGN

Parental  ICLDILKDKWSALYDVRTILLSIQSLLGEPNI-DSPLNTHAAELWKNPT
          ICLDILKDKWS.LY.V.TI..SI.SLLGE.NI....LNTHAA.LWKN.T
Retrocopy ICLDILKDKWSTLYEVKTIFFSI*SLLGELNI<FNSLNTHAAKLWKNHT

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_902 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 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005054	1 retrocopy	retro_chof_902 ,
Choloepus hoffmanni	ENSCHOG00000005910	4 retrocopies	retro_chof_1114, retro_chof_1974, retro_chof_889, retro_chof_957,
Cavia porcellus	ENSCPOG00000014102	2 retrocopies	retro_cpor_1007, retro_cpor_211,
Loxodonta africana	ENSLAFG00000003164	1 retrocopy	retro_lafr_73,
Macaca mulatta	ENSMMUG00000021023	4 retrocopies	retro_mmul_1345, retro_mmul_170, retro_mmul_1951, retro_mmul_777,
Mustela putorius furo	ENSMPUG00000017619	2 retrocopies	retro_mputfur_103, retro_mputfur_189,
Otolemur garnettii	ENSOGAG00000004989	3 retrocopies	retro_ogar_2347, retro_ogar_249, retro_ogar_3067,
Pan troglodytes	ENSPTRG00000013564	1 retrocopy	retro_ptro_38,
Sarcophilus harrisii	ENSSHAG00000002117	1 retrocopy	retro_shar_832,