RetrogeneDB ID: | retro_chof_1074 | ||
Retrocopy location | Organism: | Sloth (Choloepus hoffmanni) | |
| Coordinates: | scaffold_19438:15530..17101(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | STT3B | ||
| Ensembl ID: | ENSCHOG00000002273 | ||
| Aliases: | None | ||
| Description: | STT3B, subunit of the oligosaccharyltransferase complex (catalytic) [Source:HGNC Symbol;Acc:30611] |
Retrocopy-Parental alignment summary:
>retro_chof_1074
TTTAACTATAGATCAATGCATCATCTTGTGTGTCATGGGTTCTATGAATTTTTAAATTGATTTGATGGAAGAGCACACTA
TCCACTAGGAAGAATAGTAGGTGATTCTGTTTACCCAGGCTTGATAGTAACAGCTGGCCTTATTCATTGAATTTTACATA
TATTGAACATAACAGTTCATATAAGAGATGTCTGTGTGTTCCTTGAACCAACTTTTAGTGGCCTGACATCTAAATCTACT
TTTCTGCTTACCAGAGAACTTTGGAACCAAGAAGGATTTTTAGCTGCTTGTTTCATTGCTATTGAACGAGGTTATATCTC
TCAGTCAGTAGCTAGATCCTTTGATAATGAAGGCATTGCTATTTTTGCACTTCAGTTCACATACTACTTGTGGGTAAAAT
CTGTAAAAATTGGGTCAGTGTTTTGAATAGTGTGCTGCTGCTTATCCTATTTCTATATGCTCTCTGCTTGGGGTGGTTAT
GTGTTTATCATCACCCTTATTCTACTGCATGTGTTTGTGTTGCTACCAATGTAGAGATAAAGCCAAAGAGTCTATATATC
ATATAGCAGTTGTTACATTGTGGGTTTAATATTACCCATGCAAATACCCTTTGTGGTATTCCATCCTATCTGAACAATTG
AACACATGGCAGCTGCAAGTATATTTGTATTTTGTTACAAGCTTATGCTTCCTTGCAGTATCTGAGAGACCAACTAACAA
AACAATAGTTCCAGACCCTTTTCTTTTTGGGTGTTATCACTAACTGCAGGTGCCATATCCCTTAGTGTCATCTATTTGAC
TCACACAGGTTACATTGTGCCATGGAGTAGCAGGTTTTACTCATTGTGGGACACTGGATATGCAAAAACACACACTCCAA
TTATTGCATCAGTGTCTGGGCATCAACTTATGTCTTGGGTGTCTTTCTTCTTTGATCTACATACTCTTGTATATACTTCC
CAGCAGGCCTATGGTTCTGCAACAGAAATATCAATGATGAAAGAGTATTTGTTGCTCTGTACGCAATCAGCACCGTCTAC
TTTGCCAGAGTGATATTGCGACTAATGTTGACTCCAGTTGTCTGTTTGCTTTCCCAGTCGCCTTCTCAAATATTTTTGAG
CGCTATTTGGGGATGATATGAAAAGGGAAAATCTACCTGTAGAAGACAGCAGTGATGAGGATGACAAAAGAAACCCAAGA
AATTTGTATGATAAGGCAGTAAAAGTAAGGAAACATGTAACTGAACAGAAAAAAAATGAAGAAAGATTACGTCCTCATAT
AAAAAGCACTGTCACCATGTGGATGCTGATGTCATTGATGAGTCTGCAGTCCACTGTATCTGGGTAACAAGCAATGCCTA
CTCCAGTCCAAGTGTGGAACTGGCTTCTTATAATCATAATGGCACCAGGAAAATCTTAGATGATTTTAGAGAAGCTTACT
TTTGGCTAAGGCAAAATACAGATGAACATGCCCGAGTGATATCTTGGTGGGATTATGGCTATCAGATAGCTGGGATGGTA
ACAGAACTACTTTTGGTGGGTAATAACACATGGAGTAACAGCCACATAAGC
ORF - retro_chof_1074 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 77.34 % |
| Parental protein coverage: | 65.75 % |
| Number of stop codons detected: | 7 |
