RetrogeneDB ID: retro_chof_2110

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_50117:4936..6121(+)
• 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_2110
ATAGATGAAACTGAAAGCTACCAGCCTGTGATGACAAGCAGCCAATATTTTAAAGAAGCAGTAAGAAAATGCCAAAATTC
AGCACAGAATTCTGGAGGAAGTGATTCTTCTAGGTTTTCCAGGAAAAGCTTCAAACTGGATTACAGATTAGAGGAATATA
TAACTAAATCAAAAAAGGAAAAGATGGGAGCTTTGTTAACCCTTGGCCAACTTGGAGAAATCCCTCTATTCCAAATGCCC
TAAGATTGTTGATTATAGAAAAAGATCACAGCAATATTCTACATTCCAAAGAGGAACTTCATAAAGAACCCTCAGTGCTT
AAGCCCTATTTCAGCAATGACTCTGAAGAAGCTGGAATGAAGGAAGCTGGCTTAAGAGTCACATGGCTGGGACATGCAAC
AGTAATGGTAGAAATGGATGAGCTCATAATTCTCATGGATCCCAGTTTTAGCCATCATGCTTCACCACCACAGTACATGG
GTCCAAAATGCTTTTATCATCCTCCATGCACAATAAGCAAGCTGCCTCCAATAGATGTGGTCCTTATCAGTCAAAACCAC
TGTGATCACCTGGACTACAATTCTGTCATTGTTCTGAATGAGTGATTCAGTAATGAGTTGAGATGATTTGTGCCTTTGGG
TCTCCTTGACTGGATGCAGAAATACAGCTGAGAGAATATGATTGAGCTGGACCAGTGGGAGGAGAATTGTGTCTCCAGAC
ATGATAAGGTCACCTTTGTCTATTCACCATCCCAGCACTGCTGCAAGAGGACTCTAATGGATGACAATAGGGTTCTGTGG
GGCAGCTGGTATGTCTTGAGACCTTGGAATACTTTCTTTTTTTTTGCAGGAGATACTGGTTATTGCCCTGCTTTTGAAGA
GATAGGAAAAAGATTTGGACCTTTTGGCCTTGCAGCTATTCTTATTGGACCTTATGAACCCAGGTGGTTTATGAAATGGC
AGCACATAGACCCAGAAGAAGCTGTAAGGATTCACACTGATGTTCAAGCAGAGAAATCTGTGGCAATTCACTGGGGAACT
TTTGTCTTAGAAAAATGAGCACTACTTAGACCCTCCAGTGAAACTGCATGAAGCTCTAGGAAGATACAGACTTACGACTG
AAGAGTTTTTTGTCTTGAAGCATGGAGAATCAAGATACCAAAATAGTGATGATAAAAACCTTGAA

Alignment

ORF - retro_chof_2110 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEENESNQPLMTSSQYPKEVVRKRQNSARNSGGSDSSRFSRKSFKLDYRLEEDVTKSKK-GKDGRFVNPW
          ..E.ES.QP.MTSSQY.KE.VRK.QNSA.NSGGSDSSRFSRKSFKLDYRLEE..TKSKK.GKDG.FVNPW
Retrocopy IDETESYQPVMTSSQYFKEAVRKCQNSAQNSGGSDSSRFSRKSFKLDYRLEEYITKSKK<GKDGSFVNPW

Parental  PTWKNPSIPNALRWLIMEKDHSNVPRSKEELDKELPVLKPYFINDPEKAGVKEAGLRVKWLGHATVMLEM
          PTW.NPSIPNALR.LI.EKDHSN...SKEEL.KE..VLKPYF.ND.E.AG.KEAGLRV.WLGHATVM.EM
Retrocopy PTWRNPSIPNALRLLIIEKDHSNILHSKEELHKEPSVLKPYFSNDSEEAGMKEAGLRVTWLGHATVMVEM

Parental  GEILFLTDPIFSQCVSPSQ-VGLKYFCCPPCTIFELPPADVVLISHNHYDHLDYNSVIALNERFGNELRW
          .E...L.DP.FS...SP.Q..G.K.F..PPCTI..LPP.DVVLIS.NH.DHLDYNSVI.LNE.F.NELR.
Retrocopy DELIILMDPSFSHHASPPQYMGPKCFYHPPCTISKLPPIDVVLISQNHCDHLDYNSVIVLNE*FSNELR*

Parental  FVPLGLLDWMQKCGCENVIELDWWEENCVPRHDKVTFVFTPSQHWCKRTLMDDNKVLWGSWSVLGPWNRF
          FVPLGLLDWMQK...EN.IELD.WEENCV.RHDKVTFV..PSQH.CKRTLMDDN.VLWGSW.VL.PWN.F
Retrocopy FVPLGLLDWMQKYS*ENMIELDQWEENCVSRHDKVTFVYSPSQHCCKRTLMDDNRVLWGSWYVLRPWNTF

Parental  -FFAGDTGYCPAFEEIGKRFGPFDLAAIPVGAYEPRWFMKWQHIDPEEAVRIHIDVQAKKSVAIHWGTFV
          ...AGDTGYCPAFEEIGKRFGPF.LAAI..G.YEPRWFMKWQHIDPEEAVRIH.DVQA.KSVAIHWGTFV
Retrocopy XXXAGDTGYCPAFEEIGKRFGPFGLAAILIGPYEPRWFMKWQHIDPEEAVRIHTDVQAEKSVAIHWGTFV

Parental  L-ANEHYLDPPVKLREALGRYGLTTEDFFVLKHGESRYLNSDDKNVE
          L..NEHYLDPPVKL.EALGRY.LTTE.FFVLKHGESRY.NSDDKN.E
Retrocopy L>KNEHYLDPPVKLHEALGRYRLTTEEFFVLKHGESRYQNSDDKNLE

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_2110 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,