RetrogeneDB ID: retro_chof_1945

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_43031:8106..8840(+)
• 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_1945
TTGGAACTTGGGAACAAACCCTGATTGGATGTGTTTTGTTGTTGTTGTTTTGCTGAGATATTCATGTTTAATTGTGCACA
TTGGCAAACAAATGTTTCTGGAACACTGAGATTCAGAATAATTGATGTGACTGAGATGCAAATCTTCATAATAATCATGC
ATTTGCTAGTGGTAATTGGAGGACCACCTTTCTGGCAATCCATGATTCCAGTGCTGTATATTCAAATGAAATTTTTTCAT
GCACTTTGTACTGTAGCAGGGACCATATTTTCCTGCACAAATTATTCCATGTAATCTTCACAGGTCGTGTTGGCAAAAAT
GGATCAATGATAGCAGGAACAACTGTTTTTTTTCCTTTTCTCCATATTGGATCAGTGATTTTATTAGCTGCAATGATCTA
CAAAAAATCAGCAGTTCAGCTTATTGAAAAGCATCCCTGCCTTTGTATACTGACATTTGGTTTTGTATCTGCTAAAATCA
CTAATAAGCTTGTGGTTGCATGCAAGATGAAAAGTGAAATGCATTTGCATGACACAGTGTTCATAGATCCAGCACTTTTG
TTCTTGGACCAGTATTTTAACAGCTTTATTGAGTATATTGTACTTTGGATTGCCCCATTTTTCTCTTTCTTTGATTTGAT
CTGCTACTGTGTCAGTGTTTGCAATTAGACTGCATTTCACCTGCATATACATGTCTTCAGAATCAAGGTCTCTATAGCTC
ATTCTGATCATCAT

Alignment

ORF - retro_chof_1945 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.78 %
• Parental protein coverage: 58.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VQLGTNP--DWMFFCCFAGTFMFYCAHWQTYVSGTLRFGIIDVTEVQIFIIIMHLLAVIGGPPFWQSMIP
          ..LG..P..D....CCFA..FMF.CAHWQT.VSGTLRF.IIDVTE.QIFIIIMHLL.VIGGPPFWQSMIP
Retrocopy LELGNKP*LDVFCCCCFAEIFMFNCAHWQTNVSGTLRFRIIDVTEMQIFIIIMHLLVVIGGPPFWQSMIP

Parental  VLNIQMKIFPALCTVAGTIFSCTNY-FRVIFTGGVGKNGSTIAGTSVLSPFLHIGSVIILAAMIYKKSAV
          VL.IQMK.F.ALCTVAGTIFSCTNY.F.VIFTG.VGKNGS.IAGT....PFLHIGSVI.LAAMIYKKSAV
Retrocopy VLYIQMKFFHALCTVAGTIFSCTNY<FHVIFTGRVGKNGSMIAGTTXXXPFLHIGSVILLAAMIYKKSAV

Parental  QLFEKHPCLYILTFGFVSAKITNKLVVAHMTKSEMHLHDTAFIGPALLFLDQYFNSFIDEYIVLWIALVF
          QL.EKHPCL.ILTFGFVSAKITNKLVVA...KSEMHLHDT.FI.PALLFLDQYFNSFI.EYIVLWIA..F
Retrocopy QLIEKHPCLCILTFGFVSAKITNKLVVACKMKSEMHLHDTVFIDPALLFLDQYFNSFI-EYIVLWIAPFF

Parental  SFFDLIRYCVSVCNQIASHLHIHVFRIKVSTAHSNHH
          SFFDLI.YCVSVCN..A.HLHIHVFRIKVS.AHS.HH
Retrocopy SFFDLICYCVSVCN*TAFHLHIHVFRIKVSIAHSDHH

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_1945 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,