RetrogeneDB ID: retro_chof_1315

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_260161:13..1298(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS45
• Ensembl ID: ENSCHOG00000000501
• Aliases: None
• Description: vacuolar protein sorting 45 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:14579]

Sequence

>retro_chof_1315
CAACCAGAGATTCTTCAGAGGAAATGTACCTCTTTGAATACATTGATTCTCAAAATTAAGAGATCGTAAAATACCTGAGG
ACAATTTGTTTTCTTCATCCTGTGAAGGAGAATGTGGATTATTTAATTCAGGAGCATTGAAGACCCTAATGTAGCATATA
TTTTATTTATTTTGGTAATGTGATCAGCAAGAGTGATGTGAAGTCAATGGCTGAAGCTGATGAACAGGAAGTTGTGGCTG
AGGTTCAGGAATTTTACGGTGATGACATTGTTGTGAATTCACGTTTTTTTCCCTGAATATTTTGGGTTGTTTTCATGGTC
AAAATTGGGATCCAGCCCAGCTATCAAGAGCAACTCAAGGATTGACAGCTCTCCTTTTATCACTGAAGAAATGTCCCATG
ATTCATTATCACCTTCCATCAGAGGCAGCAAAGAGACATGCTGAATGTGTTGAGCAAGTGATACCTCAAGAATATGAACT
GTTTGAATTCTGGCAGACTGAGATTCCTCCATTGCTACTTATTTTAGATTAGTGTGATGATGCCATCACCCCATTGCTAA
ACCAGTGGACATATAGGGCCATTATCCATGAACTATTGGGCATAATCAGCAACTGGATTGACCTTTCTAGAGTGCCAGGG
ATCCATAAAGACTTGAGAGAGGTGGTCCTATCTGCTGAAAATGATGAATTCTATGCTAATAATATGTACCTGAACTTTGC
TGAGATTGGTAGCAATATATAGAATTTCATGGAAGACTTTCAGAAGAAGAAACCAAAAGAATGGCAAAAACTGGATGGAA
TCAATAGTAGACATGAAGGCCTTTGTTGAAAATAGTCCACAATTTAAGAAGATGTCTGGTACTTTATCAAAGCATGTGAC
AGTGTTTGGAGAGTTCTCTCAGTTGGCCAGTGAGCAGAATCTACTGGAGGTTTCAGAGGCTGAGCAATAACTGGCCTGTC
AAAATGACTGTTCTAGTGCTCTCCAGAATGTAAAGAGGCTCCTGCAGAGCCCCAAAGTGACAGAGTTTGATGCTGCCTGC
CTGGTGATGCTTTATGCTCTGCATTATGAGCGACATAGCAGCAATCACCCGCCAGGGCTAACGATGGATCTCAGGAATAA
AGGTGTTTCTGAGAAGTATTGAAAGCTCGTGTCTACAGTCATTGAATATGGTGGTAAACAGGTCAGAGGGAGTGACCTCT
TTAGCTTCAAAGATGCTGTGGCTATTACCAAACAGTTCCTCAAAGGATTGAAGGAGTAGAAAATGTATATGCACAGCATC
AACCC

Alignment

ORF - retro_chof_1315 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.99 %
• Parental protein coverage: 75.35 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QSEILQK-EVYLFERIDSQNREIMKHLKAICFLRPTKENVDYLIQELRRPKYSIYFIYFSNVISKSDVKS
          Q.EILQ..E.YLFE.IDSQN.EI.K.L..ICFL.P.KENVDYLIQE..RP..SIYFIYF.NVISKSDVKS
Retrocopy QPEILQR<EMYLFEYIDSQN*EIVKYLRTICFLHPVKENVDYLIQEH*RP*CSIYFIYFGNVISKSDVKS

Parental  LAEADEQEVVAEVQEFYGDYIAVNPHLF-SLNILGCFQGRNWDPAQLSRTTQGLTALLLSLKKCPMIRYQ
          .AEADEQEVVAEVQEFYGD.I.VN...F.SLNILGCF.G.NWDPAQLSR.TQGLTALLLSLKKCPMI.Y.
Retrocopy MAEADEQEVVAEVQEFYGDDIVVNSRFF<SLNILGCFHGQNWDPAQLSRATQGLTALLLSLKKCPMIHYH

Parental  LSSEAAKRLAECVKQVITKEYELFEFQRTEVPPLLLILDRCDDAITPLLNQWTYQAMVHELLGINNNRID
          L.SEAAKR.AECV.QVI..EYELFEF..TE.PPLLLILD.CDDAITPLLNQWTY.A..HELLGI..N.ID
Retrocopy LPSEAAKRHAECVEQVIPQEYELFEFWQTEIPPLLLILD*CDDAITPLLNQWTYRAIIHELLGIISNWID

Parental  LSRVPGISKDLREVVLSAENDEFYANNMYLNFAEIGSNIKNLMEDFQ-KKKPKEQQK-LESIADMKAFVE
          LSRVPGI.KDLREVVLSAENDEFYANNMYLNFAEIGSNI.N.MEDFQ.KK....Q....ESI.DMKAFVE
Retrocopy LSRVPGIHKDLREVVLSAENDEFYANNMYLNFAEIGSNI*NFMEDFQKKKPKEWQKL>MESIVDMKAFVE

Parental  NYPQFKKMSGTVSKHVTVVGELSRLVSERNLLEVSEVEQELACQNDHSSAFQNVKRLLQSPKVTEFDAAR
          N.PQFKKMSGT.SKHVTV.GE.S.L.SE.NLLEVSE.EQ.LACQND.SSA.QNVKRLLQSPKVTEFDAA.
Retrocopy NSPQFKKMSGTLSKHVTVFGEFSQLASEQNLLEVSEAEQ*LACQNDCSSALQNVKRLLQSPKVTEFDAAC

Parental  LVMLYALHYERHSSNSLPGLVMDLRNKGVSEKYRKLVSTVVEYGGKRVRGSDLFSPKDAVAITKQFLKGL
          LVMLYALHYERHSSN..PGL.MDLRNKGVSEKY.KLVSTV.EYGGK.VRGSDLFS.KDAVAITKQFLKGL
Retrocopy LVMLYALHYERHSSNHPPGLTMDLRNKGVSEKY*KLVSTVIEYGGKQVRGSDLFSFKDAVAITKQFLKGL

Parental  K-GVENVYTQHQP
          K.GVENVY.QHQP
Retrocopy K<GVENVYAQHQP

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_1315 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000501	1 retrocopy	retro_chof_1315 ,
Tupaia belangeri	ENSTBEG00000010744	1 retrocopy	retro_tbel_107,
Tursiops truncatus	ENSTTRG00000005060	1 retrocopy	retro_ttru_1807,