RetrogeneDB ID: | retro_chof_1417 | ||
Retrocopy location | Organism: | Sloth (Choloepus hoffmanni) | |
| Coordinates: | scaffold_28694:14120..14709(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LIN7C | ||
| Ensembl ID: | ENSCHOG00000000111 | ||
| Aliases: | None | ||
| Description: | lin-7 homolog C (C. elegans) [Source:HGNC Symbol;Acc:17789] |
Retrocopy-Parental alignment summary:
>retro_chof_1417
ATGATGGCACTGGAGGAAACTGTGTGGCTGGAGAGAGATATTTGTAGAGCAATTGTATTGTTAGAAAAACTACAAAGGAG
TGAAGTACCACCACAAAAACTTCAGGCTTTACAAAGGGTCCTTCAAAGTGAGTTGTGCAATGCTGTTAGGGAGGTATATG
AACACATCTATGAAACTGTGGACATCAGTAGCAGTTCTGAAGTGAGAGCTAATGCAACTGCAAAGGCTACAGTCACTGCA
TTTGCTGCCAGTGAAAGGAGATTCTCATCCTTGAGTGGCTGAGCTGCCAAAAACAGAAGATGGCCTTAGAGTCAATATTG
TGGGAGGGAAAAAATGAAACTGTCCAATCTGTGTATCTTGAATAATTCCAGGTGGTATTGCTGATAGACATGGGGGCCTC
AAACGAGGAGACCAACTCCTTTCTGATAATGGAGTTAGAATTGAAGGAGAAAATCATGAGAAAGCTGTAGAGCTACTGAA
AGCAGCTCAAGCAAAGGTTAAATTAGTAGTATGATATACACCCAAAGTCTTAGAAGAAATGGAGTCACAATTTGAAAAAA
TGAGATCAGCAAAACACAGGCAACAAACC
ORF - retro_chof_1417 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.84 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MAALGEPVRLERDICRAIELLEKLQRSGEVPPQKLQALQRVLQSEFCNAVREVYEHVYETVDISSSPEVR |
| M.AL.E.V.LERDICRAI.LLEKLQRS.EVPPQKLQALQRVLQSE.CNAVREVYEH.YETVDISSS.EVR | |
| Retrocopy | MMALEETVWLERDICRAIVLLEKLQRS-EVPPQKLQALQRVLQSELCNAVREVYEHIYETVDISSSSEVR |
| Parental | ANATAKATVAAFAASE-GHSHPRVVELPKTEEGLGFNIMGGKEQNSPIYISRIIPGGIADRHGGLKRGDQ |
| ANATAKATV.AFAASE.G.SHP.V.ELPKTE.GL..NI.GGK..N.PI..S.IIPGGIADRHGGLKRGDQ | |
| Retrocopy | ANATAKATVTAFAASE>GDSHP*VAELPKTEDGLRVNIVGGKK*NCPICVS*IIPGGIADRHGGLKRGDQ |
| Parental | LLSVNGVSVEGEHHEKAVELLKAAQGKVKLVVRYTPKVLEEMESRFEKMRSAKRRQQT |
| LLS.NGV..EGE.HEKAVELLKAAQ.KVKLVV.YTPKVLEEMES.FEKMRSAK.RQQT | |
| Retrocopy | LLSDNGVRIEGENHEKAVELLKAAQAKVKLVV*YTPKVLEEMESQFEKMRSAKHRQQT |
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_1417 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 2 parental genes, and 9 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000000111 | 7 retrocopies |
retro_chof_1046, retro_chof_1062, retro_chof_1417 , retro_chof_2399, retro_chof_2401, retro_chof_2515, retro_chof_864,
|
| Microcebus murinus | ENSMICG00000005165 | 2 retrocopies |