RetrogeneDB ID: retro_chof_1110

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_20302:12218..12686(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM38B
• Ensembl ID: ENSCHOG00000002467
• Aliases: None
• Description: transmembrane protein 38B [Source:HGNC Symbol;Acc:25535]

Sequence

>retro_chof_1110
GGAGCAGAGGCAGTGGCATGGAAGAATCCTCTTTCAACCTGGTTTACTGCTATGCTCCACTGTTTTGGTGGAGGAATTTT
AACGTGTATACTGCTTGCAGAGCCTCATCTGAGATTTCTTACAAACCACACTAACATATTACTGGCATCTTCAATCTGGA
ATATTATATATTTTTGTCCATGTGACCTAGTTTGCCAGGGCTATTCTTTCTTACCTTTTCAACTCTTGGCTGCAGGAATG
AAGGAAGTGACCAGAGCTTGGAAAATAATAGGTGGAGTCACTCATGCTAATAGCTATTACAAAAATGGCTGGATACTCAT
GATAGCTGTTGGATGGGCCTGAGGTACAGGTGACAGCATTGTCATGAATTTTGAACAGTTGGTAAAAGGAAATTGGAAAT
CACAAACTGAAGAATTGCTGAAATTGTCATACTCTGCCAAGGTGACCCTGCTGGGGTAAGTTATCTTC

Alignment

ORF - retro_chof_1110 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.13 %
• Parental protein coverage: 53.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GAEAVALKNPLSSWFTAMLHCFGGGILSCILLAEPPLRFLADYTNVLLATSIWYVVFFCPCDLVFQGYSF
          GAEAVA.KNPLS.WFTAMLHCFGGGIL.CILLAEP.LRFL...TN.LLA.SIW....FCPCDLV.QGYSF
Retrocopy GAEAVAWKNPLSTWFTAMLHCFGGGILTCILLAEPHLRFLTNHTNILLASSIWNIIYFCPCDLVCQGYSF

Parental  LPVQLLAAGMKEVTRTWKIVGGVTDANSYYKNGWIVMIAVGWARGAGGSIVTNFEQLVKGSWKPETEEWL
          LP.QLLAAGMKEVTR.WKI.GGVT.ANSYYKNGWI.MIAVGWA.G.G.SIV.NFEQLVKG.WK..TEE.L
Retrocopy LPFQLLAAGMKEVTRAWKIIGGVTHANSYYKNGWILMIAVGWA*GTGDSIVMNFEQLVKGNWKSQTEELL

Parental  KLSYPAKVTLLGSAVF
          KLSY.AKVTLLG...F
Retrocopy KLSYSAKVTLLG*VIF

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_1110 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002467	1 retrocopy	retro_chof_1110 ,
Ictidomys tridecemlineatus	ENSSTOG00000003014	7 retrocopies	retro_itri_1553, retro_itri_1708, retro_itri_1789, retro_itri_1823, retro_itri_1824, retro_itri_1826, retro_itri_1845,