RetrogeneDB ID: retro_chof_2277

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_62883:8406..9589(+)
• Located in intron of: None

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_2277
ATGGGTGAAACTGAAAGCAATCAGCCCCTGATGAAAAGCAGCCAATATCCTAAAGAAGCCTAAGAAAATGCCAGAATTCA
GCACAGAATTCTGGAGGAAGTAATTCTAGGTTTTCCAGGAAAAGCTTCAAACTGGATTACAGATTAGAGAAATATATAAC
TAAATCAAAGAAAGGAAAAGATGAGAGCTTTGTTAATCCTTGGCCAACTTGAAAAAGCCCCTCTATACCAAATGCCCTCA
GATTGATGATTATAGAAAAAGATCATGGCAATATTCCACATTCCAAAGAGGAACTTGATAAAGAACTCCCAGGGCTTAAG
CCCTATTCCAGCAATGACTCTGAAGAAGTTGGAGTGAAGGAAGCTGGCTGAAGAGACACATGGCTGGGACATTCAACAGT
TATGGTAGAAATGGATGAGCTCATATTTCTCATGGATCCCATTTTTAGCCATCGTGTTTCACCACCACAGTACATGGGTC
CAAAATGCTTTTGTCATCCTCAATGCACAATAAGCAAGCTGTCTCCAATATATGTGGTCCTTATCAGTCAAAACCACTAT
GATCACCTGGACTACAATTCTGTCATTGCTCTGAATGAGTGATTCAGTAATGAGTTGAGAGGGGTTGTGCCTTTGGGTCT
CCTTGACTGGGTCGTGCAGAAATGCAGCTGAGAGAATGTGATTGAGCTGGACCAGCGGGAGGAGAATTGTGTCCTCAGAC
ATGATAAGGTCATCTTTGTCTTTCCGCCATCCAAGCACTGGTGAAAGAGGACTCTGATGGATGACAATAAGGTTCTGTGG
GGCAGCTTGTCTGTCTTGGGACCTTGGAATAGATTCTTTTTTTGCAGGAGATACTAGTTGTTGCCCTGCTTTTGAAGAGA
TAGGAAAAAAAATTTGAACCTTTTGACCTTGCAGCTATTCTTATTGGAGCTTATGAACCCAGGTGGTTTATGAAATGGCA
GCACATAGACCCAGAAGAAGCTGTAAGGATTCACACTGATGTTCAAGCAGAGAAATCTGTGGCAATTCACTGGGGAACAT
TTGTCTTAGCAAATGAGCATTACTTAGACCCTCCTGTGAAACTTCATTAAGCTCTAGGAAGATACAGACTTATGACTGAA
GATTTCTTTGTCTTGAAGCATGGAGAATCAAGATACCTAACTAGAGATGATAAAAACTTCGAA

Alignment

ORF - retro_chof_2277 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MEENESNQPLMTSSQYPKEV-VRKRQNSARNSGGSDSSRFSRKSFKLDYRLEEDVTKSKKGKDGRFVNPW
          M.E.ESNQPLM.SSQYPKE...RK.QNSA.NSGGS..SRFSRKSFKLDYRLE...TKSKKGKD..FVNPW
Retrocopy MGETESNQPLMKSSQYPKEA<LRKCQNSAQNSGGSN-SRFSRKSFKLDYRLEKYITKSKKGKDESFVNPW

Parental  PTWKNPSIPNALRWLIMEKDHSNVPRSKEELDKELPVLKPYFINDPEKAGVKEAGLRVKWLGHATVMLEM
          PT.K.PSIPNALR..I.EKDH.N.P.SKEELDKELP.LKPY..ND.E..GVKEAG.R..WLGH.TVM.EM
Retrocopy PT*KSPSIPNALRLMIIEKDHGNIPHSKEELDKELPGLKPYSSNDSEEVGVKEAG*RDTWLGHSTVMVEM

Parental  GEILFLTDPIFSQCVSPSQ-VGLKYFCCPPCTIFELPPADVVLISHNHYDHLDYNSVIALNERFGNELRW
          .E..FL.DPIFS..VSP.Q..G.K.FC.P.CTI..L.P..VVLIS.NHYDHLDYNSVIALNE.F.NELR.
Retrocopy DELIFLMDPIFSHRVSPPQYMGPKCFCHPQCTISKLSPIYVVLISQNHYDHLDYNSVIALNE*FSNELRG

Parental  FVPLGLLDW-MQKCGCENVIELDWWEENCVPRHDKVTFVFTPSQHWCKRTLMDDNKVLWGSWSVLGPWNR
          .VPLGLLDW..QKC..ENVIELD..EENCV.RHDKV.FVF.PS.HW.KRTLMDDNKVLWGS.SVLGPWNR
Retrocopy VVPLGLLDWVVQKCS*ENVIELDQREENCVLRHDKVIFVFPPSKHW*KRTLMDDNKVLWGSLSVLGPWNR

Parental  F-FFAGDTGYCPAFEEI-GKRFGPFDLAAIPVGAYEPRWFMKWQHIDPEEAVRIHIDVQAKKSVAIHWGT
          F.FFAGDT..CPAFEEI....F.PFDLAAI..GAYEPRWFMKWQHIDPEEAVRIH.DVQA.KSVAIHWGT
Retrocopy F>FFAGDTSCCPAFEEI>XXXFEPFDLAAILIGAYEPRWFMKWQHIDPEEAVRIHTDVQAEKSVAIHWGT

Parental  FVLANEHYLDPPVKLREALGRYGLTTEDFFVLKHGESRYLNSDDKNVE
          FVLANEHYLDPPVKL..ALGRY.L.TEDFFVLKHGESRYL..DDKN.E
Retrocopy FVLANEHYLDPPVKLH*ALGRYRLMTEDFFVLKHGESRYLTRDDKNFE

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_2277 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,