RetrogeneDB ID: | retro_chof_2583 | ||
Retrocopy location | Organism: | Sloth (Choloepus hoffmanni) | |
| Coordinates: | scaffold_87632:8104..8707(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LHX9 | ||
| Ensembl ID: | ENSCHOG00000000991 | ||
| Aliases: | None | ||
| Description: | LIM homeobox 9 [Source:HGNC Symbol;Acc:14222] |
Retrocopy-Parental alignment summary:
>retro_chof_2583
CCTGCCGGTTCCACCACGATGCTGTTCCACAGTCTGTCGGTCCCCGAGGTGCACAGGATCATCAACGAGATGGACTGCAG
GGCCAAGAGTGAGGCTCCCGCCATCAGTTCCGCCATTGACCATGGTGACGTGGAGATGACCGTGCCTTCCATCAGCAGTG
ACTGTGCTGCACTGTGTGCTGGCTGCATGGGCAAGATTTCGGACCACTACTACCTGCTGGCAGTGGATAAACAGTGGCAC
ATGCACTGCCTCAAGTGCTGCGAGTGCAAGTTCAATCTAGAGTCAGAGCTCACCTGTTTTAGCAAGGACAGCAGCATCTA
CTGCAAGGAAGACTACTACAGGTAGTTCTCTGTGCAGCATTGCGCCCGCTGCCATCTGGGCATCTCGGCCTCAGAGATGG
TGATGTGCACCCAGAACTTGGTTTATCACCTCAACTGCTTCACTTGCACCACGTGTAACAAAATGCTGACCACCGGCAAC
CACTTTGGTATGAAGGACAGCCTGGTCTACTGCCGCTTGCACTTCGAGGCACTGCTGCAAGGTGAGTATCCCACTCATTT
TAACCATGCTGACGTGGCAGCCACAGCCAAGAGCGTGGGGCTG
ORF - retro_chof_2583 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 62.69 % |
| Parental protein coverage: | 50.38 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | PFRPPAMLFHGISGGHIQGIMEEMERRSKTEARLAKGSQLNGR-DAGMPPLSPEKPALCAGCGGKISDRY |
| P.....MLFH..S......I..EM..R.K.EA.........G......P..S....ALCAGC.GKISD.Y | |
| Retrocopy | PAGSTTMLFHSLSVPEVHRIINEMDCRAKSEAPAISSAIDHGDVEMTVPSISSDCAALCAGCMGKISDHY |
| Parental | YLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDYYRRFSVQRCARCHLGISASEMVMRARDS |
| YLLAVDKQWH..CLKCCECK..LESELTCF.KD.SIYCKEDYYR.FSVQ.CARCHLGISASEMVM..... | |
| Retrocopy | YLLAVDKQWHMHCLKCCECKFNLESELTCFSKDSSIYCKEDYYR*FSVQHCARCHLGISASEMVMCTQNL |
| Parental | VYHLSCFTCSTCNKTLTTGDHFGMKDSLVYCRAHFETLLQGEYPPQLSYTELAAKSGGLAL |
| VYHL.CFTC.TCNK.LTTG.HFGMKDSLVYCR.HFE.LLQGEYP........AA......L | |
| Retrocopy | VYHLNCFTCTTCNKMLTTGNHFGMKDSLVYCRLHFEALLQGEYPTHFNHADVAATAKSVGL |
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_2583 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 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000000991 | 1 retrocopy |
retro_chof_2583 ,
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