RetrogeneDB ID: retro_chof_664

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_13287:11925..12364(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EXOSC8
• Ensembl ID: ENSCHOG00000009005
• Aliases: None
• Description: exosome component 8 [Source:HGNC Symbol;Acc:17035]

Sequence

>retro_chof_664
GAGCTTGCATGGGTTCTATACTGTGATCTCATTTGCCTCAACTATGATGATAACATTTTGGATGCCTGTATGTTTGCTTT
ATTAGCTGCTTTAAAAGATGTACAGTTGCCTGAAGTTACTGTAAATGAAGAAACTGCCTTAGCAGAAGTTAATTTTAAAG
AAGAGTCATTTGAATATTAGAACGCATCCAGTCGCAACCTCCTTTGCCACATTTGATGACACTTTACTCATAGTTGACCC
TACTGGCGAAGAGGAGCACCTGGCCACTGGAAACTTAACAGTAGTAATGGATGAAGAGGGCAAGCTGCACTGTCTTTACA
AACCAGGTGGAAGTGGGCTGACAGGAGCTAAACTTCAGGACTGTATGAGCCGAGCAGTTACAAGACATAGAGAAGCTAAA
AAACTGATGGATGAAGTAATTCAGAGTATGAAACCCAAA

Alignment

ORF - retro_chof_664 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.22 %
• Parental protein coverage: 54.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KLAWVLYCDLICLDYDGNILDACTFALLAALKDVQLPEVTINEETALAEVN-LKKKSHLNIRTHPVATSF
          .LAWVLYCDLICL.YD.NILDAC.FALLAALKDVQLPEVT.NEETALAEVN.LKK.SHLNIRTHPVATSF
Retrocopy ELAWVLYCDLICLNYDDNILDACMFALLAALKDVQLPEVTVNEETALAEVN>LKK-SHLNIRTHPVATSF

Parental  AIFDDTLLIVDPTGEEEHLATGSLTVVMDEEGKLCCLHKPGGSGLTGAKLQDCISRAVTRHREVKKLMDE
          A.FDDTLLIVDPTGEEEHLATG.LTVVMDEEGKL.CL.KPGGSGLTGAKLQDC.SRAVTRHRE.KKLMDE
Retrocopy ATFDDTLLIVDPTGEEEHLATGNLTVVMDEEGKLHCLYKPGGSGLTGAKLQDCMSRAVTRHREAKKLMDE

Parental  VIQSMKPK
          VIQSMKPK
Retrocopy VIQSMKPK

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_664 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009005	2 retrocopies	retro_chof_2014, retro_chof_664 ,
Dasypus novemcinctus	ENSDNOG00000019133	1 retrocopy	retro_dnov_1273,
Tupaia belangeri	ENSTBEG00000012040	9 retrocopies	retro_tbel_1492, retro_tbel_1680, retro_tbel_2932, retro_tbel_349, retro_tbel_3712, retro_tbel_4030, retro_tbel_419, retro_tbel_4649, retro_tbel_527,