RetrogeneDB ID: retro_chof_712

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_138654:4657..5222(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHPT1
• Ensembl ID: ENSCHOG00000013377
• Aliases: None
• Description: choline phosphotransferase 1 [Source:HGNC Symbol;Acc:17852]

Sequence

>retro_chof_712
CCTATTCTAGAAATAAAATGGAAGATCTTTCCAATTCTTGGAGTAGTGGATGGAACAACTTTTTCCTGTCCAAATTATTT
CCATGTCATCATTCATGGTGGTTTTGGCAAGAAGGGATCCACTATAGCAGGCACTAGTGTCTTGTCACCCGGACTCCACA
TAGGACTAATGAGCATACTGGCAATAATGATCTATAAAAGTCGGCAACTAATGTGTTTGAAAAACATGCTTGTCTTTATA
CCCTAATGTTTGGATGTGGCTTTACTAAAGTTACACCAAAATTGATGGCAGCTCATATGACCAAAAGTGAACTATACCTC
AAGACACTGTCTTTATTGGGCCAGGTCTTTTATTTCTAGACCAGTATTTTAATAACTTTGTAGACAAATATGTGGCTTTC
TGGATAGCAATGGTCATTGCTCCATTTGATATGATGGCATACTTTAGTGATTTGTGCCTGCAAATTTCAAGACACCTTCA
TTTAGGTATTTTCAAGACTTCATGTCATCAATCACGTGAACAGGTTCAAGTTCTTTCTTCAAAGAGTCATCCGAATAAAA
TGGAT

Alignment

ORF - retro_chof_712 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.82 %
• Parental protein coverage: 60.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PILEIKWKIFPVLGVVGGAIFSCSNYFHVILHGGVGKNGSTIAGTSVLSPGLHIGLIIILAIMIYK-KSA
          PILEIKWKIFP.LGVV.G..FSC.NYFHVI.HGG.GK.GSTIAGTSVLSPGLHIGL..ILAIMIYK.KSA
Retrocopy PILEIKWKIFPILGVVDGTTFSCPNYFHVIIHGGFGKKGSTIAGTSVLSPGLHIGLMSILAIMIYK<KSA

Parental  TNVFEKHPCLYTLMFGCVFAKVAQKLVVAHMTKSELYL-QDTVFIGPGLLFLDQYFNNFVDEYVVLWIAM
          TNVFEKH.CLYTLMFGC.F.KV..KL..AHMTKSELYL.QDTVFIGPGLLFLDQYFNNFVD.YV..WIAM
Retrocopy TNVFEKHACLYTLMFGCGFTKVTPKLMAAHMTKSELYL<QDTVFIGPGLLFLDQYFNNFVDKYVAFWIAM

Parental  VIALFDMMAYFSALCLQISRHLHLSIFKTSCHQAPEQVQVLSSKSHQNNMD
          VIA.FDMMAYFS.LCLQISRHLHL.IFKTSCHQ..EQVQVLSSKSH.N.MD
Retrocopy VIAPFDMMAYFSDLCLQISRHLHLGIFKTSCHQSREQVQVLSSKSHPNKMD

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_712 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 ,
Loxodonta africana	ENSLAFG00000004678	1 retrocopy	retro_lafr_586,
Monodelphis domestica	ENSMODG00000002564	1 retrocopy	retro_mdom_1135,