RetrogeneDB ID: retro_chof_165

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_3713:23426..24149(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEH1L
• Ensembl ID: ENSCHOG00000000545
• Aliases: None
• Description: SEH1-like (S. cerevisiae) [Source:HGNC Symbol;Acc:30379]

Sequence

>retro_chof_165
ATTATCGATGTGAAATTTGCTCCCAAGCATATGGGTCTTATGTTGGCAACCTGTTCAGCGGATGGTATGGTAAGTATATA
CGAGGTGCCCGACGTGACGAACCTCAGTCAGTGGTCTCTGCAGCATGAAATTTCATGTAAGCTCAGCTGTAGTTGTATTT
CCTGGAACCCTTCAAGCTCCCGTGCTCATTCTCCCATGATACCTGTAGAAAGTGATGACAGTGGTCCCAATGCAATGGCC
AAGGTGCAGATTTTTGAATATAATGAAAACACCAGGAAATATGCAAAAGCAAAAACTCTTGTGGCCGTCACTGATCCTGT
GCGTGATACTGCGTTTACTCCGAATTTGGGAAGGTCTTTCCATATTCCGGCTATAGCCACCAAAGATATGAGAATTTTTA
CTCTAAAACCTGTGAGGAAAAAACTGACTTCCTCTGGTGGGCCAACAAAATTTGAAATCCATGTAGTGGCTCAGTTTAAT
AATCATAATTCTCAGGTCTGGAGAGTGAGTTGGAATATAACAGGAACAGTCCTAGCATCTTCAGGAAATGATGGCTGTGT
GAGATTGTGGAACGCCAATTACATGGACAGCTGGAAGTGCACTGGTATCCTGAAAGGTAACGGGAGCCCAGTCAGTGGGA
GTTCCCAGCAGGGAAACCCAAACCCTACCCTAGGCTCAAATGTTCCAAATCTACAAAATTCATTACATGACACTTCTGCT
GGC

Alignment

ORF - retro_chof_165 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.63 %
• Parental protein coverage: 63.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VTDVKFAPKHMGLMLATCSADGIVRIYEAPDVMNLSQWSLQHEISCKLSCSCISWNPSSSRAHSPMIAVG
          ..DVKFAPKHMGLMLATCSADG.V.IYE.PDV.NLSQWSLQHEISCKLSCSCISWNPSSSRAHSPMI.V.
Retrocopy IIDVKFAPKHMGLMLATCSADGMVSIYEVPDVTNLSQWSLQHEISCKLSCSCISWNPSSSRAHSPMIPVE

Parental  SDDSGPNAMAKVQIFEYNENTRKYAKAETLMTVTDPVHDIAFAPNLGRSFHILAIATKDVRIFTLKPVRK
          SDDSGPNAMAKVQIFEYNENTRKYAKA.TL..VTDPV.D.AF.PNLGRSFHI.AIATKD.RIFTLKPVRK
Retrocopy SDDSGPNAMAKVQIFEYNENTRKYAKAKTLVAVTDPVRDTAFTPNLGRSFHIPAIATKDMRIFTLKPVRK

Parental  ELTSSGGPTKFEIHVVAQFDNHNSQVWRVSWNITGTVLASSGDDGCVRLWKANYMDNWKCTGILKGNGSP
          .LTSSGGPTKFEIHVVAQF.NHNSQVWRVSWNITGTVLASSG.DGCVRLW.ANYMD.WKCTGILKGNGSP
Retrocopy KLTSSGGPTKFEIHVVAQFNNHNSQVWRVSWNITGTVLASSGNDGCVRLWNANYMDSWKCTGILKGNGSP

Parental  VSGSSQQGNANPSLGSNVPNLQNSLHGPSAG
          VSGSSQQGN.NP.LGSNVPNLQNSLH..SAG
Retrocopy VSGSSQQGNPNPTLGSNVPNLQNSLHDTSAG

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_165 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 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000545	2 retrocopies	retro_chof_165 , retro_chof_2594,
Oryctolagus cuniculus	ENSOCUG00000006858	2 retrocopies	retro_ocun_1723, retro_ocun_1801,
Sus scrofa	ENSSSCG00000030252	2 retrocopies	retro_sscr_178, retro_sscr_186,