RetrogeneDB ID: retro_chof_2456

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_77537:3611..4609(-)
• 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_2456
TTTGATGAGATAAAGATTGATATTTTGTTTGTGAGATTATCACTGCAGACTATTCCAGAAGGTTTGGTTCTATGAGATGA
CTAGTCTGAATAAACATGTAGATATAAGATGCATAAGAAGTCTTAATGGTTGCAGAGTATCCAATGAAATTTTACATCTA
GTACCAAACATTTGCAACTTCAGGTTAACTCTGAAAATAAGACTGTGGGTCAAATGCCACAATAACTATTCCAATATATT
AGGTTTCCTCAGTGGAATTTTCTGGACTATGCAAGTAGCAAGAACTTGCCACATTTATCCAAATACAATAGCATCTACAC
TTGTATATAATTTTTTAGGTATTTTCTAAATGTGAATGGCTAAATTGAGTCTTCTGAAACAGCTGAAGAATGCAATCATA
ATTTGTCTGTAGGGGGTGCAAAGGTAAACCCCAGTGACAGGTACCATCTTGTGCCTATAATCACACCAGCATATCCACAG
CAGCAGAACTCCATATACAATGTATCCACTTCAACACGGATGGTCATGGGTGAGGTGTTTAACCAAGATTTTGCTGTCAC
AGATGAAATTTTGCTGTGTAAGGCAGTGTGTTCCAAACATTTTGAAGCTCCAAACTTCTTTAAAAATACAAGTATTATTT
GTACTTCTAGCAAGTTCACTAACAGGAAAGCAATGGCTGGAATAAGTGAGCTAGGTGGAATAAAAACTCCAAATCCTGTT
TGGAATCTTGGAGAAACATGATTTTATTACACTGGCTCATTGAATCCTCAGTCATTTCCAGCTCCCGAAGAGGATGATGA
CAAGGAAGAATTTCATACAATGTGGGTAATTGGGTTTGTGTTCAAAGAGAACAACAGAAAACTCTGAAAACCTCAGTGTT
GTTCTTACTTATGATATCTAGACTGAAAGATACAGTTTATAGGCAAGCAATAAACTGCAAGATATTTGAGGTGAATATGA
AAATTTATGCAATACATGTAAGAAAAAAACAACTCCAT

Alignment

ORF - retro_chof_2456 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.52 %
• Parental protein coverage: 50.76 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  FDGIEIDLVFARLAIQSISDNLDLRDD-SRLRSLDIRCIRSLNGCRVTDEILHLVPNKETFRLTLRAVKL
          FD.I.ID..F.RL..Q.I...L.L.DD.S.....DIRCIRSLNGCRV..EILHLVPN...FRLTL....L
Retrocopy FDEIKIDILFVRLSLQTIPEGLVL*DD>SLNKHVDIRCIRSLNGCRVSNEILHLVPNICNFRLTLK-IRL

Parental  WAKRRGIYSNMLGFLGGVSWAMLVARTCQLYPNAAASTLVHKFFL-VFSKWEWPNPV-LLKQ-PEESNLN
          W.K....YSN.LGFL.G..W.M.VARTC..YPN..ASTLV...FL.VFSK.EW.N.V.LLKQ..EE.N.N
Retrocopy WVKCHNNYSNILGFLSGIFWTMQVARTCHIYPNTIASTLVYN-FL>VFSKCEWLN*V<LLKQ<AEECNHN

Parental  LPVWDPRVNPSDRYHLMPIITPAYPQQ-NSTYNVSTSTRTVMVEEFKQGFTVTDEILQGKSDWSKLLEPP
          L.V....VNPSDRYHL.PIITPAYPQQ.NS.YNVSTSTR.VM.E.F.Q.F.VTDEIL..K...SK..E.P
Retrocopy LSVGGAKVNPSDRYHLVPIITPAYPQQQNSIYNVSTSTRMVMGEVFNQDFAVTDEILLCKAVCSKHFEAP

Parental  NFFQ-KYRHYI-VLTASASTEENHLEWVGLVESKIRVLVGNLERNEFITLAH-VNPQSFPGNKEHHKDN-
          NFF..KY..Y..VL.AS..T....LE.V..VE.K...L.G.LE...FITLAH..NPQSFP...E......
Retrocopy NFFK<KYKYYL<VLLASSLTGKQWLE*VS*VE*KLQILFGILEKHDFITLAH<LNPQSFPAPEEDDDKE>

Parental  NYVSMWFLGI-IFRRVENAESVNIDLTYDIQSFTDTVYRQANNINMLKEGMKIEATHVKKKQLH
          N......LG....R...............I....DTVYRQA.N.......MKI.A.HV.KKQLH
Retrocopy NFIQCG*LGL>VQREQQKTLKTSVLFLLMISRLKDTVYRQAINCKIFEVNMKIYAIHVRKKQLH

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_2456 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,