RetrogeneDB ID: retro_chof_1564

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_3267:20067..20527(+)
• Located in intron of: ENSCHOG00000012633

Retrocopy information

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

Parental gene information

• Parental gene symbol: MGST1
• Ensembl ID: ENSCHOG00000013004
• Aliases: None
• Description: microsomal glutathione S-transferase 1 [Source:HGNC Symbol;Acc:7061]

Sequence

>retro_chof_1564
GTTGACCTCACTCAGCTAAAGGAGAATGACGTATTCATGGCCTTTGCCTCCTACACAATGATTATTCTTTCGAAAATGAT
ATTAATGAGTATTGTAACTGCATTCCATAGAGCGTCAAGAAAGGTTTTTGCCAACCAAGAAGACTGTGCATCCTTTGGCA
AAGGAGAAAATGCCAAGAAGTTTCTAAGGACAGATGACAGGGTGGAATGTGTATGAAGAGCCCACCTGAATGACCTTGAA
AATATTGTGCCATTTCTTGGTATTGGCCTTCTGTATTCCCTGAGTGAACGAGATCTCTCTACAGCTCTCCTGCACTTCAT
ACTCTGTTGGAGCACGGATCTTCCATTCACTTGCATATTTGACACCCCTTCCCCAGCCAAATCGAGGTTTGGCTTTTTTT
GTTGGATATGGAGTTACTTTTTCAATGGCTTACAGGTTGCTGAAGAATAAATTGTACCTG

Alignment

ORF - retro_chof_1564 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.28 %
• Parental protein coverage: 98.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VDLTQLKENEVFMAFASYATIILSKMMLMSIITAFHRMSRKVFANPEDCASFGKGENAKKFLRTDDTVER
          VDLTQLKEN.VFMAFASY..IILSKM.LMSI.TAFHR.SRKVFAN.EDCASFGKGENAKKFLRTDD.VE.
Retrocopy VDLTQLKENDVFMAFASYTMIILSKMILMSIVTAFHRASRKVFANQEDCASFGKGENAKKFLRTDDRVEC

Parental  VRRAHLKENENIVPFLSIGLRYSLSESDLSTAILHFRLFVGAQIYHTIAYLT-PFP-QPNQALAFFVEYG
          V.RAHL...ENIVPFL.IGL.YSLSE.DLSTA.LHF.L........T....T.PFP.QPN..LAFFV.YG
Retrocopy V*RAHLNDLENIVPFLGIGLLYSLSERDLSTALLHFILCWSTDLPFTCIFDT<PFP<QPNRGLAFFVGYG

Parental  VTFSMAYK-LKNKLYL
          VTFSMAY..LKNKLYL
Retrocopy VTFSMAYRLLKNKLYL

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_1564 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013004	3 retrocopies	retro_chof_1564 , retro_chof_1842, retro_chof_2298,
Callithrix jacchus	ENSCJAG00000021590	1 retrocopy	retro_cjac_745,
Echinops telfairi	ENSETEG00000007466	7 retrocopies	retro_etel_142, retro_etel_1541, retro_etel_1615, retro_etel_1727, retro_etel_2045, retro_etel_789, retro_etel_989,
Loxodonta africana	ENSLAFG00000002693	1 retrocopy	retro_lafr_976,
Myotis lucifugus	ENSMLUG00000002358	1 retrocopy	retro_mluc_1078,
Tupaia belangeri	ENSTBEG00000016248	6 retrocopies	retro_tbel_1229, retro_tbel_2494, retro_tbel_3452, retro_tbel_3654, retro_tbel_366, retro_tbel_4500,