RetrogeneDB ID: retro_chof_241

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_5246:84317..85222(+)
• Located in intron of: ENSCHOG00000001406

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_241
ATGAGTGGGCATCAATCAGCAAGGAAATGATGTAGAGGTTCTCACCCAGAGTCCCCTGTGGGCTTCAGGCATATGAGTCC
TACAGGGTGTGTATTAAATAAATTGTTTCACTTACCTACACCACCATTGTCAAGACACCAACTAAAGCGACTAGAAGATC
ACAAATATCAGAGTGTTGGATGGTCCCTACACGAACCTTTAACACAGGAGTATTGGGAAGGGCTAGTTGGAAGAGTTCCC
TCCTGGACTGCCCCAGTCTCATTACCATCACTGGACTATCAATAAACATCTGTACAACTGTTTTATTAGTCTACTACTGC
CTACAGCTACCGATCAGGCACCTCTGTGGGCATATATTGCTTGTGCAATATATGCATATATTGTTTGTGCATGTGGATGC
TATAGATGGGAAACAAGCAAGAAGAACCTATAGTAATTCTCCTTTAGGAGGACTTTTTGATCATGATTATGATTCACTAT
CAACAGTTTTTGTGGTCCTTGGAACTTGTATTGCAGTGCAATTGGGAACAAACCCTGATTGAATGGTTTTTGTTGTTTTG
CTGGGACATTCACATTTTATTGTGCACAATGGCAAACATGTTTCTGGAACACTGAGATTAGGAATAATTGATGTGACTGA
GGTGCAAATCTTCCTAATAATCATGCATTTGCTGGCAGAGATTGGAGGACCACCTTTTCGGCAATCCATGATTCCAGTGC
TGAATATTCAAATGAAAATTTTTCTTGCACTTTGAACTGTAGCAGGGACCATATTTTCCTGTACAAATTACTTCCATACA
ATCTTCACAGGTGGTGTTGGCAAAAATAGATCAACAATAGCAGGAACAAGTGTCCTTTCTCCTTTTTTCCATATTTGATC
AGTGATTACATTAGCTGCAATGATC

Alignment

ORF - retro_chof_241 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.76 %
• Parental protein coverage: 72.84 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSGHRSARKRCGDSHPESLVGFGHMSTTGCVFNKLFQLPTPPLSRHQLKRLEEHKYQSAGRSLLEPLMQG
          MSGH.SARK.C..SHPES.VGF.HMS.TGCV.NKLF.LPTPPLSRHQLKRLE.HKYQS.G.SL.EPL.Q.
Retrocopy MSGHQSARK*CRGSHPESPVGFRHMSPTGCVLNKLFHLPTPPLSRHQLKRLEDHKYQSVGWSLHEPLTQE

Parental  YWEWLVGRVPSWIAP-NLITIIGLSINICTTVLLVYYC-PTATEQAPLWAYVACACGLFI-YQSLDAIDG
          YWE.LVGRVPSW.AP..LITI.GLSINICTTVLLVYYC.PTAT.QAPLWAY.ACA....I.....DAIDG
Retrocopy YWEGLVGRVPSWTAP<SLITITGLSINICTTVLLVYYC<PTATDQAPLWAYIACAIYAYI>FVHVDAIDG

Parental  KQARRTNSSSPLGELFDHGCDSLSTVFVVLGTCIAVQLGTNPDWMFFCCFAGTFMFYCAHWQTYVSGTLR
          KQARRT.S.SPLG.LFDH..DSLSTVFVVLGTCIAVQLGTNPD.M.F....G...F...H....VSGTLR
Retrocopy KQARRTYSNSPLGGLFDHDYDSLSTVFVVLGTCIAVQLGTNPD*MVFVVLLGHSHFI-VHNGKHVSGTLR

Parental  FGIIDVTEVQIFIIIMHLLAVIGGPPFWQSMIPVLNIQMKIFPALCTVAGTIFSCTNYFRVIFTGGVGKN
          .GIIDVTEVQIF.IIMHLLA.IGGPPF.QSMIPVLNIQMKIF.AL.TVAGTIFSCTNYF..IFTGGVGKN
Retrocopy LGIIDVTEVQIFLIIMHLLAEIGGPPFRQSMIPVLNIQMKIFLAL*TVAGTIFSCTNYFHTIFTGGVGKN

Parental  GSTIAGTSVLSPFLHIGSVIILAAMI
          .STIAGTSVLSPF.HI.SVI.LAAMI
Retrocopy RSTIAGTSVLSPFFHI*SVITLAAMI

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_241 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,