RetrogeneDB ID: retro_chof_1686

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_358798:77..1117(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAPSS2
• Ensembl ID: ENSCHOG00000002724
• Aliases: None
• Description: 3'-phosphoadenosine 5'-phosphosulfate synthase 2 [Source:HGNC Symbol;Acc:8604]

Sequence

>retro_chof_1686
CTGAAAACAGACTCCTGTGATGTAAATGACTGCATTCAGCAAATTGTGGAGTTCCTACAGGAAAGGGACATTGTACCTGT
GGATGCTTCTTATGAAGTAAAAGAACTTTATGTGCCAGAAAATAAACTTCGTTTGGCAAAAACAGATGCAGAAACATTAC
CGGCACTGAAAATTAATAAAGTACACATGCAGTGAGTGCAAGTTTTGGCTGAAGGTTGGGCAACACCACTGAATGGCTTT
ATGAGAGAGAGGCAGTACTTGCAGCACCTTCATTTTGTCTTCGATGGGGGTGTCATTAACTTGTCATACCTATAGTTCTG
ACAGCTACCCAAGAAGACAAAGAGAGGCTGGATGGCTGTGCAGCATTTGCTCCGATGTATGAGGGCTACCGCATGGCTAT
TCTTCTTACATCAGGGTTTTTTGAGCACAGAAAGGAAGAGTACTGTGCCAGACAGTGGGGGACCACGTGCAAGAACCACC
CCTACATCAAGATGGTTATGGAACAAGGAGATTGGCTGATTGGAGGAGATCTTCAAGTCCTGGACCAAATTTATTGGAAT
GATGGTCTGATCATATCATCTTACTCCCACTGAGCTAAAGCAGAGTTTAAAGATATGAATGCTGATGCTGTCTTGCTTTT
CAGTTATGCAACCCAGTGCACAATGGATATGCACTATTAATGCAGGACACCTATAAGCAGCTCCTAGAGAGGGGCTACCA
GCACCTCATCTGTCTCCTTCATCCCCTTGGTGACTGGACAAAGGATGATGATGTTCCTTTGATGTGGCATATGAAGCAGC
ATGCTGCAGTGCTGGAGGAAGGAGTCCTGAATCCTGAAACAACAGTGGTGGCCATCTGCCCATCTCCTATGATGTGTGCT
GGAGCAACTGAGGTCCAGTGCCTTGCAGGGCATGAATGGTCATGGGGCCAATTTTTACATTGTTGGACAAGACCCTGCCA
GTGTGCCTCATCCAGAAACAGGGAAGGATCTTTGCCACCCAACTCATAGTGCCAAAGTGCTGACAATGGCCCCTGGCCTA

Alignment

ORF - retro_chof_1686 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.54 %
• Parental protein coverage: 57.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  LKTSVSSVSDCVQQVVELLQEQNIVPHTVIKGIHELFVPENKLDQVRAEAETLPSLSITKLDLQWVQVLS
          LKT....V.DC.QQ.VE.LQE..IVP........EL.VPENKL......AETLP.L.I.K...Q.VQVL.
Retrocopy LKTDSCDVNDCIQQIVEFLQERDIVPVDASYEVKELYVPENKLRLAKTDAETLPALKINKVHMQ*VQVLA

Parental  EGWATPLKGFMREKEYLQALHFGTLLDGMILDGVINLS-IPIVLPVSVDDKKWLEGCSEFALEHGGRRVA
          EGWATPL.GFMRE..YLQ..H.....DG....GVINLS.IPIVL.....DK..L.GC..FA....G.R.A
Retrocopy EGWATPLNGFMRERQYLQ--HLHFVFDG----GVINLS<IPIVLTATQEDKERLDGCAAFAPMYEGYRMA

Parental  ILQNPEFYEHRKEERCSRVWGTTCAKHPHIKMVMESGDWLVGGDLKVLERIRWNDGL-DQYRLTPL-ELK
          IL....F.EHRKEE.C.R.WGTTC..HP.IKMVME.GDWL.GGDL.VL..I.WNDGL.D...L.PL.ELK
Retrocopy ILLTSGFFEHRKEEYCARQWGTTCKNHPYIKMVMEQGDWLIGGDLQVLDQIYWNDGL<DHIILLPL<ELK

Parental  Q-KCKDMNADVV-FAFQLRNPVHNGHALLMQDTHRQLLERGYKHPVLLLHPLGGWTKDDDVPLDWRMKQH
          Q...KDMNAD.V..AFQL.NPVHNG.ALLMQDT..QLLERGY.H...LLHPLG.WTKDDDVPL.W.MKQH
Retrocopy Q<EFKDMNADAV<LAFQLCNPVHNGYALLMQDTYKQLLERGYQHLICLLHPLGDWTKDDDVPLMWHMKQH

Parental  AAVLEEGVLDPKSTIVAIFPSPMLYAGPTEVQW-HCRSRMIA-GASFYIVGRDPAGMPHPENKKDLYEPT
          AAVLEEGVL.P..T.VAI.PSPM..AG.TEVQ...CR..M...GA.FYIVG.DPA..PHPE..KDL..PT
Retrocopy AAVLEEGVLNPETTVVAICPSPMMCAGATEVQC<PCRA*MVM<GANFYIVGQDPASVPHPETGKDLCHPT

Parental  QGGKVLSMAPGL
          ...KVL.MAPGL
Retrocopy HSAKVLTMAPGL

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_1686 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002724	2 retrocopies	retro_chof_1510, retro_chof_1686 ,