RetrogeneDB ID: retro_chof_1249

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_23690:3897..4340(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMX1
• Ensembl ID: ENSCHOG00000011305
• Aliases: None
• Description: thioredoxin-related transmembrane protein 1 [Source:HGNC Symbol;Acc:15487]

Sequence

>retro_chof_1249
ATGGCGCTCTCCGGGTGTCTCATGGTTCCTTTGGCAGTCTGGTGGTCTTACTCTGTGGGGCTCCCTGGATCCACGGGCCG
CGGGGCGACGTGCGCATCATCACTGATGCTAACTGGGAAGAGTTGCTGGAAGGAGAGTGGATGATAGAATTTTATGCTCC
ATGGTGTCCTGCTTGCCAGAATCTTCAACCAGAATGGGAAAGTTTTGCTGAATGGGGAGAAGATCTTGAGATTAATGTTG
CAAAAGTAGATGTCACAGAGCAGCCAGGACTGAGTGGACGATTTATCATAATTGCTCTTTCTACTATTTATCATTGTAAA
GATGATGAATTTAGGCGCTATCAGGGCCCAAGAACTAAGAAGGACTTCATAAACTTTATAAGTGAAAAAGAGTATAAGAG
TATTGAACTTGTTTCATCCTGGCTTGGTCCAGGTTCTGTTCTG

Alignment

ORF - retro_chof_1249 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.93 %
• Parental protein coverage: 53.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAPSGSLVVPLAV-LVLLLCEAPWIHGRRSDVRIITDANWKELLEGEWMIEFYAPWCPACQNLQPEWESF
          MA.SG.L.VPLAV.LV.LLC.APWIHG.R.DVRIITDANW.ELLEGEWMIEFYAPWCPACQNLQPEWESF
Retrocopy MALSGCLMVPLAV<LVVLLCGAPWIHGPRGDVRIITDANWEELLEGEWMIEFYAPWCPACQNLQPEWESF

Parental  AEWGEDLEINVAKVDVTEQPGLSGRFIITALPTIYHCKDGEFRRYQGLRTKKDFINFISEKEWKSIEPVS
          AEWGEDLEINVAKVDVTEQPGLSGRFII.AL.TIYHCKD.EFRRYQG.RTKKDFINFISEKE.KSIE.VS
Retrocopy AEWGEDLEINVAKVDVTEQPGLSGRFIIIALSTIYHCKDDEFRRYQGPRTKKDFINFISEKEYKSIELVS

Parental  SWLGPGSVL
          SWLGPGSVL
Retrocopy SWLGPGSVL

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_1249 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 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015041	1 retrocopy	retro_amel_719,
Canis familiaris	ENSCAFG00000014626	1 retrocopy	retro_cfam_796,
Choloepus hoffmanni	ENSCHOG00000011305	1 retrocopy	retro_chof_1249 ,
Callithrix jacchus	ENSCJAG00000006893	1 retrocopy	retro_cjac_1453,
Dasypus novemcinctus	ENSDNOG00000016496	1 retrocopy	retro_dnov_78,
Felis catus	ENSFCAG00000002780	1 retrocopy	retro_fcat_333,
Homo sapiens	ENSG00000139921	2 retrocopies	retro_hsap_3840, retro_hsap_3970,
Gorilla gorilla	ENSGGOG00000009768	1 retrocopy	retro_ggor_2587,
Loxodonta africana	ENSLAFG00000013251	1 retrocopy	retro_lafr_1214,
Macaca mulatta	ENSMMUG00000001901	1 retrocopy	retro_mmul_1618,
Nomascus leucogenys	ENSNLEG00000012362	2 retrocopies	retro_nleu_1976, retro_nleu_2524,
Oryctolagus cuniculus	ENSOCUG00000003980	1 retrocopy	retro_ocun_571,
Pongo abelii	ENSPPYG00000005810	2 retrocopies	retro_pabe_3058, retro_pabe_3264,
Pan troglodytes	ENSPTRG00000006339	2 retrocopies	retro_ptro_2522, retro_ptro_2695,