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 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_2184
CTGCTGGCCTTCTTCCTTGCACTGCAAGTTCTAATAGGAGATGAAGATGCCGTCTGTTTCCAAACCTTTTTCCACACCGT
ATGAAACGATATGGGGCACTCCCTGAGAGGTTTAACTGGCAGGTACAGGCCCCTGATGATCTCTTTTATCCACTGAGACC
AGAGTTGGTGAAATCTACATGTGTTCTCTACCAGGCAACCAAGAATCCCTTCTACTTCCATGTAGGAATGGAAATTCTAC
AGAGTCTGGAAAAGTACCCCAAACTCAAATGTGGGTACGTTAGGCTGCGTCATATCATAGACAAATCTAAAGAGGACTGG
ATGGAGAGCTTCTTTCTCAGCGAGACCTGTAAATACTTTTATCTGCTATTTGATGAGAATCCAGTCGGCAAATCTGGAAG
CAGATAATGTCTACAACAGAGGGACACGTTGTATCTGTGGACAAACATCTACTGGAATCACCCTGGAAAGAATTCTTTTC
TGAAGAAGGAGAGCACAACTAAGGGGGAGAATCTCTGCACAGGCCTAAATCTCATGAATTAAAAGTCATCAACCCCAACT
CCAATTGCAATCATGTTCCTGATGAGAGGAGATACTGCCTGCCCTTAAAGAGCATCTACATCCAACAGATTGACCAGATG
GTTGGC
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 |
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_2184 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,
|