RetrogeneDB ID: retro_chof_355

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_859:170313..170947(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EAF1
• Ensembl ID: ENSCHOG00000007449
• Aliases: None
• Description: ELL associated factor 1 [Source:HGNC Symbol;Acc:20907]

Sequence

>retro_chof_355
AAAGGAGATGAGGTCACATTTCCACTGCCACATATCCCTGGATCCACACCACCAGTGACTTGTGTTCAAAGGGAACAAAT
GACCATATCAAAAAGACTGTGTGCTTATTATTAATCATGACACTGGTGAATACATACTGGAAAAACTCAATAGCAGCATT
CAGGTCAAGAAGACAAATGCTGAAGGGAGCAGTAGAATGGAACAGCAATCCGCTGATCCCCCACAGCCATCGCAGCCGCC
ACCGCCGCCACCACCTAGCCCATTCAGAGCTCCAAGGAAGCCTCCTGGTTGGACCCCAAACTTCTCCCTTGAAAGCTAAC
CCCTCACCCGAACGTCAGCTGGATGGCGTCCAAAGAGAGCTGAGGGCCGAAGTTGACATTACTGAGCAGATGAGTGGCAG
CAGTGGGAGCAGCTCCTCAGACTCTGGGAGCTCCCCGGGCAGTGATGGCGACAGGTCCAGCTCCGGAGGCAGGGACGGTG
CCCCGGCGGGTCCTCCACGACCTCACACCAGCAGCCCCACCTCAGCAGATTCACTGTCAGCAGCGGACCCAGCTGGCGGC
AAGGAAGCAACCAGCTTATGAACACCCTCAGAAATGACTTGCAGTTGAGTGAGTCTGGCAGTGACAGTGATGAC

Alignment

ORF - retro_chof_355 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.9 %
• Parental protein coverage: 80.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KGDEVTITLPHIPGSTPPMT-VFKGNKRPYQKDCVLIINHDTGEYVLEKLSSSIQVKKTRAEGSSKIQAR
          KGDEVT..LPHIPGSTPP.T.VFKGNK.PYQKDCVLIINHDTGEY.LEKL.SSIQVKKT.AEGSS....R
Retrocopy KGDEVTFPLPHIPGSTPPVT>VFKGNK*PYQKDCVLIINHDTGEYILEKLNSSIQVKKTNAEGSS----R

Parental  MEQQSTRPPQSSQPPPPPPPIPFRAPTKPP-VGSKTSPLKDNPSPEPQLDDIKRELRAEVDLIEQMSSSS
          MEQQS..PPQ.SQPPPPPPP.PFRAP.KPP.VG..TSPLK.NPSPE.QLD...RELRAEVD..EQMS.SS
Retrocopy MEQQSADPPQPSQPPPPPPPSPFRAPRKPP>VGPQTSPLKANPSPERQLDGVQRELRAEVDITEQMSGSS

Parental  GSSSSDSESSSGSDDDSSSSGGEDNAPASPPQP-SHQQPYNSRPTVANGTSRPQGSTQLMNTLRNDLQLS
          GSSSSDS.SS.GSD.D.SSSGG.D.APA.PP.P.SHQQP..SR.TV..G.S..QGS.QLMNTLRNDLQLS
Retrocopy GSSSSDSGSSPGSDGDRSSSGGRDGAPAGPPRP<SHQQPHLSRFTVSSGPSWRQGSNQLMNTLRNDLQLS

Parental  ESGSDSDD
          ESGSDSDD
Retrocopy ESGSDSDD

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_355 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 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006017	1 retrocopy	retro_cfam_1658,
Choloepus hoffmanni	ENSCHOG00000007449	4 retrocopies	retro_chof_1039, retro_chof_2342, retro_chof_355 , retro_chof_883,
Erinaceus europaeus	ENSEEUG00000002084	1 retrocopy	retro_eeur_254,
Monodelphis domestica	ENSMODG00000014543	1 retrocopy	retro_mdom_290,
Otolemur garnettii	ENSOGAG00000013964	1 retrocopy	retro_ogar_2142,
Sarcophilus harrisii	ENSSHAG00000006597	2 retrocopies	retro_shar_485, retro_shar_56,