RetrogeneDB ID: retro_chof_2097

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_48808:5175..5751(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SH3YL1
• Ensembl ID: ENSCHOG00000013307
• Aliases: None
• Description: SH3 domain containing, Ysc84-like 1 (S. cerevisiae) [Source:HGNC Symbol;Acc:29546]

Sequence

>retro_chof_2097
TGGTCTGCACCTCCAGCAGTTGGGGTAGCTGGGCTTGGTGGAGGATTTAAAATAGGAATTGAGGTATCAGATCTGGTAAT
AATTCTGAATTACGACAGAGCAGTAGAAGCCTTTGCAAAAGGTGGTAACCCAACATTTGGAGGGAATTTTACTGTGGCGG
TTCAGCCCTTGGGAAGGAATTTGGAAGGAAACGTAGCCTTAAGAAGCTCTGCAGCTGTCTTCACACATTGTAAATCAAGA
GGACTGTTCGCTGGCATATCTTTAGAAGGTGGCTATTTGACAGAGAGAAAAAATTCAAATCAAAAATTTTATTGTCAAGG
TACTCATGCTTATGATGTTTTACTTGGAGATATACCACAGTCAGCTCAAGCAGAAGATTTTCATGAAGTTCTTGATTACT
TTGCTGAAAAGTATGAAAATGAAGAACAACGGATCGATGCAAGAAAAGAGGCAAGGGAACAGAGAAAGGCTTTCGCTAAA
AAACTGCCTCCAAAAGTATTGCCAAGACTACAGCGATCACCTGCACCAGTCCAGCTGAACTCTGGCTCTCAAAGTAACAG
AAATGAATATAAGCTC

Alignment

ORF - retro_chof_2097 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.21 %
• Parental protein coverage: 56.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WSAPSAIGIAGLGGGFEIGIEVSDLVIILNYDRAVEAFAKGGNLTLGGNLTVAVGPLGRNLEGNLALRSS
          WSAP.A.G.AGLGGGF.IGIEVSDLVIILNYDRAVEAFAKGGN.T.GGN.TVAV.PLGRNLEGN.ALRSS
Retrocopy WSAPPAVGVAGLGGGFKIGIEVSDLVIILNYDRAVEAFAKGGNPTFGGNFTVAVQPLGRNLEGNVALRSS

Parental  AAVFTYCKSRGLFAGLSLEGSCLIERKETNRKFYCQDIRAYDILFGDIPRPAQAEDLYEILDSFTEKYEN
          AAVFT.CKSRGLFAG.SLEG..L.ERK..N.KFYCQ...AYD.L.GDIP..AQAED..E.LD.F.EKYEN
Retrocopy AAVFTHCKSRGLFAGISLEGGYLTERKNSNQKFYCQGTHAYDVLLGDIPQSAQAEDFHEVLDYFAEKYEN

Parental  EEQRINARKAAREQRKASAKELPPKPLSRPQQSSAPVQLNSGSQSNRNEYKL
          EEQRI.ARK.AREQRKA.AK.LPPK.L.R.Q.S.APVQLNSGSQSNRNEYKL
Retrocopy EEQRIDARKEAREQRKAFAKKLPPKVLPRLQRSPAPVQLNSGSQSNRNEYKL

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_2097 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	ENSCHOG00000013307	1 retrocopy	retro_chof_2097 ,
Dasypus novemcinctus	ENSDNOG00000003742	1 retrocopy	retro_dnov_1005,