RetrogeneDB ID: retro_chof_528

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_11857:8009..8559(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GEM
• Ensembl ID: ENSCHOG00000006332
• Aliases: None
• Description: GTP binding protein overexpressed in skeletal muscle [Source:HGNC Symbol;Acc:4234]

Sequence

>retro_chof_528
GATACATATGAGTGAACCCTGATTGTTGATGGAGAAAGTGCAACAATTATACTCCTGGACATATGGGAAAATAAGGGAGA
GAATGAATGGCTCCAAGACCACTGCATGCAAGTTGGGGATGCGTACTTCATTGTCTTCTCTATCACTGACCGAACGAGCT
TTGAAAAAGCACCTGAACTTCAAATCCAGCTGCGCAGGGCCTGTCAGACAGAAGACATTCCTATAGTCTTGGTTGGCAAC
AAAAGTGACCTGGTGCAGTGTTAAAAAGTGTCTGTATCAAAAGGGAAAGCATGTGCTGTGGTGTTCAACTGCAAGTTCAC
TGAAACCTCCACGGCTGTCCAGCACAACGCCAAAGAACTGTTTGAGGGCATTGTGTGTCAGGTTCACCTTCCATTGGACA
GCAAGGAAAAGAACCAGCAGCAGCTGGCCTACCAGAAGAAGGAGAGTATCCCCCAGGCAAGCCAGGCATTTGGGGCAAGG
TCATGGTCAAAACGACATAAATAAGGCCTTCAAGCTCAAGTCCAAATCCTGCCATGAACTCTCTGTTCTC

Alignment

ORF - retro_chof_528 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.61 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DTYERTLIVDGESATIILLDIWENKGENEWLQDHCMQVGDAYLIVYSITDRASFEKASELRIQLRRARQT
          DTYE.TLIVDGESATIILLDIWENKGENEWLQDHCMQVGDAY.IV.SITDR.SFEKA.EL.IQLRRA.QT
Retrocopy DTYE*TLIVDGESATIILLDIWENKGENEWLQDHCMQVGDAYFIVFSITDRTSFEKAPELQIQLRRACQT

Parental  EDIPIILVGNKSDLVRCREVSVSEGRACAVVFDCKFIETSAAVQHNVKELFEGIVRQVRLRRDSKEKNER
          EDIPI.LVGNKSDLV.C..VSVS.G.ACAVVF.CKF.ETS.AVQHN.KELFEGIV.QV.L..DSKEKN..
Retrocopy EDIPIVLVGNKSDLVQC*KVSVSKGKACAVVFNCKFTETSTAVQHNAKELFEGIVCQVHLPLDSKEKNQQ

Parental  RLAYQKRRESIPRKARRF-WGKIVAK-NNKNMAFKLKSKSCHDLSVL
          .LAYQK..ESIP.....F.WGK...K.N..N.AFKLKSKSCH.LSVL
Retrocopy QLAYQK-KESIPQASQAF<WGKVMVK<NDINKAFKLKSKSCHELSVL

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_528 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	ENSCHOG00000003135	7 retrocopies	retro_chof_111, retro_chof_1639, retro_chof_2065, retro_chof_2644, retro_chof_2706, retro_chof_389, retro_chof_521,
Choloepus hoffmanni	ENSCHOG00000006332	1 retrocopy	retro_chof_528 ,