RetrogeneDB ID: retro_chof_817

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_151457:3449..3964(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000013902
• Aliases: None
• Description: None

Sequence

>retro_chof_817
GAATTCATCATTGACTGCGTTATTAAAGCCATGAATGACAACAGCTGGCATTGTGAGTATTTCCACTGTAATCTCTGTCA
GGAAGTTTTGCACATATTGGGTTGCTCATGAATGTTGGGAGACATCTCTGTAACCCCTGTCATAATTGTCAGAAAGACAG
AGGACTTGGAAAATACATTTGCCAGAAATGCCATGCCATCACTGATGAACAACTTCTGACAGTCAAGAATGACCCTTACT
ATCCAGATCATTTCATCTGTGCCAACTGTGAGAACGAGCTGACTGCCAATGCCCAGGAGCTGAAAGGGGAACTGCATTGC
TTGCCATGCCATGATAAAAGGGACATCCCCATTTGTGGTGCTTGTCAATGGCCCATTAAAGGGCATGTGGCAAATGCCAT
GGGCAAGCCGTGGCATATGGAGCAATTTGTTTATACCAAGTGTAGGCCATTTCTAGGACATCAGCACTGTGAGAGGAAGG
ACTTTGCATATTGTGACACCCACTGAAACCAGCTG

Alignment

ORF - retro_chof_817 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.84 %
• Parental protein coverage: 69.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EFIIGRVIKAMN-NSWHPECFRCDLCQEVL-ADIGFVKNAGRHLCRPCHNREKARGLGKYICQKCHAIID
          EFII..VIKAMN.NSWH.E.F.C.LCQEVL.A.IG...N.GRHLC.PCHN..K.RGLGKYICQKCHAI.D
Retrocopy EFIIDCVIKAMNDNSWHCEYFHCNLCQEVL<AHIGLLMNVGRHLCNPCHNCQKDRGLGKYICQKCHAITD

Parental  EQPLIFKNDPYHPDHFNCANCGKELTADARELKGELYCLPCHDKMGVPICGACRRPIEGRVVNAMGKQWH
          EQ.L..KNDPY.PDHF.CANC..ELTA.A.ELKGEL.CLPCHDK...PICGAC..PI.G.V.NAMGK.WH
Retrocopy EQLLTVKNDPYYPDHFICANCENELTANAQELKGELHCLPCHDKRDIPICGACQWPIKGHVANAMGKPWH

Parental  VEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQL
          .E.FV..KC..PFLGH.H.ERK..AYC.TH.NQL
Retrocopy MEQFVYTKC-RPFLGHQHCERKDFAYCDTH*NQL

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_817 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013902	1 retrocopy	retro_chof_817 ,
Dasypus novemcinctus	ENSDNOG00000004334	1 retrocopy	retro_dnov_1229,
Otolemur garnettii	ENSOGAG00000001879	1 retrocopy	retro_ogar_2992,
Rattus norvegicus	ENSRNOG00000037765	1 retrocopy	retro_rnor_432,