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 symbol: STT3B
• Ensembl ID: ENSCHOG00000002273
• Aliases: None
• Description: STT3B, subunit of the oligosaccharyltransferase complex (catalytic) [Source:HGNC Symbol;Acc:30611]

Sequence

>retro_chof_1074
TTTAACTATAGATCAATGCATCATCTTGTGTGTCATGGGTTCTATGAATTTTTAAATTGATTTGATGGAAGAGCACACTA
TCCACTAGGAAGAATAGTAGGTGATTCTGTTTACCCAGGCTTGATAGTAACAGCTGGCCTTATTCATTGAATTTTACATA
TATTGAACATAACAGTTCATATAAGAGATGTCTGTGTGTTCCTTGAACCAACTTTTAGTGGCCTGACATCTAAATCTACT
TTTCTGCTTACCAGAGAACTTTGGAACCAAGAAGGATTTTTAGCTGCTTGTTTCATTGCTATTGAACGAGGTTATATCTC
TCAGTCAGTAGCTAGATCCTTTGATAATGAAGGCATTGCTATTTTTGCACTTCAGTTCACATACTACTTGTGGGTAAAAT
CTGTAAAAATTGGGTCAGTGTTTTGAATAGTGTGCTGCTGCTTATCCTATTTCTATATGCTCTCTGCTTGGGGTGGTTAT
GTGTTTATCATCACCCTTATTCTACTGCATGTGTTTGTGTTGCTACCAATGTAGAGATAAAGCCAAAGAGTCTATATATC
ATATAGCAGTTGTTACATTGTGGGTTTAATATTACCCATGCAAATACCCTTTGTGGTATTCCATCCTATCTGAACAATTG
AACACATGGCAGCTGCAAGTATATTTGTATTTTGTTACAAGCTTATGCTTCCTTGCAGTATCTGAGAGACCAACTAACAA
AACAATAGTTCCAGACCCTTTTCTTTTTGGGTGTTATCACTAACTGCAGGTGCCATATCCCTTAGTGTCATCTATTTGAC
TCACACAGGTTACATTGTGCCATGGAGTAGCAGGTTTTACTCATTGTGGGACACTGGATATGCAAAAACACACACTCCAA
TTATTGCATCAGTGTCTGGGCATCAACTTATGTCTTGGGTGTCTTTCTTCTTTGATCTACATACTCTTGTATATACTTCC
CAGCAGGCCTATGGTTCTGCAACAGAAATATCAATGATGAAAGAGTATTTGTTGCTCTGTACGCAATCAGCACCGTCTAC
TTTGCCAGAGTGATATTGCGACTAATGTTGACTCCAGTTGTCTGTTTGCTTTCCCAGTCGCCTTCTCAAATATTTTTGAG
CGCTATTTGGGGATGATATGAAAAGGGAAAATCTACCTGTAGAAGACAGCAGTGATGAGGATGACAAAAGAAACCCAAGA
AATTTGTATGATAAGGCAGTAAAAGTAAGGAAACATGTAACTGAACAGAAAAAAAATGAAGAAAGATTACGTCCTCATAT
AAAAAGCACTGTCACCATGTGGATGCTGATGTCATTGATGAGTCTGCAGTCCACTGTATCTGGGTAACAAGCAATGCCTA
CTCCAGTCCAAGTGTGGAACTGGCTTCTTATAATCATAATGGCACCAGGAAAATCTTAGATGATTTTAGAGAAGCTTACT
TTTGGCTAAGGCAAAATACAGATGAACATGCCCGAGTGATATCTTGGTGGGATTATGGCTATCAGATAGCTGGGATGGTA
ACAGAACTACTTTTGGTGGGTAATAACACATGGAGTAACAGCCACATAAGC

Alignment

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

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_1074 was not experimentally validated.

Homology

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.

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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 ,