RetrogeneDB ID: retro_chof_431

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_107843:2665..3413(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000010418
• Aliases: None
• Description: None

Sequence

>retro_chof_431
GTCATAAAGTATTTTTTAAGTTTCTTATTTTTAGAAGACTGCCAATGAGATGAACTCTTAGAGAAGAGCTCAGAAAACCA
AGGCAAACACTTGTGGCAAATTTTATTCTCCAGCAAAATGTTGACTGCAGAGCAAGAGAACATCTCAGGAACACCATATT
ATATGGACATAAACATTTTTCCTTCAAGAATAATACCCTATACATGTGACATTGCAGGACCTACTTACCTTGGTCATACC
TCATTGATGGCACACTGTCAGTACCCAAGAGAGAAGGGTGATGAGTTTAATGTCTGTGAGAAATGGCACCTCCTTATTAA
GGACAGCAGAATTAATGGAGATAAGGGTTTTCCGTATAATAAAAATGTGAAAGCTCACAGTCCAGAGGAGGAAGTTATTC
AACATCAGACAGTTCACACTTTTGGGCAAGATTTTAAATATGAAGGAGGAGGAAAATCTTCCCTTGAGAAGACTGCCCTC
GGTACATCTAAGAGTACACACACAAAAGAGAAATCCTGTAAATACGAGTTTTAGAAAAATGTGACAAATCTACTTTTATT
GTCTCAAGAAACATTCATAAAGAGGATAGCAATCACTATGAAGTAAATAAATATAATTGTAATGAAAATGGGGATGATTT
CAGTAGCATCACACAAATTCCAAGAACTGACATAGGAAGGAAAACTTTCAGCCCAAAATCCCACCTCAAAGAAAATCAAA
GAATTCGTATAGGATAAAATCTTTTCAT

Alignment

ORF - retro_chof_431 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.89 %
• Parental protein coverage: 56.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LLKGFLNKSYTEDCQQDELLKKSSENQGKQLWQILFSNKLLTAEQENISGTPYYMDINIFPSRITPYTCD
          ..K.FL.....EDCQ.DELL.KSSENQGK.LWQILFS.K.LTAEQENISGTPYYMDINIFPSRI.PYTCD
Retrocopy VIKYFLSFLFLEDCQ*DELLEKSSENQGKHLWQILFSSKMLTAEQENISGTPYYMDINIFPSRIIPYTCD

Parental  XXXXXXXXXXXXXXHCQYSREKADEFNVCEKWHLLIKDSRINGDKGFPYNKNVKAPSPEEEVIQHQTVQT
          ..............HCQY.REK.DEFNVCEKWHLLIKDSRINGDKGFPYNKNVKA.SPEEEVIQHQTV.T
Retrocopy IAGPTYLGHTSLMAHCQYPREKGDEFNVCEKWHLLIKDSRINGDKGFPYNKNVKAHSPEEEVIQHQTVHT

Parental  FGQNFEYEGGGKTSLEKTALSTSKSTHTKEKSYKYVFERNVCDKSTLTVSQNIHK-EDNNHYEVNEYNCN
          FGQ.F.YEGGGK.SLEKTAL.TSKSTHTKEKS.KY.F..NV.....L.....I.....N..YEVN.YNCN
Retrocopy FGQDFKYEGGGKSSLEKTALGTSKSTHTKEKSCKYEF*KNVTNLLLLSQETFIKR<DSNH-YEVNKYNCN

Parental  ENGDDFSSITQIPRTDIGGKTFSPKSHLKENQRIHIG-IKSFH
          ENGDDFSSITQIPRTDIG.KTFSPKSHLKENQRI.IG.IKSFH
Retrocopy ENGDDFSSITQIPRTDIGRKTFSPKSHLKENQRIRIG<IKSFH

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_431 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010418	2 retrocopies	retro_chof_431 , retro_chof_969,
Choloepus hoffmanni	ENSCHOG00000012100	1 retrocopy	retro_chof_12,