RetrogeneDB ID: retro_chof_2603

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_89616:4227..5296(-)
• 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_2603
AGAACTTGTAGGGTTGCTGCCACCACCATGCTACCACAACAGCTTCTTCTCACTTCTTTCCCTTCACAGGCCCTGCCAGG
CAGCTTTCCTGCACTACTGCCTCCACTCACTCCCTGCCTTGCTGCCCTACTCCATTACTGTAAAATGGGGAAAGGAGAAA
TTTGAGGATTTAGAATTGAATATTGATGAAACTTCAATGGTGTTCAAGGCTCAGCTTTTTGCACTAACTGGAGTCCAGTT
GGCCAGACAGAAAGTTATGGTGAAAGGAGAACTGTTGAAGGATGATGATTGGGGAAACATCAAAATAAAACATGGAATTA
CTCTACTAATGGTGTGGCCAGCAGATGCACTCCAGGAGGAACCATCAGCTAAAACTGTGTTTGTAGAAGACATGACAGAA
CAGTTAGCATCTGCTATGGAATTACCATGTGGATTGACAAATCTTGGTAACATGAATGCCACAGTTCAGTGTATCCAGAC
TGTGCCTAAACTCACAGATGCCCTTAAAAGGTGTGTGGGAGCCTTGAGAGCTCCAGGGGAAATGACTTCAGCCCCGTATA
TTACTGCAGCCCTTAGGATTTTTCTGATTCCATGGATAAACTTCTTCCAGTATTCCACCTATTAGTCTACTGCAGTTTTT
GCACATGGCTTTCCCACACTTTGTGGAGAAGGGTGAACAAGGACAGTATCTTCAACAGGATGCATATGTATGTTGGATAA
AAATTATGTGAGTATTGCAACAGAAATTGGAAGCCATAGAGGATGACTCTGTTAAAGAAACAGATTCTTCATCTAAATCA
ACAGGGACACCTTCTGAAAAAAAATTAATTCATCATTTCTTCAGTGTTGAGTTTAAACTACCATGAAATGTACAGAATCT
GAAAAAGTCACAAAAGAAAATGAAAATCAGCCTCAGCTTAGCTGTTTTATCAATCAAGAAGTTAAGAATCTTTTTACAAG
ACTTAAATTGGGACTTCAAGAAGAAATAACTAAACAATCTCCAACATTACAAAGATATGCTTTGTATATCAAATATTCAA
AAATCAGCTGGCTTCCTGCTTATGTGACT

Alignment

ORF - retro_chof_2603 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.0 %
• Parental protein coverage: 65.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RRSGAAAAAPPPPLSLLAAFPSQALP-AAFLRYRRSWHPAMPLYSVTVKWGKEKFEGVELNTDEPPMVFK
          R....AA....P...LL..FPSQALP.AAFL.Y.....PA...YS.TVKWGKEKFE..ELN.DE..MVFK
Retrocopy RTCRVAATTMLPQQLLLTSFPSQALP>AAFLHYCLHSLPALLPYSITVKWGKEKFEDLELNIDETSMVFK

Parental  AQLFALTGVQPARQKVMVKGGTLKDDDWGNIKIKNGITLLMMGSADALPEEPSAKTVFVEDMTEEQLASA
          AQLFALTGVQ.ARQKVMVKG..LKDDDWGNIKIK.GITLLM...ADAL.EEPSAKTVFVEDMTE.QLASA
Retrocopy AQLFALTGVQLARQKVMVKGELLKDDDWGNIKIKHGITLLMVWPADALQEEPSAKTVFVEDMTE-QLASA

Parental  MELPCGLTNLGNTCYMNATVQCIRSVPELKDALKRYAGALRASGEMASAQYITAALR-DLFDSMDK-TSS
          MELPCGLTNLGN...MNATVQCI..VP.L.DALKR..GALRA.GEM.SA.YITAALR.D..DSMDK.TSS
Retrocopy MELPCGLTNLGN---MNATVQCIQTVPKLTDALKRCVGALRAPGEMTSAPYITAALR<DFSDSMDK<TSS

Parental  SIPPIILLQFLHMAFPQFAEKGEQGQYLQQDANECWIQMMRVLQQKLEALEDDSIKETDTSSALAVTPSK
          SIPPI.LLQFLHMAFP.F.EKGEQGQYLQQDA..CWI..M.VLQQKLEA.EDDS.KETD.SS....TPS.
Retrocopy SIPPISLLQFLHMAFPHFVEKGEQGQYLQQDAYVCWIKIM*VLQQKLEAIEDDSVKETDSSSKSTGTPS-

Parental  KKSLIDQFFGVEFE-TSMKCTESEEEEVTKGKENQLQLSCFINQEVKYLFTGLKLRLQEEITKQSPTLQR
          ...LI..FF.VEF..T.MKCTES..E.VTK..ENQ.QLSCFINQEVK.LFT.LKL.LQEEITKQSPTLQR
Retrocopy XXXLIHHFFSVEFK<TTMKCTES--EKVTKENENQPQLSCFINQEVKNLFTRLKLGLQEEITKQSPTLQR

Parental  NALYIKSSKISRLPAYLT
          .ALYIK.SKIS.LPAY.T
Retrocopy YALYIKYSKISWLPAYVT

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_2603 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,