RetrogeneDB ID: retro_chof_159

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_3564:33363..34308(-)
• Located in intron of: ENSCHOG00000004236

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAPEPLD
• Ensembl ID: ENSCHOG00000002097
• Aliases: None
• Description: N-acyl phosphatidylethanolamine phospholipase D [Source:HGNC Symbol;Acc:21683]

Sequence

>retro_chof_159
AATGCCCTCAGATGGTTGATAATGGAGAAAAATCACAGCAATGTTCCACGTTCCAAAGAGGAACTTGATAAAGAACTACC
AGTGCTTAAACCCTATTTTATCAATGACCCTGAAAAAGCTGGAGTGAAGGAAGCTGGCTTAAGAGTCAAGTGGCTGGGAC
ATGCAACAGTAATGCTAGAAATGGGTGAGATCTTATTTCTCACGGATCCCATTTTTAGCCAATGTGTTTCACCGTCCCAG
TAAGTGGGTCTGAAATACTTTTGTTGTCCTCCATGCACAATATTTGAGCTGCCCCCAGCAGATGTAGTCCTTTTCAGTCA
CAACCACTATGACCACCTGGACTACAATTCTGTCATTGCTCTGAACGAGTGATTCGGTGATGAGTTGAGATGGTTTGTGC
CTTTGGGTCTCCTCAACTGGATCCAAAAATGTGGCTGTGAGAATGTGATTGAGCTGGACTGGTGGGAGGAGAACTGTGTC
CCCAGACATGACGAAGTCACCTTTGTCTTTACACCTTCCAAGCACTGGTGTTAAGAGGACTCTAATTGATGGCAATAAGG
TTCTGTGGGGCAGCTGGTCTGTCTTGGGGCCTTGGAATAGAGTCTTTTTGCAGGAGATACTGGTTATTGCTCTGCTTTCA
AAGAGATAGGAGAAAGATTTGGATCTTTCAACCTTGCAGCTACTCCTATTGGAGCTTACAAACCCAGGTGGTTTATGAAA
TGCCAGCATATAGACCTAGAATTTGTAAGGATTCACAATGATGTTCAAGCAAACAAATCTGTGGCAATTCACTGGAGGAA
TTTTGTCTTAGTAAATGAGCATTATTTAGAGCCTCCAGTGAAATAGAGTGAAGCTCTATAAAAATATGGACCTACGACTG
AAGATCTTTTTGTCTTGAAGCATGGAGAATCAATATTCCTAAATACTGATGACAAAAACTTTGAA

Alignment

ORF - retro_chof_159 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.79 %
• Parental protein coverage: 80.15 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NALRWLIMEKDHSNVPRSKEELDKELPVLKPYFINDPEKAGVKEAGLRVKWLGHATVMLEMGEILFLTDP
          NALRWLIMEK.HSNVPRSKEELDKELPVLKPYFINDPEKAGVKEAGLRVKWLGHATVMLEMGEILFLTDP
Retrocopy NALRWLIMEKNHSNVPRSKEELDKELPVLKPYFINDPEKAGVKEAGLRVKWLGHATVMLEMGEILFLTDP

Parental  IFSQCVSPSQ-VGLKYFCCPPCTIFELPPADVVLISHNHYDHLDYNSVIALNERFGNELRWFVPLGLLDW
          IFSQCVSPSQ.VGLKYFCCPPCTIFELPPADVVL.SHNHYDHLDYNSVIALNE.FG.ELRWFVPLGLL.W
Retrocopy IFSQCVSPSQ*VGLKYFCCPPCTIFELPPADVVLFSHNHYDHLDYNSVIALNE*FGDELRWFVPLGLLNW

Parental  MQKCGCENVIELDWWEENCVPRHDKVTFVFTPSQHWC-KRTLMDDNKVLWGSWSVLGPWNRFF-FAGDTG
          .QKCGCENVIELDWWEENCVPRHD.VTFVFTPS.HWC.KRTL.D.NKVLWGSWSVLGPWNR.F.FAGDTG
Retrocopy IQKCGCENVIELDWWEENCVPRHDEVTFVFTPSKHWC>KRTLIDGNKVLWGSWSVLGPWNRVF<FAGDTG

Parental  YCPAFEEIGKRFGPFDLAAIPVGAYEPRWFMKWQHIDPEEAVRIHIDVQAKKSVAIHWGTFVLANEHYLD
          YC.AF.EIG.RFG.F.LAA.P.GAY.PRWFMK.QHID..E.VRIH.DVQA.KSVAIHW..FVL.NEHYL.
Retrocopy YCSAFKEIGERFGSFNLAATPIGAYKPRWFMKCQHID-LEFVRIHNDVQANKSVAIHWRNFVLVNEHYLE

Parental  PPVKLREALGRYGLTTEDFFVLKHGESRYLNSDDKNVE
          PPVK..EAL..YG.TTED.FVLKHGES..LN.DDKN.E
Retrocopy PPVK*SEAL*KYGPTTEDLFVLKHGESIFLNTDDKNFE

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_159 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 1 parental gene, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002097	7 retrocopies	retro_chof_159 , retro_chof_1769, retro_chof_2110, retro_chof_2178, retro_chof_2277, retro_chof_2441, retro_chof_2660,