RetrogeneDB ID: retro_chof_2311

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_65355:2857..3247(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIGA
• Ensembl ID: ENSCHOG00000006415
• Aliases: None
• Description: phosphatidylinositol glycan anchor biosynthesis, class A [Source:HGNC Symbol;Acc:8957]

Sequence

>retro_chof_2311
GATTTGCTTATTGGTATAATACCTGAACTCTGTCAAAAATATCTAGACTTAAATTCATAATTGGGGGAGAGGGACCAAAG
AGAGTCATTTTGGAAGAAGTATGGGAAAGAAATAGCTACATGACAGGGTATGTCTCTTGGGAGCCTTATAACACAAAGAT
GTTAGAAATGTCTTAGTTCAAGGACATATTTTTCTTAATACCTCCCTTACCAAAGCGTTCTGCATGGCAATTGTAGAAGC
GGCCAGTTGTGGTTTATAGGTTGTAAGTTCCAAGATTGGTGGAATTCCTGAGGTACTTCTGGAAAATCTTACTATTTTAT
ATGAAACTTCTGTAAAATCTTTGTGTGAAGGAATGGAAAAGTTATTTACCAACTGAAGTCAGGGGCTTTG

Alignment

ORF - retro_chof_2311 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.09 %
• Parental protein coverage: 53.69 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DLLSGIIPELCQKYPDLN-FIIGGEGPKRVILEEVRERYQ-LHDRVRLLGALEHKDVRNVLVQGHIFLNT
          DLL.GIIPELCQKY.DLN.FIIGGEGPKRVILEEV.ER...LHDRV.LLGAL.HKDVRNVLVQGHIFLNT
Retrocopy DLLIGIIPELCQKYLDLN<FIIGGEGPKRVILEEVWERNS<LHDRVCLLGAL*HKDVRNVLVQGHIFLNT

Parental  SLTEAFCMAIVEAASCGLQVVSTRVGGIPEVLPENLIILCEPSVKSLCEGLE-KAIYQLNSTTL
          SLT.AFCMAIVEAASCGL.VVS...GGIPEVL.ENL.IL.E.SVKSLCEG.E.K.IYQL.S..L
Retrocopy SLTKAFCMAIVEAASCGL*VVSSKIGGIPEVLLENLTILYETSVKSLCEGME<KVIYQLKSGAL

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_2311 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006415	1 retrocopy	retro_chof_2311 ,
Homo sapiens	ENSG00000165195	1 retrocopy	retro_hsap_1050,
Gorilla gorilla	ENSGGOG00000007293	1 retrocopy	retro_ggor_828,
Nomascus leucogenys	ENSNLEG00000009352	1 retrocopy	retro_nleu_2070,
Ochotona princeps	ENSOPRG00000015381	1 retrocopy	retro_opri_1065,
Pongo abelii	ENSPPYG00000020142	1 retrocopy	retro_pabe_876,
Pan troglodytes	ENSPTRG00000021684	1 retrocopy	retro_ptro_716,
Rattus norvegicus	ENSRNOG00000003554	1 retrocopy	retro_rnor_2566,