RetrogeneDB ID: retro_chof_1542

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_31837:12427..13295(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000008888
• Aliases: None
• Description: None

Sequence

>retro_chof_1542
ATGGCGCGGACCCCGGGGCCCGCTCCGCCGTGTCCCGGAAGCCGCAGAAAACAACTTTCCACCGCTTCTGCCGCTGGGAC
CAGGATCCTGCTGCCGCCACCGACGCCTCTGCCGCTGCTACTGATGCTGTTCCCGCTGCTGCTCCTCTCGGGGCTCTGTG
GTGCCTCAGCTCTACCAGTCATCGTGCAGCCCAGTGTCTTCGCGGTTTGGGGAAAGAATGTGTCTTTGAAATGCTTCATT
GAAGCGAAGGACAGTATAACCCAGATTTCTTGGGAGAAGATCAATGGCAAAAGTTCACAGACTGTTGCGGTTCATCATCC
TCAATATGGATTTTCTGTTGTAGGGGAATATCAGGGAAGAATCTTGTTTAAGAACCTGTCAATGAGTGATGCAACAATTA
CTCTACATAATATAGGAGTCTCTGATTCCGGACAATATATATGCAAAGCTGTTACATTCCCAGGTGGAATTGTGGAGTCC
TCAACAACTGTAACTTTTAGTTGAACCCACTGTAAGCCTGATGAAAGGGCCAGATTCTTTAATTGATGGAGGAAATGAAA
CAGTAGCAGCCATTTGTACAGCAGCCACTGGCAAACCAGTTGCACATATTGACTGGGAAGGTGATCTTGGTGAAATGGAA
TCGATTACAACTTCTTTTCCAAATGAAACGGTGACAATTGTCAGCCAGTACAAGCTGTTTCCAACCAGATTTGCTCAAGG
AAGACGAATTACCTGTGTCGTAAAGCATCCAACCTTGGACAAGGACATTCGATATTCTTTCATATCAGATATACTGTACG
CTCCTGAGGTTTCTGTAACAGGATAAGATGGAAATTGGTTTGTAGGAAGAAAAGGTGTTAATCTTCAG

Alignment

ORF - retro_chof_1542 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.54 %
• Parental protein coverage: 52.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAWTPGPAPPCPGSRRKQLSTASAAGTRILLPPPTPLPLLLMLFPLLLLSGLCGALAGPIIVEPHIIAVW
          MA.TPGPAPPCPGSRRKQLSTASAAGTRILLPPPTPLPLLLMLFPLLLLSGLCGA.A.P.IV.P...AVW
Retrocopy MARTPGPAPPCPGSRRKQLSTASAAGTRILLPPPTPLPLLLMLFPLLLLSGLCGASALPVIVQPSVFAVW

Parental  GKNVSLKCLIEVNETITHILWEKIQGQNSQIVAVHHPQDGFSVQGAYQGRVLFKSYSLTDATITLHNIGF
          GKNVSLKC.IE....IT.I.WEKI.G..SQ.VAVHHPQ.GFSV.G.YQGR.LFK..S..DATITLHNIG.
Retrocopy GKNVSLKCFIEAKDSITQISWEKINGKSSQTVAVHHPQYGFSVVGEYQGRILFKNLSMSDATITLHNIGV

Parental  SDSGKYICKAVTFPGGNAQSSTTVT-VLVEPTVSLIKGPDSLIDGGNETVAAICTAATGKPVAHIDWEGD
          SDSG.YICKAVTFPGG....S.T....LVEPTVSL.KGPDSLIDGGNETVAAICTAATGKPVAHIDWEGD
Retrocopy SDSGQYICKAVTFPGGIVE-SSTTV>LLVEPTVSLMKGPDSLIDGGNETVAAICTAATGKPVAHIDWEGD

Parental  LGEMESTTTSFPNETVTIVSQYKLFPTRFARGRRITCVVKHPTLDKDIRYSFILDIQYAPEVSVTGYDGN
          LGEMES.TTSFPNETVTIVSQYKLFPTRFA.GRRITCVVKHPTLDKDIRYSFI.DI.YAPEVSVTG.DGN
Retrocopy LGEMESITTSFPNETVTIVSQYKLFPTRFAQGRRITCVVKHPTLDKDIRYSFISDILYAPEVSVTG*DGN

Parental  WFVGRKGVNLK
          WFVGRKGVNL.
Retrocopy WFVGRKGVNLQ

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_1542 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008888	1 retrocopy	retro_chof_1542 ,