RetrogeneDB ID: retro_chof_2406

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_72488:7460..8389(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: USP14
• Ensembl ID: ENSCHOG00000010588
• Aliases: None
• Description: ubiquitin specific peptidase 14 (tRNA-guanine transglycosylase) [Source:HGNC Symbol;Acc:12612]

Sequence

>retro_chof_2406
GCCACCAGCACCGCACCACTGCCGCAGCCTCTTCTCGCTGCTTTCCCTTCGCAGGCCCTGCCAGGCCAGCCTTCCTGCAG
TACCGTCGCTCCTGGCTCCCCGCCATGCCGCTCTACTCCGTTACTGTAAAATGGGGAAAGGAGAAATTTGAAGGTGTGGA
ATTGAATACTGATGAACCTCCAATGGTGTTCAAGACTCAGCTGATTGCACTGACTGGACTCCAGCCGGCCAGACAGAAAG
TTATGGTGAAAGGGGGGAACGTTGAAGGATGATGATTGGGGAAACATCGAAATAAAAAATGGAATTTCTCTACTAATTAT
GGGGTCAGCAGATGCTCTCCCGGAAGAACCATCAGCTAAAACTGTCTTTGTAGAAGATATGACAGAAGAACAGTTAACAT
CTGCTATGGGATTACCATGTGGATTGACAAATCTTGGTAACACTTGTTACATGAATGCCACAGTTCAGTGTATCTGGTCT
GTGCCTGAAGTCAAAATGCCCTTAAAAGGTATGCAGGTGCCTTGAGAGCTTCAGGGGAAATGGCTTCAGCACAGTATATT
ACTGCAACCCTTAGAGATTTGTTTGACTCCGTGGATAAAACTACTTCTAGTACTCCACCTATTATTCTACTGCAGTTTTT
GCACATGGCTTTTCCACAGTTTGCAGAGAAGGGTGAACAAGGACAGTATCTTCAACAGGATGCAAATGAATGTTGGATAC
AAATTATGTGAGTATTACAACAGAAATTGGAAGCCTTAGAGGATGATTCTGTTAAAGAAATAGATTCCTCATCTGCATCA
GCAGTGACACCTACTAAAAAGAAAAGTTTAATTGATCAGTTCTTTGGTGTTGAGATTGAAACTACCATGAAATGTACAGA
ATGTGAAGAAGAAGTAACAAAAGGAAAGGAAAATCAGCTTCAGCTTAGC

Alignment

ORF - retro_chof_2406 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 56.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AAAAAP-PPPL-SLLAAFPSQALPAAFLRYRRSWHPAMPLYSVTVKWGKEKFEGVELNTDEPPMVFKAQL
          A...AP.P.PL.S....F...A.PA.FL.YRRSW.PAMPLYSVTVKWGKEKFEGVELNTDEPPMVFK.QL
Retrocopy ATSTAPLPQPL<SRCFPFAGPARPA-FLQYRRSWLPAMPLYSVTVKWGKEKFEGVELNTDEPPMVFKTQL

Parental  FALTGVQPARQKVMVKGG-TLKDDDWGNIKIKNGITLLMMGSADALPEEPSAKTVFVEDMTEEQLASAME
          .ALTG.QPARQKVMVKGG.TLKDDDWGNI.IKNGI.LL.MGSADALPEEPSAKTVFVEDMTEEQL.SAM.
Retrocopy IALTGLQPARQKVMVKGG>TLKDDDWGNIEIKNGISLLIMGSADALPEEPSAKTVFVEDMTEEQLTSAMG

Parental  LPCGLTNLGNTCYMNATVQCIRSVPELK-DALKRYAGALRASGEMASAQYITAALRDLFDSMDKTSSSIP
          LPCGLTNLGNTCYMNATVQCI.SVPE.K..ALKRYAGALRASGEMASAQYITA.LRDLFDS.DKT.SS.P
Retrocopy LPCGLTNLGNTCYMNATVQCIWSVPEVK<NALKRYAGALRASGEMASAQYITATLRDLFDSVDKTTSSTP

Parental  PIILLQFLHMAFPQFAEKGEQGQYLQQDANECWIQMMRVLQQKLEALEDDSIKETDTSSALAVTPSKKKS
          PIILLQFLHMAFPQFAEKGEQGQYLQQDANECWIQ.M.VLQQKLEALEDDS.KE.D.SSA.AVTP.KKKS
Retrocopy PIILLQFLHMAFPQFAEKGEQGQYLQQDANECWIQIM*VLQQKLEALEDDSVKEIDSSSASAVTPTKKKS

Parental  LIDQFFGVEFETSMKCTESEEEEVTKGKENQLQLS
          LIDQFFGVE.ET.MKCTE..EEEVTKGKENQLQLS
Retrocopy LIDQFFGVEIETTMKCTEC-EEEVTKGKENQLQLS

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_2406 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 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008213	1 retrocopy	retro_acar_108,
Choloepus hoffmanni	ENSCHOG00000010588	4 retrocopies	retro_chof_1736, retro_chof_2406 , retro_chof_2529, retro_chof_2603,
Echinops telfairi	ENSETEG00000004949	1 retrocopy	retro_etel_966,