RetrogeneDB ID: retro_chof_356

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_871:92797..93136(+)
• Located in intron of: ENSCHOG00000005274

Retrocopy information

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

Parental gene information

• Parental gene symbol: MGST3
• Ensembl ID: ENSCHOG00000012723
• Aliases: None
• Description: microsomal glutathione S-transferase 3 [Source:HGNC Symbol;Acc:7064]

Sequence

>retro_chof_356
TATCCTACCATGTACAGCACAGACCCAGAAAATGGGCACCTCTTCAACTGCATTCAGCGAGCCCACCAGAACACGTTGGA
AATATATCCTCCCTTCTTATTTTTTCTAACTGTTGGAGGTGTTTACCACCCGCGTATAGCTTCTGGTTTGGGCTTGGCTT
GGATTGTTGGACAAGTTCTCTATGCTTATGGCTATTACACGGGAGAACCCAGCAAGCGGACTCGAGGAACCCTGGGATCC
ATTGCACTCATGGGCTTGTTGGGCACCACTGTGTGCTCTGCTTTCCAGCATCTTGGCTGGGTGAAAACTGGCTTAAACAG
TGGGGCCAAAGGCTGCCAT

Alignment

ORF - retro_chof_356 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.35 %
• Parental protein coverage: 68.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YPTMYSTDPENGHLFNCIQRAHQNTLEIYPPFLFFLAVGGVYHPRIASGLGLAWIVGRVLYAYGYYTGEP
          YPTMYSTDPENGHLFNCIQRAHQNTLEIYPPFLFFL.VGGVYHPRIASGLGLAWIVG.VLYAYGYYTGEP
Retrocopy YPTMYSTDPENGHLFNCIQRAHQNTLEIYPPFLFFLTVGGVYHPRIASGLGLAWIVGQVLYAYGYYTGEP

Parental  SKRTRGALGSIALMGLLGTTVCSAFQHLGWVKTGLNSGAKGCH
          SKRTRG.LGSIALMGLLGTTVCSAFQHLGWVKTGLNSGAKGCH
Retrocopy SKRTRGTLGSIALMGLLGTTVCSAFQHLGWVKTGLNSGAKGCH

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_356 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 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006658	1 retrocopy	retro_amel_1210,
Canis familiaris	ENSCAFG00000013353	1 retrocopy	retro_cfam_35,
Choloepus hoffmanni	ENSCHOG00000012723	2 retrocopies	retro_chof_1872, retro_chof_356 ,
Echinops telfairi	ENSETEG00000003507	3 retrocopies	retro_etel_1328, retro_etel_1527, retro_etel_1544,
Mustela putorius furo	ENSMPUG00000003817	1 retrocopy	retro_mputfur_1251,
Mus musculus	ENSMUSG00000026688	1 retrocopy	retro_mmus_2709,
Oryctolagus cuniculus	ENSOCUG00000010376	1 retrocopy	retro_ocun_270,
Procavia capensis	ENSPCAG00000015774	2 retrocopies	retro_pcap_385, retro_pcap_393,
Rattus norvegicus	ENSRNOG00000004245	1 retrocopy	retro_rnor_195,
Tupaia belangeri	ENSTBEG00000005299	2 retrocopies	retro_tbel_2989, retro_tbel_752,