RetrogeneDB ID: retro_chof_2710

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_99730:2712..3634(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CEPT1
• Ensembl ID: ENSCHOG00000007908
• Aliases: None
• Description: choline/ethanolamine phosphotransferase 1 [Source:HGNC Symbol;Acc:24289]

Sequence

>retro_chof_2710
CTCGCCATCAGCCTGCTCACCACACTCCTGCTCATCTCTGCCTCCCCCACAGCACGGAGGAGGCACCACACTGGGCATTT
TATGTGCCCGGGGACTCTATCTACCAGTCACTGGATGTGTTGATGGGAAACAGGCCAGAAGAGCAAATTCTTGTTCTCTT
TTAGGGACCTTTTTGACTATGAACGTGACTCTTTCCACAGTGTTTATGGCAGTTGGAGCTTCAATTTCCTTTCAATATCC
TAAGCATCCTGACTGGTTGTTTTTCTGCTCTTTTATTGGGATGTTCATGTTTTATTGTGCTCACTGGCAGATTTATGTTT
CAGGCATGTTGAGGTTTGGAAAAGTGGATGTAACTGAAATTCTGGTAGCTGTAATAATCTTGCTTGTGTTGTCTACATTT
GGAGGAGCAAAAATGTGTGACTATATGATACCTACTTTAGAAATAAAATGGAAGATATTTCTGGTTCTCAGAGTAGTAGG
GGGAGCAATGTTTTTCTTGTTCAAATTATTTCCATGTCATCCTTCATGGTGGCATTGGCAAAAATGGATCCACTATAACA
GGTACTAGTGCCTTGTCACCTGAACTCCACATAGGACTAATGATCACCCTGGCAATAATGAGCTATAAAAGTCAGCAGCT
AATATGTTTCAAAAACATTCTTATCTTTATACCCTAATGTTTGGATGTGTCTTTGCTAAAGTTGCACAAAAATTGGCAGT
AGCTCATATGACCAAAAGTGAACTATACCTTCAAGATACTGTCTTTATTGGGCCAGGCATTTTATTTTTAGACCAGTACT
TTAATAATTTTGTAGACAAATATGTGGCTGTTTGGATAGTAATGGTCATTGCTTCATTTGATATGATGTCATACTTAAGT
GCTTTGTGCCTGCAAATTTCAAGACACCTTCATTTAAGTATT

Alignment

ORF - retro_chof_2710 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.24 %
• Parental protein coverage: 74.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LSINICTTVLLVYYCPTA-TEQAPLWAYVACACGLFIYQSLDA-IDGKQARRTNSSSPLGELFDHGCDSL
          L.I...TT.LL....PTA.TE.AP.WA......G..IYQSLD...DGKQARR.NS.S.LG.........L
Retrocopy LAISLLTTLLLISASPTA<TEEAPHWAFYVP--GDSIYQSLDV<VDGKQARRANSCSLLGTFLTMNV-TL

Parental  STVFVVLGTCIAVQLGTNPDWMFFCCFAGTFMFYCAHWQTYVSGTLRFGIIDVTEVQIFIIIMHLLAVIG
          STVF...G..I..Q....PDW.FFC.F.G.FMFYCAHWQ.YVSG.LRFG..DVTE.....II...L...G
Retrocopy STVFMAVGASISFQYPKHPDWLFFCSFIGMFMFYCAHWQIYVSGMLRFGKVDVTEILVAVIILLVLSTFG

Parental  GPPFWQSMIPVLNIQMKIFPALCTVAGTIF-SCTNYFRVIFTGGVGKNGSTIAGTSVLSPFLHIGSVIIL
          G......MIP.L.I..KIF..L..V.G..F.SC.NYF.VI..GG.GKNGSTI.GTS.LSP.LHIG..I.L
Retrocopy GAKMCDYMIPTLEIKWKIFLVLRVVGGAMF>SCSNYFHVILHGGIGKNGSTITGTSALSPELHIGLMITL

Parental  AAMIYK-KSAVQLFEKHPCLYILTFGFVSAKITNKLVVAHMTKSEMHLHDTAFIGPALLFLDQYFNSFID
          A.M.YK.KSA...F.KH..LY.L.FG.V.AK...KL.VAHMTKSE..L.DT.FIGP..LFLDQYFN.F.D
Retrocopy AIMSYK<KSAANMFQKHSYLYTLMFGCVFAKVAQKLAVAHMTKSELYLQDTVFIGPGILFLDQYFNNFVD

Parental  EYIVLWIALVFSFFDLIRYCVSVCNQIASHLHIHV
          .Y...WI..V...FD...Y....C.QI..HLH...
Retrocopy KYVAVWIVMVIASFDMMSYLSALCLQISRHLHLSI

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_2710 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007908	3 retrocopies	retro_chof_1945, retro_chof_241, retro_chof_2710 ,
Choloepus hoffmanni	ENSCHOG00000013377	1 retrocopy	retro_chof_712,
Dasypus novemcinctus	ENSDNOG00000017013	1 retrocopy	retro_dnov_3,
Otolemur garnettii	ENSOGAG00000010799	1 retrocopy	retro_ogar_2444,