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 summary: | ||
| Parental gene symbol: | EDEM1 | ||
| Ensembl ID: | ENSCHOG00000011489 | ||
| Aliases: | None | ||
| Description: | ER degradation enhancer, mannosidase alpha-like 1 [Source:HGNC Symbol;Acc:18967] |
Retrocopy-Parental alignment summary:
>retro_chof_474
GTCCTGGGAAGCCGTCTTTCTGCCCACAGAAAAACAACTGACTCCAAGAAGCCCTTTGGTGGCAGGACAACTAAGGATTA
CGATAACAAACTGTTGCATACGGCTCATAACCTGGCCATGCGACGACTCCCTGCCTTTGAAAACACCAAGACAGGCATCC
CCTATCCTTGGGTGAATCTAAAGACAAGCGTCCCTCCTGACAGCAATAATGAGATGTGTACGGCAGGAGCTGGTTTCCTT
CTGATGGAATTTGGGATTCTGAGCCCACTGCTGGGGGATTCTGCATTTCAATGGGTGGCCAAATGAGCAGCGAAAACCCT
TTGGAACCTCTGGAGCAACGACACAGGATTAATAGGCAATGTTGTGAATATTCAGATGGGCCATTGGGTTGGAAAGCAGT
GTGGCTTAGTTGCTGGTCTGGACTCCTTCTATGAGTACTTCTTCAATCCTACATTCTTTTTGGAAAAAAAGAAGACCTAC
AAATGTTTAATGCCACATATGAGAATATTCAGAACTACTTAAGAGGAGGTTGGGAGGCCTGTAAGGAGGGAGGAGACCCC
CCCACACACACACTATGTCAATGTGACATGTTCAGTGGACAGCTGAGGAGCACCTGGATTGACTCTCTGCAGGCCTTCTC
GCCTGGACTGCACGTTCTAACAGGAGATGTGGAAGATGGCAGCTGCCCCCATGCCTTTTACTAAGCTATATGGAAAAGAT
ATGGGGCTCTCCCTGAGAGGTATAACTGGAGCTACAGGCCCCTGACCTTCTCTTCTACCTACTGAGACCAGAGTTGGTGG
AATCTACATACGTCCTCTACTAAGCAAACAAGAATCCCTTCTACCTCCATGTAGGAATGATATTCTGCAGAGTCTAGAAA
AGTATGCAAGTCAAATGTGGGTACATGATGCTACACCATGTCATAGACAAATCCAAAGAGGACCGGATGGAGAACTTCTT
TCTCAGTGAGACCTGTAAATACTTATACCTATTTGATGAAAACAATCTAGTACACAAATCTAGAACCAGGTACATATTTA
CAACTGAGGGACACATTGTATCTGCGGACAAACATCTATGGGAATCACCCTAGAAGGAATTCTTTTCTAAAGGAAAGCAG
AACCAAGAGGGAAAATCTGTGCACAGGCCTAAATCTCATGAATTAAAGGTCATTAACTCCAGCCCAATTGCAATCATGCT
CCTGATGAGAGATACTTCCTGCCCTTAAAGAGAATCTACATGTGACACACTGACCAGATCCTCGTTTTGATT
ORF - retro_chof_474 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.86 % |
| Parental protein coverage: | 100.0 % |
| 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 |
Choloepus hoffmanni was not studied using RNA-Seq expression data.
Choloepus hoffmanni was not studied using ChIP-Seq data.
Choloepus hoffmanni was not studied using EST data.
Choloepus hoffmanni was not studied using FANTOM5 data.
retro_chof_474 was not experimentally validated.
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 ,
|