RetrogeneDB ID: retro_chof_1510

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_311305:7..1281(-)
• 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_1510
CAGAGAGCAACTAGTGTCACCCATCAAGCCCACCATGTCAGCAGGAACAAGAGAGGTCAGGTGGTAGGGATCAAAAGTGG
CTTTCATGTTTGCACAGTTTGGCTAACAGGCTTATCTGGAGCACAGAAGACCACAGTGGACATGGCTTTGGAGGAATACT
TAGTTTGCCATGGTATTCCATGTTGTACCTTGGATGGTGACAACATTCTTCAGGGTCTCAATAAGAATCTTGGTTTTAGT
CCTGAAGACAGGGAAGAGAATGTTTGATGCATTGCAGAAGTTGCTAAGCTAGTTGCAGATGCCAGCCTAGTGTGTATCAC
AAGTTATATATCACCTTATACTCAGGATTGCAACAATGCATGGCAAATTCATGAGGGTTCAAGTTTACCTTTTTTTGAAA
TATTTGTTGATGCTCCTCTGCATGTTTGTGAACAGAGGGATGTTAAGGGACTGTACAAAAAAGCACAGGCTGGAGAAATT
AAAGGTTTCACTGGGATTGATTCTGACTATGAAAAATCAGAGGCCCCTGAATTCTTGCTGAAAACAGACTCCTTGATGTA
ATTGACTGCATTCAGCAAGTTATGGAACTCCTACAAGAAAGGGACATTGTACCTGTGGATGCTTCTTATGAAGTAAAAGA
ACTGTATGTGCCAGAAAATAAACTTCATTTGGCAAAAACAGATGCAGAAACGTTACCGGCACTGAAAATTAATAAAGCGG
ATATGCAGTGGGTGCAAGTTTTGGCTGAAGGTTGAGCAACACCACTGAATGGCTTTATGAGAGAGAGGGAGTACTTGCAG
TGCCTTCATTTTGATTGTCTTCTGGATGGGGGTGTCATTAACTTGTCAGTACCTATAGTTCTGACAGCTACCCAAGAAGA
TAAAGAGAGGCTGGATGGCTGCACAGCATTTGCTCTGATGCATGAGGGCTACCGCGTGGCTATTCTTCGTAATCCAGAGT
TTTTTGAGCACAGGAAGGAAGAGCGCTGTGCCAGACAGTAGGGGACCACGTGCAAGAACCATCCCTACATCAAGATGGTT
ATGGAACAAGGAGATTGGCTGGTTGTAGGAGATCTTCAGGTCCTGGACCAAATTTATTGGAATGATGGTCTTGATCAATA
TCTTACTTACTCCCACTGAGCTAAAGTTTAAAGCTATGAATGCTGATGTTATGCTGATGCTGTCTTTGCATTACCTGGTG
CACAATGGACATGCTCTATTAAGCAGGACACTCATAAGCAGCTCATGGAGAGGGCTACCAGTGCCCCCACCCTT

Alignment

ORF - retro_chof_1510 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.05 %
• Parental protein coverage: 69.74 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QKSTNVVYQAHHVSRNKRGQVVGTRGGFRGCTVWMTGLSGAGKTTISFALEEYLVSHAIPCYSLDGDNIR
          Q..T.V..QAHHVSRNKRGQVVG...GF..CTVW.TGLSGA.KTT...ALEEYLV.H.IPC..LDGDNI.
Retrocopy QRATSVTHQAHHVSRNKRGQVVGIKSGFHVCTVWLTGLSGAQKTTVDMALEEYLVCHGIPCCTLDGDNIL

Parental  HGLNKNLGFSAGDREENIRRIAEVARLFADAGLICITSFISPFAKDRANARKIHESTGLPFFEIFIDAPL
          .GLNKNLGFS..DREEN...IAEVA.L.ADA.L.CITS.ISP...D..NA..IHE...LPFFEIF.DAPL
Retrocopy QGLNKNLGFSPEDREENV*CIAEVAKLVADASLVCITSYISPYTQDCNNAWQIHEGSSLPFFEIFVDAPL

Parental  NICESRDVKGLYKRARAGEIKGFTGIDSDYEKPEAPECVLKTS-VSSVSDCVQQVVELLQEQNIVPHTVI
          ..CE.RDVKGLYK.A.AGEIKGFTGIDSDYEK.EAPE..LKT.....V.DC.QQV.ELLQE..IVP....
Retrocopy HVCEQRDVKGLYKKAQAGEIKGFTGIDSDYEKSEAPEFLLKTD<LLDVIDCIQQVMELLQERDIVPVDAS

Parental  KGIHELFVPENKLDQVRAEAETLPSLSITKLDLQWVQVLSEGWATPLKGFMREKEYLQALHFGTLLDGMI
          ....EL.VPENKL......AETLP.L.I.K.D.QWVQVL.EG.ATPL.GFMRE.EYLQ.LHF..LLDG..
Retrocopy YEVKELYVPENKLHLAKTDAETLPALKINKADMQWVQVLAEG*ATPLNGFMREREYLQCLHFDCLLDG--

Parental  LDGVINLSIPIVLPVSVDDKKWLEGCSEFALEHGGRRVAILQNPEFYEHRKEERCSRVWGTTCAKHPHIK
          ..GVINLS.PIVL.....DK..L.GC..FAL.H.G.RVAIL.NPEF.EHRKEERC.R..GTTC..HP.IK
Retrocopy --GVINLSVPIVLTATQEDKERLDGCTAFALMHEGYRVAILRNPEFFEHRKEERCARQ*GTTCKNHPYIK

Parental  MVMESGDWLVGGDLKVLERIRWNDGLDQY-RLTPLELKQKCKDMNADVVFAFQLRNPVHNGHALL-MQDT
          MVME.GDWLV.GDL.VL..I.WNDGLDQY..LTP.ELK.K...MNADV.....L...VHNGHALL..QDT
Retrocopy MVMEQGDWLVVGDLQVLDQIYWNDGLDQY>LLTPTELKFKA--MNADVMLMLSLHYLVHNGHALL<KQDT

Parental  HRQLLERGYKHPVL
          H.QL.ER....P.L
Retrocopy HKQLMERATSAPTL

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_1510 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,