RetrogeneDB ID: retro_chof_2529

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_82805:8118..9362(-)
• 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_2529
CTCCCTGAGGAGCATCAGCTAAAACTGGCTTCACAGAAGAGAGGACAGAAGAACAGTTACCATCTGCTGTGGAATTACCA
TGTGGATTGACAAATCTTGGTAACATTTACCACATGAATGCCACAGTTCGGTGTGTCCGGTCTGTGCCTGAACTCAAAGA
TGCCCTTAAAAGGTAGGGCAGATGTGTTGAGAGCTTCAGGGGAAATGGCTTCAGCACAGTATGTTACTGTAGTCCCTAGA
CATTTGTTTGACTCCACGGGTAAAAATCCTTCTAGTGTTCCACCTACTATTCTACTGCATTTTTTGCACATGATTTTCCC
ACAGTTGCAGAGAACGGTGAGCATGGACAATATCTTCAATGGGATGCAAATAAATGTTGGAGACAAATGATGTGAGTATT
ACAACAGAAACTGGAAGCCTTAGAAGACGATTCTGTTAAAGAAACAGATTCTTCACCTCAATCAGCAGTGACAACTTCTA
ATAAGAAAAGTTTAATTGATAAGTTCTTCAGTGTTGAGTTTTAAACTGCCAAGAAATGTATAGAAACTGAAGAAGATGTC
ACTAAAGAAATGAAAATCAGCTTCAGCTTAGCTGCTTTATCAATCAAGAAGTCAAGCCTCTTTTTACAGGACTTAAATTG
TGACTTTGGGAAGAAAACACTAAACAGTCTCCAACATTGCAAAGAAATGCTTTGTATATCAAACCTTCCAAAATCAGCTA
ACAAGCTGCTTACTTGACTATTCAGATGGTTCAATTTTTTTTTTATAAAGAGAAGGAATCTGTGAATGCCAAAGTTCTTA
AGAATGTTAAATCTCCTCTTATTTTGGATGTGTACAAAGTATGTACACCAGAACTTCAAAAGAAAATGATTTCTTTTCAA
ATTTCAAAAATCCATAAGATTAAAAAAAGTGAATCAGAAGCCAAAGACAAATGACAAAAAGAGTACTCCCCAGAAGGAAG
TTACGGACGAACCATTTTCTTTTGCTGATGACACTGGCTCCAATAACTGTGAATACTATGACTTACAAGCAGTGCTAAGA
CATCAGGGAAGGTCTGGTTCTTCAGGTCATTATGTATCATGGGTGAAAAGGAAACAAAATGAATGGATTAATTTGGATGA
TGATAAGGGTAGCATGGTTATACCAGAAGAAATTCTGTGGCTTTCTGGTGGTGGAGCCTGGCATATAGCTTATGTTCTAC
TCTATGGGCATCACAGAGTTGAAATATTACAAGAAGAAAGTGAA

Alignment

ORF - retro_chof_2529 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.22 %
• Parental protein coverage: 74.95 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LPEE-PSAKTVFVEDMTEEQLASAMELPCGLTNLGNTCYMNATVQCIRSVPELKDALKR-YAGALRASGE
          LPEE..SAKT.F.E..TEEQL.SA.ELPCGLTNLGN...MNATV.C.RSVPELKDALKR..A..LRASGE
Retrocopy LPEE<ASAKTGFTEERTEEQLPSAVELPCGLTNLGNIYHMNATVRCVRSVPELKDALKR>RADVLRASGE

Parental  MASAQYITAALRDLFDSMDKTSSSIPPIILLQFLHMAFPQF-AEKGEQGQYLQQDANECWIQMMRVLQQK
          MASAQY.T...R.LFDS..K..SS.PP.ILL.FLHM.FPQ..AE.GE.GQYLQ.DAN.CW.QMM.VLQQK
Retrocopy MASAQYVTVVPRHLFDSTGKNPSSVPPTILLHFLHMIFPQL<AENGEHGQYLQWDANKCWRQMM*VLQQK

Parental  LEALEDDSIKETDTSSALAVTPSKKKSLIDQFFGVEFETSMKCTESEEEEVTK-GKENQLQLSCFINQEV
          LEALEDDS.KETD.S...AVT.S.KKSLID.FF.VEF.T..KC.E..EE.VTK...ENQLQLSCFINQEV
Retrocopy LEALEDDSVKETDSSPQSAVTTSNKKSLIDKFFSVEF*TAKKCIET-EEDVTK<RNENQLQLSCFINQEV

Parental  KYLFTGLKLRLQEEITKQSPTLQRNALYIKSSKISRLPAYLTIQMVR-FFYKEKESVNAKVLKDVKFPLM
          K.LFTGLKL.L.EE.TKQSPTLQRNALYIK.SKIS...AYLTIQMV.....KEKESVNAKVLK.VK.PL.
Retrocopy KPLFTGLKL*LWEENTKQSPTLQRNALYIKPSKIS*QAAYLTIQMVQXXXXKEKESVNAKVLKNVKSPLI

Parental  LDVYELCTPALQEKMVSFRSKFKDLEDKKVNQQPK-TSDKKSSPQKEVKYEPFSFADDIGSNNCGYYDLQ
          LDVY..CTP.LQ.KM.SF....K....KK.....K.T.DKKS.PQKEV..EPFSFADD.GSNNC.YYDLQ
Retrocopy LDVYKVCTPELQKKMISFQIS-KIHKIKKSESEAK>TNDKKSTPQKEVTDEPFSFADDTGSNNCEYYDLQ

Parental  AVLTHQGRSSSSGHYVSWVKRKQDEWIKFDDDKVSIVTPEDILRLSGGGDWHIAYVLLYGPRRVEIIEEE
          AVL.HQGRS.SSGHYVSWVKRKQ.EWI..DDDK.S.V.PE.IL.LSGGG.WHIAYVLLYG..RVEI..EE
Retrocopy AVLRHQGRSGSSGHYVSWVKRKQNEWINLDDDKGSMVIPEEILWLSGGGAWHIAYVLLYGHHRVEILQEE

Parental  SE
          SE
Retrocopy SE

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_2529 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,