RetrogeneDB ID: retro_chof_2361

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_68332:5363..6545(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PAPOLG
• Ensembl ID: ENSCHOG00000014028
• Aliases: None
• Description: poly(A) polymerase gamma [Source:HGNC Symbol;Acc:14982]

Sequence

>retro_chof_2361
GGAAAAATGTTTACCTTTGGATCTTATAGATTAGGAGTATACACAAAATGAGCTGATATTGATGCATTGTGCCTTTCACA
AAGACAAATTGATTGAAGTGGCTTTTCCCCTCATTCTATGATAAATTGAAATTACAAGAAGAATAAAAGATTTGTGAGCT
ACTGATGAGGCATTTGTTCCAGTTATCAAACTGTATTTTGATGGGATAGAGATTGATATTTTGTTTGCAAGATTAGCACT
GCAGACTATTCCAGAAGATTTGGATCTATGTGATGACAGTATGAATAAAAATGCACATACAAGATTCATAAGAAGTCTTA
ATGGTTTACAGAGTACCCAATGAAATTTTACACCCAGGACAAAACAATGACAACTTCAGGTTAACTCTGAGAGCTATCAA
ACTGTAGGTAAAATGCACAACAGCTATTCCAATATATTAGGTTTCCTCAGTGGCATTTCCTGGGCTATGCTAGTAGCAAG
AACTTGCCAGCTTTATCCAAATGCAATAGCATCAACTTTTGTACACAGATATTTTTTGGTATTTTCTAAATGAGAACAGT
GAAATTGAGTATTTTGAAACAGCTGAAGAATTCACCCTTAATTTGCCTGTATGGGACCTAAGGGTAAACCCAGTGATAGG
AAACAACTTATGCTTACAATCCCACCAGCATACCCACAGCAGAACTCCACATTACAGTGTGTCCATTTCAACATGGATGG
TCATGGTTGAGGAGTTTAAACAAGGTCTTGCTCTCACTGATGAAATTTTCCTTTGTAAGAGAGAGTGTTCCAAAATTTTG
AAGCTCCAAACTTCTTTCAGAAGTACAAGTATTATACTGTACTTCTAGGAAGTGCACAAACAGGAAAACAATGCCAGAAA
TGGGTGGACTAGGTAGAATCCAACATCTGAATCCTGGTTGGAATCTTGGAGAATGGATTTATTGCACTGGCCCATTGAAT
CCCTAGGCATTTTCAGCATCCAAAGAAGATCATGACATGGAATAATTTCATGCAGTGTAGGTGATTGGGTTAGTGTTTAT
AAAAACAGAAAACTGAGAAAATCTCAAGCTTGGTCTCACATATGACATTCAGTCTTTCACAGAAACAGTTTTCAGGCAAA
CAAGAAACTGCAAGATAATTGAGGTGGATATGTAAATTGATGCAATGCATGTAAAAAGGCAA

Alignment

ORF - retro_chof_2361 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.48 %
• Parental protein coverage: 60.33 %
• Number of stop codons detected: 13
• Number of frameshifts detected: 10

Retrocopy - Parental Gene Alignment:

Parental  GKIFTFGSYRLGVHTKGADIDALCVAPRHVERSDF-FQSFFEKLKHQDG-IRNLRAVEDAFVPVIKFEFD
          GK.FTFGSYRLGV.TK.ADIDALC...R....S.F.F.SF..KLK.Q...I..L.A...AFVPVIK..FD
Retrocopy GKMFTFGSYRLGVYTK*ADIDALCLSQRQID*SGF<FPSFYDKLKLQEE<IKDL*ATDEAFVPVIKLYFD

Parental  GIEIDLVFARLAIQSISDNLDLRDDSRLRSLDIRCIRSLNGC-RVTDEILHLVPNKETFRLTLRAVKL-W
          GIEID..FARLA.Q.I...LDL.DDS.......R.IRSLNG..RV..EILH...N...FRLTLRA.KL..
Retrocopy GIEIDILFARLALQTIPEDLDLCDDSMNKNAHTRFIRSLNGL>RVPNEILHPGQNNDNFRLTLRAIKL<V

Parental  AKRRGIYSNMLGFLGGVSWAMLVARTCQLYPNAAASTLVHKFFLVFSKWEWPNPV-LLKQ-PEESNLNLP
          .K....YSN.LGFL.G.SWAMLVARTCQLYPNA.AST.VH..FLVFSK.E..N.V..LKQ..EE..LNLP
Retrocopy GKMHNSYSNILGFLSGISWAMLVARTCQLYPNAIASTFVHRYFLVFSK*EQ*N*V<ILKQ<AEEFTLNLP

Parental  VWDPRVN-PSDRYHLMPIITPAYPQQNST-YNVSTSTRTVMVEEFKQGFTVTDEILQGKSDWSKLL-EPP
          VWD.RVN.PSDR..LM..I.PAYPQQNST.Y.VS.ST..VMVEEFKQG...TDEI...K...SK.L.E.P
Retrocopy VWDLRVN<PSDRKQLMLTIPPAYPQQNST>YSVSISTWMVMVEEFKQGLALTDEIFLCKRECSKIL<EAP

Parental  NFFQKYRHYIVLTASASTEENHLEWVGLVESKIRVLVGNLERNEFITLAH-VNPQSFPGNKEHHKDNNYV
          NFFQKY..Y.VL..SA.T......WV..VES.I..LVG.LE.N.FI.LAH..NP..F...KE.H......
Retrocopy NFFQKYKYYTVLLGSAQTGKQCQKWVD*VESNI*ILVGILE-NGFIALAH<LNP*AFSASKEDHDME*FH

Parental  SMWFLGIIFRRVENAESVNIDLTYDIQSFTDTVYRQANNINMLKEGMKIEATHVKKK
          .....G..F...EN.E.....LTYDIQSFT.TV.RQ..N.......M.I.A.HVK..
Retrocopy AV*VIGLVFIKTEN*ENLKLGLTYDIQSFTETVFRQTRNCKIIEVDM*IDAMHVKRQ

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_2361 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 4 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000014028	4 retrocopies	retro_chof_2125, retro_chof_2361 , retro_chof_2456, retro_chof_2571,
Ochotona princeps	ENSOPRG00000009630	4 retrocopies	retro_opri_208, retro_opri_395, retro_opri_827, retro_opri_861,
Ictidomys tridecemlineatus	ENSSTOG00000010861	1 retrocopy	retro_itri_1616,
Tursiops truncatus	ENSTTRG00000006237	1 retrocopy	retro_ttru_475,