RetrogeneDB ID: retro_chof_2058

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_46960:8305..8960(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000010080
• Aliases: None
• Description: None

Sequence

>retro_chof_2058
TCTATGATGCTACAACTGCTGGGACTAGTTTGGAGACTTGTTTGACTTGTGTGATAGAACATTTTCTCTTAAAACAGGTT
GCATGATAGGTATCCAACTAATTTCTCATATGGAATTTGTCCATTCAAAGAATTTAATATACAGAGATGTAAAACATGAG
GAATTCTTAATAGGACAACAAGGAAACAAAACCCAAAAAAATTATTCCCATTATAGATTTTGGTTTGGTAAGGATATATC
AATCCAGAGACAAAGAAACACATACCATACAGTGAACACAAGAGTCTTACAGGATCAGCTGAGATATATAAACATGAACA
CACATTTAGGAAAGAAACAAAGTAGAAGGAATGATTTAGAACTTTTAGGAAACATGTTTATGAATTTTCTGAGAAGACAT
CATCCTTGGCAAGGCTTAAAGGCTGACACATTAAAAAAAGAAATATCAGAAAATTGGAGATACAAAATGAGCCACACTAA
TAGAAGTGCTATGTGAAAATTTTTCAGAAGAAATGGCAACATATCTTTGTTATGAAAGATGGTAAGATTTTTTTGAAAAA
CCAGAATATGGCTACCTAAGAAAACTTTTTAATGACTTGTGTGATCAAAAAGGCATGTGTCAGAGTATAAATATGACAGG
ATCAGTAAACAGTTG

Alignment

ORF - retro_chof_2058 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.22 %
• Parental protein coverage: 54.21 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  AMVLELLG-PSLE-DLFDLCDRTFTLKTVLMIAIQLLSRMEYVHSKNLIYRDVKPENFLIGRQGNKKEHV
          .M.L.LLG..SLE.DLFDLCDRTF.LKT..MI.IQL.S.ME.VHSKNLIYRDVK.E.FLIG.QGNK....
Retrocopy SMMLQLLG<TSLE<DLFDLCDRTFSLKTGCMIGIQLISHMEFVHSKNLIYRDVKHEEFLIGQQGNKTQKN

Parental  IHIIDFGLAKE-YIDPETKKHIPYREHKSLTGTA-RYMSINTHLGKEQSRRDDLEALGHMFMYFLRGSLP
          .....F...K..YI.PETKKHIPY.EHKSLTG.A.RY...NTHLGK.QSRR.DLE.LG.MFM.FLR...P
Retrocopy YSHYRFWFGKD<YINPETKKHIPYSEHKSLTGSA>RYINMNTHLGKKQSRRNDLELLGNMFMNFLRRHHP

Parental  WQGLKADTL-KERYQKIGDTKRNTPIEALCENFPEEMATYLRYVRRLDFFEKPDYEYLRTLFTDLFERKG
          WQGLKADTL.K..YQKIGDTK..T.IE.LCENF.EEMATYL.Y.R..DFFEKP.Y.YLR.LF.DL...KG
Retrocopy WQGLKADTL>KKKYQKIGDTK*ATLIEVLCENFSEEMATYLCYERW*DFFEKPEYGYLRKLFNDLCDQKG

Parental  -YTFDYVYDWVGRPI
          .....Y.YD......
Retrocopy <HVSEYKYDRISKQL

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_2058 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003299	1 retrocopy	retro_chof_753,
Choloepus hoffmanni	ENSCHOG00000010080	3 retrocopies	retro_chof_1577, retro_chof_2058 , retro_chof_216,
Dasypus novemcinctus	ENSDNOG00000018857	1 retrocopy	retro_dnov_2386,
Rattus norvegicus	ENSRNOG00000016620	1 retrocopy	retro_rnor_2267,
Tupaia belangeri	ENSTBEG00000003013	1 retrocopy	retro_tbel_17,