RetrogeneDB ID: retro_chof_2019

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_45671:6600..7061(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C3orf33
• Ensembl ID: ENSCHOG00000013532
• Aliases: None
• Description: chromosome 3 open reading frame 33 [Source:HGNC Symbol;Acc:26434]

Sequence

>retro_chof_2019
GCAGGGTGGGCTCCTGGGAGGCCGTGAACATGGGGGGGGCAGCCCCTGGTGGTGGCGAGGATCTCACAGTGAGCAGACGG
CCACCTGCTCCTCATCTGGAACATCAGCACTGGAATGGCTGTAGTTGGAAGAATGTTACTTCCAAGAAGTTTGATTGACA
TTGAAATCCACAAGTGTTTCAGGTATTCCAGTAGAATTTATAAAAAGGAATGTTAAGCTACGTGGACAATTACACCGAAT
AACAGAGAATGGTTTAGAAACTGAACATTCTATTATTTTACCTATTATATCTTCATGGAGAAATGAGCCACATGGTGTTT
TGCTGGTTAAGTTGGCTGGAGTAGAACTCATTGAAAGTGGGAAGGTACGGTTATAAAAGGAGTTTACAACCTTCCCAACT
ACTGTGGTTGCGACTTCTTGGAAAGGAGAACTCATCATTTTTTTGATACCTTTTAGTGAAG

Alignment

ORF - retro_chof_2019 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.43 %
• Parental protein coverage: 53.63 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AASAPQLPDRDPAAPNVVARISQWADDHLRLVRNISTGMAIVGIMLLL-RSVRLTSKFTSSSGIPAEFIK
          A..AP..P......P.VVARISQ.AD.HL.L..NISTGMA.VG.M.LL...V.LT.K.TS.SGIP.EFIK
Retrocopy AGWAPGRP*TXXXQPLVVARISQ*ADGHLLLIWNISTGMAVVGRM-LL>QEV*LTLKSTSVSGIPVEFIK

Parental  RNVKLRGRLHRVTENGLEIEHIPITFPIISSWRNEPHGVLLVRLAGVELTETGKVWL-QNELKPSQLLWF
          RNVKLRG.LHR.TENGLE.EH..I..PIISSWRNEPHGVLLV.LAGVEL.E.GKV.L....L.PSQLLW.
Retrocopy RNVKLRGQLHRITENGLETEH-SIILPIISSWRNEPHGVLLVKLAGVELIESGKVRL>KRSLQPSQLLWL

Parental  QLLGKENSTLFCYLLVK
          .LLGKENS..F.YLLVK
Retrocopy RLLGKENSSFF*YLLVK

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_2019 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	ENSCHOG00000013532	1 retrocopy	retro_chof_2019 ,
Cavia porcellus	ENSCPOG00000006620	1 retrocopy	retro_cpor_882,