RetrogeneDB ID: | retro_chof_2112 | ||
Retrocopy location | Organism: | Sloth (Choloepus hoffmanni) | |
| Coordinates: | scaffold_50204:4339..4976(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PPP2CB | ||
| Ensembl ID: | ENSCHOG00000003467 | ||
| Aliases: | None | ||
| Description: | protein phosphatase 2, catalytic subunit, beta isozyme [Source:HGNC Symbol;Acc:9300] |
Retrocopy-Parental alignment summary:
>retro_chof_2112
CTGAGGGAATGCGAACAAACTTGGAACAAAGTGCGAACACCGTGCGTAAACGCTGCGGAAATCTTAACAAAGAATCAAAT
GTGCGAGAGGTTCGTGTCTGTGGAGATGTTCATGTTCAATTCCTTGATTTTAGGGAACTCTTTAGAATTGGTGGGAAATC
TCCAGATAAAAATTGTCTACTCATGGGTGACTCGGTAGGTTATTATTCAGTGGAGACTATGACTCTCTTTGTAGCATCAG
AAGTGTCTTTTTGAGATCACATTACAGTACTGAGAAGAAACCAAAAAAGCCGACAAATGACCCAAGTACATGGCTTTTAT
GATGAATGACTATGAAAATATGGAAACGCCGATATTTGTAAATATTTTACACAGCTATTTGATTATCTTCCACTAACAGC
TTTAGTAGATGGACAGATACTCTGCCTCCATAGTGGTTTCTCTACATCTGTAGATACACTGGATCATATAAGAGCCCTAG
ATCTTTTACAAGAAATTCCACATGAGGGCCCAATGTGTCATCTGTTCCTGTCAGATCCAGATGATGATGGTAGATGGGAT
ATTTTTACATGTGGTGCAGGCTACACTTTGGACAAGACACTTCTGAAGCATTTAGCCAAGCCAGTGGCCTTACACTA
ORF - retro_chof_2112 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 68.47 % |
| Parental protein coverage: | 71.66 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | LKECKQFKENQVQTLCEKAKEILTK-ESNVQEVRCPVTVCGDVHGQFHDLMELFRIGGKSPDTNYLFMGD |
| L.EC.Q...N.V.T.C..A.EILTK.ESNV.EVR....VCGDVH.QF.D..ELFRIGGKSPD.N.L.MGD | |
| Retrocopy | LRECEQ-TWNKVRTPCVNAAEILTK<ESNVREVR----VCGDVHVQFLDFRELFRIGGKSPDKNCLLMGD |
| Parental | YVDRGYYSVETVTLLVALKVRYPERITILRGNHESRQITQVYGFYDECLRKYGNANVWKYFTDLFDYLPL |
| .V..GYYSVET.TL.VA..V.....IT.LR.N..SRQ.TQV.GFYDE.L.KYGNA...KYFT.LFDYLPL | |
| Retrocopy | SV--GYYSVETMTLFVASEVSF*DHITVLRRNQKSRQMTQVHGFYDE*L*KYGNADICKYFTQLFDYLPL |
| Parental | TALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGGWGISPRGAGYT-FGQDI |
| TALVDGQI.CLH.G.S.S.DTLDHIRALD.LQE.PHEGPMC.L..SDPDD.G.W.I...GAGYT.FGQD. | |
| Retrocopy | TALVDGQILCLHSGFSTSVDTLDHIRALDLLQEIPHEGPMCHLFLSDPDDDGRWDIFTCGAGYT<FGQDT |
| Parental | SETFNHANGLTL |
| SE.F..A.GLTL | |
| Retrocopy | SEAFSQASGLTL |
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_2112 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 11 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000003467 | 9 retrocopies |
retro_chof_1247, retro_chof_1521, retro_chof_1556, retro_chof_2112 , retro_chof_2267, retro_chof_2502, retro_chof_251, retro_chof_273, retro_chof_446,
|
| Monodelphis domestica | ENSMODG00000019001 | 2 retrocopies |