RetrogeneDB ID: retro_chof_2125

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_51380:7372..8430(+)
• 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_2125
ATAAAATATTTATGAGTAAATAAAGAGACATATTTACCAGTTATCAAGCTGTTTTATGAGATAAAGATTGATATTTTGTT
TGCAAGATTATGACTGTAGACTATTCCAGAAAATTTGGATCTATGAGAACATAGTCTGAATAAAAATGTAGATAGAAGAT
GCATAAGAAGTCTTAATTGTTGCAGAGTATCCAATGAAATTTTACATCTAGCACCAAACATTCACAACTTCAGGTTAACT
CTGGGAGCCATCAAACTGTGGGTCAAATGCCACAATAGCTATTCCAATATATTAGGTTTCCTCAGTGGCATTTACTGGAC
TACATTAGTAGCAACAACTTTCCAGATTTATCCAAATGCAATATCAACCCTTGTATACAATATTTTTAGGTATTTTCTAA
ATGAGAATGACCAAATTGAGTTTTCTGAAACAGCTGAAGAATGCAATTCTAATTTGCCTGTAGGGGCTGCAAGGGTAAAC
CCCAGTGATAGGTACCATCTTATGCCTATAATCACACTAGCATACCCACAGCAGAACTCCATATACAATGTATCCATTTC
AACATGGATGGTCATGGGTGAGGTGTTTAAACAAGGTCTTGCTCTCATGGATGAAAGCTTGCTGTGTAAGGCAGAGTGTT
CCAAAGTTTTTGAAGTTCCAAACTCCTTGAAAAATACAAGTATTATATTGTACTTCTAGCAAGTTCACCAACAGGAAAAC
AATGGCTGGAATTAGTGAGCTGCGTGGAATAAAAACTCAAAGTCCTGTTTGGAATCTTGGAGAAAAATTATTTTAATACA
CTGGCTCATTGAATCCCCAGTCATTTCCAGCTTTGAAAGAAGATCATGACAAGGAAGAATTTCAGGCAATGTGGGTGATT
GGGTTTCTGTTCAAACAGAACAACAGAAAACTCTGAAAACCTCAGTGTTGATCTTACCTATGATATCTAGTCTTTCAAAG
ATACAGTTTATAGGCAAGCAATAAACTGCAAGATATTTGAGGTGGATATGAAAATTTATGCAATGCATGTAAGAAAAACA
ACTCCATTAAACTACATA

Alignment

ORF - retro_chof_2125 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.33 %
• Parental protein coverage: 53.95 %
• Number of stop codons detected: 13
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IRNLRAVEDAFVPVIKFEFDGIEIDLVFARLAIQSISDNLDLRDDSRLRSLDIRCIRSLNGCRVTDEILH
          I..L........PVIK.....I.ID..FARL....I..NLDL...S.....D.RCIRSLN.CRV..EILH
Retrocopy IKYL*VNKETYLPVIKLFYE-IKIDILFARL*L*TIPENLDL*EHSLNKNVDRRCIRSLNCCRVSNEILH

Parental  LVPNKETFRLTLRAVKLWAKRRGIYSNMLGFLGGVSWAMLVARTCQLYPNAAASTLVH-KFFLVFSKWEW
          L.PN...FRLTL.A.KLW.K....YSN.LGFL.G..W..LVA.T.Q.YPNA..STLV....F.VFSK.E.
Retrocopy LAPNIHNFRLTLGAIKLWVKCHNSYSNILGFLSGIYWTTLVATTFQIYPNAI-STLVY<QYF*VFSK*E*

Parental  PNPVL-LKQ-PEESNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSTSTRTVMVEEFKQGFTVTD
          PN.V..LKQ..EE.N.NLPV...RVNPSDRYHLMPIIT.AYPQQNS.YNVS.ST..VM.E.FKQG....D
Retrocopy PN*VF<LKQ<AEECNSNLPVGAARVNPSDRYHLMPIITLAYPQQNSIYNVSISTWMVMGEVFKQGLALMD

Parental  EILQGKSDWSKLLEPPN-FFQKYRHYIVLTASASTEENHLEWVGLVESKIRVLVGNLERNEFITLAHVNP
          E.L..K...SK..E.PN....KY..YIVL.AS..T....LE.V..VE.K..VL.G.LE.N.F.TLAH..P
Retrocopy ESLLCKAECSKVFEVPN<LLEKYKYYIVLLASSPTGKQWLELVSCVE*KLKVLFGILEKNYFNTLAH*IP

Parental  QSFPGNKEHHKDNNYVSMWFLGIIFRRV-ENAESVNIDLTYDIQSFTDTVYRQANNINMLKEGMKIEATH
          ..F...K......N......LG....R..EN.E....DLTYDI.SF.DTVYRQA.N.......MKI.A.H
Retrocopy SHFQL*KKIMTRKNFRQCG*LGFCSNRTTENSENLSVDLTYDI*SFKDTVYRQAINCKIFEVDMKIYAMH

Parental  VKKKQLHHYL
          V.K.....Y.
Retrocopy VRKTTPLNYI

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_2125 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,