RetrogeneDB ID: | retro_chof_2106 | ||
Retrocopy location | Organism: | Sloth (Choloepus hoffmanni) | |
| Coordinates: | scaffold_49556:57..729(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | THUMPD2 | ||
| Ensembl ID: | ENSCHOG00000000360 | ||
| Aliases: | None | ||
| Description: | THUMP domain containing 2 [Source:HGNC Symbol;Acc:14890] |
Retrocopy-Parental alignment summary:
>retro_chof_2106
GTTGAGTATATCTCAGGAAAGGTTTTCTTCACCACCTGTTCTTATTTGAATATGCTGATGAAATTAAAATCTGCAAAAAG
GTTATTTCTGCTGATAAAAAAGCAGTTTCCACTGACACTTTCTTCTGAAGTAAAGGAAAAATATTTAGTGATATGCAAAG
ACTTGTAAATGATGACCTAGGAAGTTGGTTGAATGCCCATTTCAATTGTGAAAAATCTTCTTGAACTTGATGCAAAAAGG
GAAGAACTTTCTCAAGGAGATTCTAACCCACTAAAAAGAAAAGCAGGAGAAAATGAAATCATTATGGCTAAAAAATTTAA
AACAGAACAAATGCAAGACATACCAGAGAACAGGGAATGTTGGCTGGAAAAACAAATAGAAGAAGAAACACTAGAGCAAA
AAGATTTTATCAATCAAAGAGACGATCTTCAAGAAGAATAGTTTCAGAGTGATGTAGAGAAAGCAAATGATACTCATAAC
TGGAGCGACTTGACTTTCAGGGTTTCTTGTTGCTGTAGTGGTGCTTTTGGAAGGACTGCACAGGAAGTAGGAAGAATAAT
TGGAATTGCTCTTAGGAAACAGCTTGGATGGAAAGCAGATTTGAGGAATCCAAATTTAGAGATCTTTATACATCTAAATG
ATGTTTACTCCATTGTGGGGATTTCTGTTTTC
ORF - retro_chof_2106 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 77.19 % |
| Parental protein coverage: | 63.74 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | VECISGKVFFTTCSDLNMLMKLKSAERLFLLIKKQFPLTVSSV-SKGKIFNEMQRLVNDDPGSWSNA-IS |
| VE.ISGKVFFTTCS.LNMLMKLKSA.RLFLLIKKQFPLT.SS..SKGKIF..MQRLVNDD.GSW.NA.IS | |
| Retrocopy | VEYISGKVFFTTCSYLNMLMKLKSAKRLFLLIKKQFPLTLSSE<SKGKIFSDMQRLVNDDLGSWLNA>IS |
| Parental | IWKNLHELDAKREELSQGDSNPLKRKAGENEIIMAKKFKTEQMQDIPENGECQLEKQVEEETLEQKDCIG |
| I.KNL.ELDAKREELSQGDSNP..................EQMQDIPEN.EC.LEKQ.EEETLEQKD.I. | |
| Retrocopy | IVKNLLELDAKREELSQGDSNPXXXXXXXXXXXXXXXXXXEQMQDIPENRECWLEKQIEEETLEQKDFIN |
| Parental | QRGDFQEE-FQSDAEKAIDTHNQCDLTFRVSCRCSGAIGRTFAAQEVGRIIGISLMKQFGWKADLRNPTL |
| QR.D.QEE.FQSD.EKA.DTHN..DLTFRVSC.CSGA.GRT..AQEVGRIIGI.L.KQ.GWKADLRNP.L | |
| Retrocopy | QRDDLQEE*FQSDVEKANDTHNWSDLTFRVSCCCSGAFGRT--AQEVGRIIGIALRKQLGWKADLRNPNL |
| Parental | EIFIHLNDVYSIVGIPVF |
| EIFIHLNDVYSIVGI.VF | |
| Retrocopy | EIFIHLNDVYSIVGISVF |
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_2106 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 | ENSCHOG00000000360 | 1 retrocopy |
retro_chof_2106 ,
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