RetrogeneDB ID: retro_chof_474

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_113157:5150..6422(-)
• 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_474
GTCCTGGGAAGCCGTCTTTCTGCCCACAGAAAAACAACTGACTCCAAGAAGCCCTTTGGTGGCAGGACAACTAAGGATTA
CGATAACAAACTGTTGCATACGGCTCATAACCTGGCCATGCGACGACTCCCTGCCTTTGAAAACACCAAGACAGGCATCC
CCTATCCTTGGGTGAATCTAAAGACAAGCGTCCCTCCTGACAGCAATAATGAGATGTGTACGGCAGGAGCTGGTTTCCTT
CTGATGGAATTTGGGATTCTGAGCCCACTGCTGGGGGATTCTGCATTTCAATGGGTGGCCAAATGAGCAGCGAAAACCCT
TTGGAACCTCTGGAGCAACGACACAGGATTAATAGGCAATGTTGTGAATATTCAGATGGGCCATTGGGTTGGAAAGCAGT
GTGGCTTAGTTGCTGGTCTGGACTCCTTCTATGAGTACTTCTTCAATCCTACATTCTTTTTGGAAAAAAAGAAGACCTAC
AAATGTTTAATGCCACATATGAGAATATTCAGAACTACTTAAGAGGAGGTTGGGAGGCCTGTAAGGAGGGAGGAGACCCC
CCCACACACACACTATGTCAATGTGACATGTTCAGTGGACAGCTGAGGAGCACCTGGATTGACTCTCTGCAGGCCTTCTC
GCCTGGACTGCACGTTCTAACAGGAGATGTGGAAGATGGCAGCTGCCCCCATGCCTTTTACTAAGCTATATGGAAAAGAT
ATGGGGCTCTCCCTGAGAGGTATAACTGGAGCTACAGGCCCCTGACCTTCTCTTCTACCTACTGAGACCAGAGTTGGTGG
AATCTACATACGTCCTCTACTAAGCAAACAAGAATCCCTTCTACCTCCATGTAGGAATGATATTCTGCAGAGTCTAGAAA
AGTATGCAAGTCAAATGTGGGTACATGATGCTACACCATGTCATAGACAAATCCAAAGAGGACCGGATGGAGAACTTCTT
TCTCAGTGAGACCTGTAAATACTTATACCTATTTGATGAAAACAATCTAGTACACAAATCTAGAACCAGGTACATATTTA
CAACTGAGGGACACATTGTATCTGCGGACAAACATCTATGGGAATCACCCTAGAAGGAATTCTTTTCTAAAGGAAAGCAG
AACCAAGAGGGAAAATCTGTGCACAGGCCTAAATCTCATGAATTAAAGGTCATTAACTCCAGCCCAATTGCAATCATGCT
CCTGATGAGAGATACTTCCTGCCCTTAAAGAGAATCTACATGTGACACACTGACCAGATCCTCGTTTTGATT

Alignment

ORF - retro_chof_474 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.86 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VLGSLLSAHRIITDSKQPFGDMTVKDYDNELLHMAHDLAVRLLPAFENTKTGIPYPRVNLKTGVPPDTNN
          VLGS.LSAHR..TDSK.PFG..T.KDYDN.LLH.AH.LA.R.LPAFENTKTGIPYP.VNLKT.VPPD.NN
Retrocopy VLGSRLSAHRKTTDSKKPFGGRTTKDYDNKLLHTAHNLAMRRLPAFENTKTGIPYPWVNLKTSVPPDSNN

Parental  ETCTAGAGSLLVEFGILSRLLGDSTFEWVARRAVKALWNLRSNDTGLLGNVVNIQTGHWVGKQSGLGAGL
          E.CTAGAG.LL.EFGILS.LLGDS.F.WVA..A.K.LWNL.SNDTGL.GNVVNIQ.GHWVGKQ.GL.AGL
Retrocopy EMCTAGAGFLLMEFGILSPLLGDSAFQWVAK*AAKTLWNLWSNDTGLIGNVVNIQMGHWVGKQCGLVAGL

Parental  DSFYEY-LLKSYILFGEKEDLEMFNAAYRSIQNYLRRGREACNEGEGD-PPL--YVNV-NMFSGQLMNTW
          DSFYEY.LL.SYILFG.KEDL.MFNA.Y..IQNYLR.G.EAC.EG.GD.PP...YVNV..MFSGQL..TW
Retrocopy DSFYEY<LLQSYILFGKKEDLQMFNATYENIQNYLRGGWEACKEG-GD>PPHTHYVNV<DMFSGQLRSTW

Parental  IDSLQAFFPGLQVLIGDVEDAICLHAFYYAIWKRYGALPERYNW-QLQAPDVLFYPLRPELVESTYLLYQ
          IDSLQAF.PGL.VL.GDVED..C.HAFY.AIWKRYGALPERYNW..LQAPD.LFY.LRPELVESTY.LY.
Retrocopy IDSLQAFSPGLHVLTGDVEDGSCPHAFY*AIWKRYGALPERYNW<ELQAPDLLFYLLRPELVESTYVLY*

Parental  ATKNPFYLHVGMDILQSLEKYTKVKCGYATLHHVIDKSKEDRMESFFLSETCKYLYLLFDEENPVHKSGT
          A.KNPFYLHVGM.I.....K...VKCGY..LHHVIDKSKEDRME.FFLSETCKYLY.LFDE.N.VHKS.T
Retrocopy ANKNPFYLHVGM-IFCRV*KSMQVKCGYMMLHHVIDKSKEDRMENFFLSETCKYLY-LFDENNLVHKSRT

Parental  RYMFTTEGHIVSVDKHLRESPWKEFFSEEGEPDEEGKSVPRPKSLELKVINSS-SNCSRVPDERRYSLPL
          RY.FTTEGHIVS.DKHL.ESP.KEFFS..G....EGKSV.RPKS.ELKVINSS..NC...PDE.RY.LPL
Retrocopy RYIFTTEGHIVSADKHLWESP*KEFFS-KGKQNQEGKSVHRPKSHELKVINSS<PNCNHAPDE-RYFLPL

Parental  KSIYMRQIDQMVGLI
          K.IYM...DQ...LI
Retrocopy KRIYM*HTDQILVLI

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_474 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.

---

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 ,