RetrogeneDB ID: retro_chof_2014

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_45490:3060..3866(+)
• 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_2014
ACGGTGGAACCTCTGGACTACTACAGGAGATTTTTGAAAGAGAACTGCCATCCTGATGGAAGAGAACTTGGTGAATTCAG
AACCACCACTGTCAACATAGGTTCAATTAGTACTGCAGATGGTTCTGCTTTAGTGAAGCTGGGAAATACTACAGTAATAT
GTGGAATTAAAGGGGAATTTGCAGTACCACCAAAACATGCCCCTGATAAAGGATATGTTGTTCCCAATGTGGATCTCCCA
CCCTGTGTTCTTCGAGATTTCCATCTGGACCTCCTGGGGAAGAGGCCCAAGTGGCTAGCCACTTCATTGCAGATGTCACT
GAAAATTCACAGATAATTCAGAAAGAGGACTTACGCATTACTCAAAGAAAGCTTGTGTGGGTTCTATACTGTGATCTCAC
TTGCCTCGACTATGATGGAAACATTTTGGATGCCTGTACATTTGCTTTGCTAGCTGCTTTAAAAGATGTGTAGTTGCCTG
AAGTTACTATAAATGAAGAAACTGCCTTAGCAGAAGTTAATTTAAAGAAGAAGAGTCATTTGAATATTACAGTGCATCTA
GTCGCAACCTCCTTTGCCATATTTGACACTTTACTCATAGTTGACCCTACTGGTGAGGAGGATCATCTGGCCACTGGAAG
CTTAACAGTAGTAATGGATGAAGAGGGCAAGCTGTGTTGTCTTCACAAACCAGGTGGAAGTGGGCTGACGGGAGCTAAGC
TTCAGGACTATATGAGCCAAGCAGTCACAAGACAGAGAGAAGTTAAAAAACTGATGGATGAAGTAATTCAGAGTATGAAA
CCCAAA

Alignment

ORF - retro_chof_2014 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.14 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TVEPLEYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGIKAEFAVPPTDAPDK
          TVEPL.YYRRFLKENC.PDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGIK.EFAVPP..APDK
Retrocopy TVEPLDYYRRFLKENCHPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGIKGEFAVPPKHAPDK

Parental  GYVVPNVDLPP-LCSSRFRSGPPGEEAQVASQFIADVIENSQIIHKEDLCITQGKLAWVLYCDLICLDYD
          GYVVPNVDLPP.LCSSRF.SGPPGEEAQVAS.FIADV.ENSQII.KEDL.ITQ.KL.WVLYCDL.CLDYD
Retrocopy GYVVPNVDLPP<LCSSRFPSGPPGEEAQVASHFIADVTENSQIIQKEDLRITQRKLVWVLYCDLTCLDYD

Parental  GNILDACTFALLAALKDVQLPEVTINEETALAEVNLKKKSHLNIRTHPVATSFAIFDDTLLIVDPTGEEE
          GNILDACTFALLAALKDV.LPEVTINEETALAEVNLKKKSHLNI..H.VATSFAIF.DTLLIVDPTGEE.
Retrocopy GNILDACTFALLAALKDV*LPEVTINEETALAEVNLKKKSHLNITVHLVATSFAIF-DTLLIVDPTGEED

Parental  HLATGSLTVVMDEEGKLCCLHKPGGSGLTGAKLQDCISRAVTRHREVKKLMDEVIQSMKPK
          HLATGSLTVVMDEEGKLCCLHKPGGSGLTGAKLQD..S.AVTR.REVKKLMDEVIQSMKPK
Retrocopy HLATGSLTVVMDEEGKLCCLHKPGGSGLTGAKLQDYMSQAVTRQREVKKLMDEVIQSMKPK

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_2014 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,