RetrogeneDB ID: retro_chof_2571

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_86860:5384..6468(+)
• 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_2571
TTCCACTGATTCTATGACAAATTGAATTTACAAGAAGAATAAAAGATTTATGAGCAAATGAAGAGGCATTTTTACCAGCT
ATCAACTGTGTTTTGATGAGATAAAGATTGATATTTTGTTTGCAAGATTATCACTGCAGACTATTCCAGAAAGATTTGGA
TCTATGAGATGATTAGTCTGAATAAAAATGTAGATATAAGATGCATAAGAAGTCTTAATTGTTTCAGAGTATCCAATGAA
ATTTTACATCTAACACCAAACATTCACAGCTTCAAGTTTAACTCTGAGAGCTACCAAACTGTGGATCAAATGCCACAATA
GCTATTCCAATATATTAAGTTTCTTTGGTGGCATTTCCTGAACTATATTAATAGCAAGAACTTGCCAGGTTTATCCAAAT
GCAATAGCATCAACCCTTGTATATAAATTTTAGGTATTTTCTAAATGAGAATGGAGAAATTGAGTCTTCTGAAACAGCTG
AAGAATGCAATCATAATTTGCCTGTAGCAGGTGCAAGTGTAAACCCCAGTGATAGGTACCATCTTATGCCTATAATCACA
CCAGCATATCCACAACGGAACTCCATATACAATGTATCCATTTCAAGATGGATGGTCACGGGTGAGGAGCTTAAAAAACG
TCTTGCTCTCACAGATGAAATTTTGCTGTGTAAGGCAGAGTGTTCCAAACTTTTTGAAGCTCCAAACTTCTTTAAAAATA
CAAGTATTATATTGTACTTCTAGCAGGTTCACCAACAGGAAAACAGTGGCTGGAATGAGTGAGCTAGGTGGAATAAAAAC
TCCAAATCCTGTTTGGAATCTTGGAGAAAAATGATTTTATTACACTGGCTCATTGAATCCCGTCATTTCCAGCTCCCAAA
GATGATCATGACAAGGAAGAATTTCATGCAATGTGGGTGATTGGGTTTGTGTTCAAAGAGAACAACAGAAAACTGAAAAC
CTCAGTGTTGATCTTACCTATGATATCTAGGCTTTCAAAAATAGTTTATAGGCAAGCAATAAACTGCAAGATATTTGAGG
TGGATACAAAAGTTTATGAAATGCATGTAAAGAAACAACTCCAT

Alignment

ORF - retro_chof_2571 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.55 %
• Parental protein coverage: 55.47 %
• Number of stop codons detected: 11
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  FQSFFEKLKHQDG-IRNLRAVEDAFVPVI-KFEFDGIEIDLVFARLAIQSISD-NLDLRDD-SRLRSLDI
          F..F..KL..Q...I..L.A.E.AF.P.I....FD.I.ID..FARL..Q.I....LDL.DD.S.....DI
Retrocopy FH*FYDKLNLQEE<IKDL*ANEEAFLPAI<QLCFDEIKIDILFARLSLQTIPE>DLDL*DD>SLNKNVDI

Parental  RCIRSLNGCRVTDEILHLVPNKETFR-LTLRAVKLWAKRRGIYSNMLGFLGGVSWAMLVARTCQLYPNAA
          RCIRSLN..RV..EILHL.PN...F..LTLRA.KLW.K....YSN.L.F.GG.S...L.ARTCQ.YPNA.
Retrocopy RCIRSLNCFRVSNEILHLTPNIHSFK>LTLRATKLWIKCHNSYSNILSFFGGIS*TILIARTCQVYPNAI

Parental  ASTLVHKFFLVFSKWEWPNPV-LLKQ-PEESNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSTS
          ASTLV.KF..VFSK.EW.N.V.LLKQ..EE.N.NLPV....VNPSDRYHLMPIITPAYPQ.NS.YNVS.S
Retrocopy ASTLVYKF*-VFSK*EWRN*V<LLKQ<AEECNHNLPVAGASVNPSDRYHLMPIITPAYPQRNSIYNVSIS

Parental  TRTVMVEEFKQGFTVTDEILQGKSDWSKLLEPPNFFQ-KYRHYIVLTASASTEENHLEWVGLVESKIRVL
          ...V..EE.K.....TDEIL..K...SKL.E.PNFF..KY..YIVL.A...T....LE.V..VE.K...L
Retrocopy RWMVTGEELKKRLALTDEILLCKAECSKLFEAPNFFK<KYKYYIVLLAGSPTGKQWLE*VS*VE*KLQIL

Parental  VGNLERNEFITLAHVNPQSFPGNKEHHKDNNYVSMWFLGIIFRRVENAESVNIDLTYDIQSFTDTVYRQA
          .G.LE.N.FITLAH..P.SFP..K..H.......MW..G..F................I......VYRQA
Retrocopy FGILEKNDFITLAH*IP-SFPAPKDDHDKEEFHAMWVIGFVFKENNRKLKTSVLILPMISRLSKIVYRQA

Parental  NNINMLKEGMKIEATHVKKKQLH
          .N........K....HV.KKQLH
Retrocopy INCKIFEVDTKVYEMHV-KKQLH

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_2571 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,