| Number of frameshifts detected: | 7 |
Retrocopy - Parental Gene Alignment:
| Parental | FNYRSTHHLASHGFYEFLNWFDERAWYPLGRIVGGTVYPGLMITAGLIHWILNTLNITVHIRDVCVSC-- |
| FNYRS.HHL..HGFYEFLN.FD.RA.YPLGRIVG..VYPGL..TAGLIH.IL..LNITVHIRDVCV.... | |
| Retrocopy | FNYRSMHHLVCHGFYEFLN*FDGRAHYPLGRIVGDSVYPGLIVTAGLIH*ILHILNITVHIRDVCVFLEP |
| Parental | TFSG-TSISTFLLEAPMWWNSAGLLAACFIAIVPGYISRSVAGSFDNEGIAIFALQFTYYLWVKSVKTGS |
| TFSG.TS.STFLL....W.N..G.LAACFIAI..GYIS.SVA.SFDNEGIAIFALQFTYYLWVKSVK.GS | |
| Retrocopy | TFSGLTSKSTFLLTRELW-NQEGFLAACFIAIERGYISQSVARSFDNEGIAIFALQFTYYLWVKSVKIGS |
| Parental | VFWTVCCCLSYFYMVSAWGGYVFIINLIPLHVFVLLLMQRYSKRVYIAYSTFYIVGLILSMQIPFVGFQP |
| VF..VCCCLSYFYM.SAWGGYVFII.LI.LHVFVLL.M.R.S.RVYI.YS..YIVGLIL.MQIPFV.F.P | |
| Retrocopy | VF*IVCCCLSYFYMLSAWGGYVFIITLILLHVFVLLPM*R*SQRVYISYSSCYIVGLILPMQIPFVVFHP |
| Parental | IRTSEHMAAAGVFA-LLQAYAFL-QYLRDRLTKQEFQTLFFLGV-SLAAGAVFLSVIYLTYTGYIAPWSG |
| I.T.EHMAAA..F........FL.QYLRD.LTKQ.FQTLFFLGV.SL.AGA..LSVIYLT.TGYI.PWS. | |
| Retrocopy | I*TIEHMAAASIFV>FVTSLCFL>QYLRDQLTKQ*FQTLFFLGV>SLTAGAISLSVIYLTHTGYIVPWSS |
| Parental | RFYSLWDTGYAKIHIPIIASVSEHQPTTWVSFFFDLHILVCT-FPAGLWFCIKNINDERVFVALYAISAV |
| RFYSLWDTGYAK.H.PIIASVS.HQ...WVSFFFDLH.LV.T.FPAGLWFC..NINDERVFVALYAIS.V | |
| Retrocopy | RFYSLWDTGYAKTHTPIIASVSGHQLMSWVSFFFDLHTLVYT<FPAGLWFCNRNINDERVFVALYAISTV |
| Parental | YFAGVMVRLMLTLTPVVCMLS-AIAFSNVFEHYL-GDDMKRENPPVEDSSDEDDKRNPGNLYDKAGKVRK |
| YFA.V..RLM..LTPVVC.LS...AFSN.FE.YL.GDDMKREN.PVEDSSDEDDKRNP.NLYDKA.KVRK | |
| Retrocopy | YFARVILRLM--LTPVVCLLS<PVAFSNIFERYL<GDDMKRENLPVEDSSDEDDKRNPRNLYDKAVKVRK |
| Parental | HVTEQEKTEEGLGPNIKSIVTMLMLMLLMMF-AVHCTWVTSNAYSSPSVVLASYNHDGTRNILDDFREAY |
| HVTEQ...EE.L.P.IKS.VTM.MLM.LM...AVHC.WVTSNAYSSPSV.LASYNH.GTR.ILDDFREAY | |
| Retrocopy | HVTEQXXXEERLRPHIKSTVTMWMLMSLMSL<AVHCIWVTSNAYSSPSVELASYNHNGTRKILDDFREAY |
| Parental | FWLRQNTDEHARVMSWWDYGYQIAGMANRTTLVDNNTWNNSHIA |
| FWLRQNTDEHARV.SWWDYGYQIAGM.....LV.NNTW.NSHI. | |
| Retrocopy | FWLRQNTDEHARVISWWDYGYQIAGMVTELLLVGNNTWSNSHIS |
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_1074 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 | ENSCHOG00000002273 | 1 retrocopy |
retro_chof_1074 ,
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