RetrogeneDB ID: retro_chof_2184

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_5669:14652..15298(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EDEM1
• Ensembl ID: ENSCHOG00000011489
• Aliases: None
• Description: ER degradation enhancer, mannosidase alpha-like 1 [Source:HGNC Symbol;Acc:18967]

Sequence

>retro_chof_2184
CTGCTGGCCTTCTTCCTTGCACTGCAAGTTCTAATAGGAGATGAAGATGCCGTCTGTTTCCAAACCTTTTTCCACACCGT
ATGAAACGATATGGGGCACTCCCTGAGAGGTTTAACTGGCAGGTACAGGCCCCTGATGATCTCTTTTATCCACTGAGACC
AGAGTTGGTGAAATCTACATGTGTTCTCTACCAGGCAACCAAGAATCCCTTCTACTTCCATGTAGGAATGGAAATTCTAC
AGAGTCTGGAAAAGTACCCCAAACTCAAATGTGGGTACGTTAGGCTGCGTCATATCATAGACAAATCTAAAGAGGACTGG
ATGGAGAGCTTCTTTCTCAGCGAGACCTGTAAATACTTTTATCTGCTATTTGATGAGAATCCAGTCGGCAAATCTGGAAG
CAGATAATGTCTACAACAGAGGGACACGTTGTATCTGTGGACAAACATCTACTGGAATCACCCTGGAAAGAATTCTTTTC
TGAAGAAGGAGAGCACAACTAAGGGGGAGAATCTCTGCACAGGCCTAAATCTCATGAATTAAAAGTCATCAACCCCAACT
CCAATTGCAATCATGTTCCTGATGAGAGGAGATACTGCCTGCCCTTAAAGAGCATCTACATCCAACAGATTGACCAGATG
GTTGGC

Alignment

ORF - retro_chof_2184 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.91 %
• Parental protein coverage: 50.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LQAFFPGLQVLIGDVEDAICLHAFYYAI-WKRYGALPERYNWQLQAPDVLFYPLRPELVESTYLLYQATK
          L.AFF..LQVLIGD.EDA.C...F......KRYGALPER.NWQ.QAPD.LFYPLRPELV.ST..LYQATK
Retrocopy LLAFFLALQVLIGD-EDAVCFQTFFHTV<MKRYGALPERFNWQVQAPDDLFYPLRPELVKSTCVLYQATK

Parental  NPFYLHVGMDILQSLEKYTKVKCGYATLHHVIDKSKEDRMESFFLSETCKYLYLLFDEENPVHKSGTR-Y
          NPFY.HVGM.ILQSLEKY.K.KCGY..L.H.IDKSKED.MESFFLSETCKY.YLLFD.ENPV.KSG.R..
Retrocopy NPFYFHVGMEILQSLEKYPKLKCGYVRLRHIIDKSKEDWMESFFLSETCKYFYLLFD-ENPVGKSGSR<I

Parental  MFTTEGHIVSVDKHLRESPWKEFFSEEGEPDEEGKSVPRPKSLELKVINSSSNCSRVPDERRYSLPLKSI
          M.TTEGH.VSVDKHL.ESPWKEFFSEEGE....G.S..RPKS.ELKVIN..SNC..VPDERRY.LPLKSI
Retrocopy MSTTEGHVVSVDKHLLESPWKEFFSEEGEHN*GGESLHRPKSHELKVINPNSNCNHVPDERRYCLPLKSI

Parental  YMRQIDQMVG
          Y..QIDQMVG
Retrocopy YIQQIDQMVG

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_2184 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011489	2 retrocopies	retro_chof_2184 , retro_chof_474,