RetrogeneDB ID: retro_chof_2007

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_45288:2807..3377(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TDP2
• Ensembl ID: ENSCHOG00000012012
• Aliases: None
• Description: tyrosyl-DNA phosphodiesterase 2 [Source:HGNC Symbol;Acc:17768]

Sequence

>retro_chof_2007
CATGAAGAAGGGTATTTCACAGCTATAATGTTGAAAAAAATCAAGAGTGAAATTAAAAAGCCAAGAGATTATTCCTTTTC
CGAGTACCAAAATGATGAGAAACCTTTTGTGTATGCATGTGAGTGTGTCAGGAAATGAACTTTGCCTTATGACTTCCTAC
TTGGAGAGCACCAAAGGGCATGCTAAGGAACAAATCAATCAGTTAAAAGTGGTTTTAAAGAAAATGCAAGAGGCTCCCAA
ATCAGCTACGGTTATATTTGCAGGTGATACAAATTTAAGGAAATCAAGAAGTTACCAAATGTGGTGGTTTTCCCAACAAC
ATTTTGGATGTTTGGGAGTTTGGGGGCAAGCTTGAGCATTGCCAGCATACATGGGATATGAAAATGAACTCTAATCTTGG
GAATACCTGGTACTTGTAAGCTTTGTTTTGATCAAATACTTTTCAGAGCAGCAGCAAAAGATGGCCACATTATTCCCCAA
AGCTGGGACCTACTTGGGCTGGAAAAACTGCACTCTGGCTGATTTCCTAGTGATCACTGGGGTTTTCTGTGCAGCTGAGA
TATAATATTG

Alignment

ORF - retro_chof_2007 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.08 %
• Parental protein coverage: 51.69 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HEEGYFTAIML-KKSRVKLKSQEIIPFPSTKMMRNLLCVNVSVSGNELCLMTSHLESTKGHTTERINQLK
          HEEGYFTAIML.KKSRVKLKSQEIIPFPSTKMMRNLLC..VSVSGNELCLMTS.LESTKGH..E.INQLK
Retrocopy HEEGYFTAIML>KKSRVKLKSQEIIPFPSTKMMRNLLCMHVSVSGNELCLMTSYLESTKGHAKEQINQLK

Parental  VVLKKMQEAPESATVIFAGDTNLR-DQEI-KC-GYPDSILDVW-FGGKPEHCQYT-DMQKNSN-LGIPSS
          VVLKKMQEAP.SATVIFAGDTNLR..QE..KC.G.P..ILDVW.FGGK.EHCQ.T.DM..NSN.LGIP..
Retrocopy VVLKKMQEAPKSATVIFAGDTNLR>NQEVTKCGGFPNNILDVWEFGGKLEHCQHTWDMKMNSN>LGIPGT

Parental  CKLGFDQIFSRAAAEGDHIIP-NLGLLVLEKLDCGRLLSDHWGLLCSLGIIL
          CKL.FDQI..RAAA...HIIP....LL.LEKL..G...SDHWG.LCS..IIL
Retrocopy CKLCFDQILFRAAAKDGHIIPQSWDLLGLEKLHSG*FPSDHWGFLCS*DIIL

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_2007 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012012	2 retrocopies	retro_chof_2007 , retro_chof_616,
Callithrix jacchus	ENSCJAG00000006074	1 retrocopy	retro_cjac_363,
Dasypus novemcinctus	ENSDNOG00000010113	1 retrocopy	retro_dnov_500,
Ochotona princeps	ENSOPRG00000016299	2 retrocopies	retro_opri_261, retro_opri_939,