RetrogeneDB ID: retro_chof_1989

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_44460:764..1097(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GSTM3
• Ensembl ID: ENSCHOG00000005380
• Aliases: None
• Description: glutathione S-transferase mu 3 (brain) [Source:HGNC Symbol;Acc:4635]

Sequence

>retro_chof_1989
GGCTACTGGTATATTCGTGAGCTGGCCCACGCCATCTGCATGCTTCTGGAGTTCACTGATACATGCTATGAGGAGAAATG
GTACATGTGTGGGGAAGCTCCTGAGTATGATAAAAGCCAATGGCTGGATATGAAATTCAAGCTAGACCTGGACTGTCCTA
ATCTGGATGGAAAGAACAAGATCACTCAGAGCAATGCCATCTTGTGTTACATTGCTCACAAGCAAAATATGTGTGGTGAC
ACAGAAGAAGAAAAGATTCCAGTGGACATCATAGAGAACCAAATAACGGATTTCCACTTGCAACTGGCACAGCTCTGCTA
CAGCCCTGAGCAT

Alignment

ORF - retro_chof_1989 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GYWDIRGLAHAIRLLLEFTDTCYEEKRYTCGEAPDYDRSQWLDVKFKLDLDFPNLPYLLDGKNKITQSNA
          GYW.IR.LAHAI..LLEFTDTCYEEK.Y.CGEAP.YD.SQWLD.KFKLDLD.PNL....DGKNKITQSNA
Retrocopy GYWYIRELAHAICMLLEFTDTCYEEKWYMCGEAPEYDKSQWLDMKFKLDLDCPNL----DGKNKITQSNA

Parental  ILRYIARKHNMCGDTEEEKIRVDIVENQIMDFRLQLVRLCYSPEH
          IL.YIA.K.NMCGDTEEEKI.VDI.ENQI.DF.LQL..LCYSPEH
Retrocopy ILCYIAHKQNMCGDTEEEKIPVDIIENQITDFHLQLAQLCYSPEH

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_1989 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 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005380	2 retrocopies	retro_chof_1850, retro_chof_1989 ,
Callithrix jacchus	ENSCJAG00000003168	1 retrocopy	retro_cjac_4,
Erinaceus europaeus	ENSEEUG00000014211	1 retrocopy	retro_eeur_112,
Echinops telfairi	ENSETEG00000005817	2 retrocopies	retro_etel_1074, retro_etel_1910,
Homo sapiens	ENSG00000134202	1 retrocopy	retro_hsap_2419,
Microcebus murinus	ENSMICG00000005185	1 retrocopy	retro_mmur_1571,
Macaca mulatta	ENSMMUG00000008029	2 retrocopies	retro_mmul_610, retro_mmul_941,
Monodelphis domestica	ENSMODG00000001899	1 retrocopy	retro_mdom_331,
Mus musculus	ENSMUSG00000004032	2 retrocopies	retro_mmus_491, retro_mmus_547,
Nomascus leucogenys	ENSNLEG00000003302	1 retrocopy	retro_nleu_1895,
Pan troglodytes	ENSPTRG00000001063	2 retrocopies	retro_ptro_1393, retro_ptro_1709,
Rattus norvegicus	ENSRNOG00000047034	1 retrocopy	retro_rnor_963,
Sus scrofa	ENSSSCG00000006821	2 retrocopies	retro_sscr_10, retro_sscr_855,
Tarsius syrichta	ENSTSYG00000006736	1 retrocopy	retro_tsyr_145,
Tursiops truncatus	ENSTTRG00000009682	1 retrocopy	retro_ttru_1828,