RetrogeneDB ID: retro_chof_1906

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_420201:503..848(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM243
• Ensembl ID: ENSCHOG00000004888
• Aliases: None
• Description: transmembrane protein 243, mitochondrial [Source:HGNC Symbol;Acc:21707]

Sequence

>retro_chof_1906
TTCTACCAGGCATCTTATGGCACCACTTGCCTGGAAAACAGACTTCTGTTCAGAGAGAGGTTGGCCATGGATGGAATCAC
CAATTTAGTTGTTGGCAGGTTAACATCTTTATTGATTCTAGTAATGCTGATTAGTGCTTTTGTTTTCCCTCAACCACCTC
CCAACCCATTGAATATACTTTTTGATGTTTGCATCTCTTTGAGTAGTAGTATTGCCTGCATAATTATCTACTGATATCAA
CAGGAAGACTTGGAACTGAAATTTAGAAATCTAATTTACTATGTCTTATTTTCTATCATCATGTTATGTATACGTGTCAA
CCTGAACTTCCATGATGTGGGAAAG

Alignment

ORF - retro_chof_1906 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.04 %
• Parental protein coverage: 97.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FSTRTYGTSGLDNRPLFGETSAKDRIINLVVGSLTSLLILVTLISAFVFPQLPPKPLNIFFAVCISLSSI
          F....YGT..L.NR.LF.E..A.D.I.NLVVG.LTSLLILV.LISAFVFPQ.PP.PLNI.F.VCISLSS.
Retrocopy FYQASYGTTCLENRLLFRERLAMDGITNLVVGRLTSLLILVMLISAFVFPQPPPNPLNILFDVCISLSSS

Parental  TACILIYWYRQGDLEPKFRNLIYYILFSIIMLCICANLYFHDVGK
          .ACI.IY.Y.Q.DLE.KFRNLIYY.LFSIIMLCI..NL.FHDVGK
Retrocopy IACIIIY*YQQEDLELKFRNLIYYVLFSIIMLCIRVNLNFHDVGK

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_1906 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004888	4 retrocopies	retro_chof_1660, retro_chof_175, retro_chof_1906 , retro_chof_821,
Microcebus murinus	ENSMICG00000014707	1 retrocopy	retro_mmur_808,
Otolemur garnettii	ENSOGAG00000000023	2 retrocopies	retro_ogar_1800, retro_ogar_383,
Rattus norvegicus	ENSRNOG00000042758	1 retrocopy	retro_rnor_2506,
Sorex araneus	ENSSARG00000002439	1 retrocopy	retro_sara_32,
Tupaia belangeri	ENSTBEG00000007846	3 retrocopies	retro_tbel_2016, retro_tbel_2828, retro_tbel_4176,