RetrogeneDB ID: retro_chof_2178

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_55808:3543..4655(+)
• 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_2178
AGAAAACACCAGAATTCAGCATGGAATTCTGCAGGAAGCAGATCTTCTAGGTTTTCCAGGAAAAGCTTCAAACTGGATTA
TAGATTAGAGGAAGATGTAACTAAATCAAAGAAAAGAAAAGATGGGAGATTTGTTAACCCTTGGCCAACTTGGAAAAATC
CCTCTATTCCAAATGCCCTCAGATGGTTGATAATGGAAAAAAATCACAGCACTGTTCCATGTTCCAAAGAGGAACTTGAT
AAAGGCCTCCCAGTGCTTAAACGCTATAATATCAATGGCCCTGAAGAAGCTGGAGTGAAGGAAGCTGCCTTAAGAGTCAC
ATGGCTGAGACATGCAACAGTAATGGTAGAAATGAATGAGCTCATATTTCTCATGAATACCATTCTTAGCCATCGTGCTT
CACCATCACAGCATGTGGGTCCAAAATGCTTTCATCACCCTCCATGCACAAGTAAGCTGCCCCCAATAGATGTGGTCCTT
ATCAGTCACAACCAGTATGATCACCTGGACTACAATTCTGTCATTGCTCTGAATGAGCAATGTGGTAATGAGTTGAGTTG
GTTTGTGACTTTGGGTCTCCTAGACTGGATGCAAAAATGTGGCTGTGAGAATGTGACTGAGCTGGATGGGTGGGAAAATT
GTGTCCCCAGACATGATAAGGTCACCTTTGTATTTACACTGTCCCTGCACTGGTGTAAGAGGACTCTAATGGATGTCAGT
AAGGTTCTGTGGGGCAGCTGGTATGTCTTGGGGCCTTGGAATAGATTTTTTTTTGCAGGAGATACTGGTTATTGCCCTGC
TTTTGAAGAGATAGGAAAAAGACTTGGATTTTTGACCTTGCAGCTATTCTTATTGGAGCTTATGAACCCAGGTGGTTTAT
GAAATGGCAGCACATAGAACCATAAGAAGTTGTAAGGATTCATACTGATGTTCAAGCAAAGAAAACTGTGGCAATTCACT
GGGGAACTTTTGTCTTAGAAAATGAGCATTACTTAGAACCTCCAGTGAAACTGCATCAAGCTCTAGGAAGATACAGACTT
ATGACTAAAGATTTTTTTGTCTTGAAGCATGGAGAATCAAGATATCTAAATAGTGATGATAAAAACTTTGAA

Alignment

ORF - retro_chof_2178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.28 %
• Parental protein coverage: 94.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RKRQNSARNSGGSDSSRFSRKSFKLDYRLEEDVTKSKKGKDGRFVNPWPTWKNPSIPNALRWLIMEKDHS
          RK.QNSA.NS.GS.SSRFSRKSFKLDYRLEEDVTKSKK.KDGRFVNPWPTWKNPSIPNALRWLIMEK.HS
Retrocopy RKHQNSAWNSAGSRSSRFSRKSFKLDYRLEEDVTKSKKRKDGRFVNPWPTWKNPSIPNALRWLIMEKNHS

Parental  NVPRSKEELDKELPVLKPYFINDPEKAGVKEAGLRVKWLGHATVMLEMGEILFLTDPIFSQCVSPSQ-VG
          .VP.SKEELDK.LPVLK.Y.IN.PE.AGVKEA.LRV.WL.HATVM.EM.E..FL...I.S...SPSQ.VG
Retrocopy TVPCSKEELDKGLPVLKRYNINGPEEAGVKEAALRVTWLRHATVMVEMNELIFLMNTILSHRASPSQHVG

Parental  LKYFCCPPCTIFELPPADVVLISHNHYDHLDYNSVIALNERFGNELRWFVPLGLLDWMQKCGCENVIELD
          .K.F..PPCT...LPP.DVVLISHN.YDHLDYNSVIALNE..GNEL.WFV.LGLLDWMQKCGCENV.ELD
Retrocopy PKCFHHPPCT-SKLPPIDVVLISHNQYDHLDYNSVIALNEQCGNELSWFVTLGLLDWMQKCGCENVTELD

Parental  WWEENCVPRHDKVTFVFTPSQHWCKRTLMDDNKVLWGSWSVLGPWNRFFFAGDTGYCPAFEEIGKRFG-P
          .W.ENCVPRHDKVTFVFT.S.HWCKRTLMD..KVLWGSW.VLGPWNR...AGDTGYCPAFEEIGKR.G..
Retrocopy GW-ENCVPRHDKVTFVFTLSLHWCKRTLMDVSKVLWGSWYVLGPWNRXXXAGDTGYCPAFEEIGKRLG<I

Parental  FDLAAIPVGAYEPRWFMKWQHIDPEEAVRIHIDVQAKKSVAIHWGTFVLANEHYLDPPVKLREALGRYGL
          FDLAAI..GAYEPRWFMKWQHI.P.E.VRIH.DVQAKK.VAIHWGTFVL.NEHYL.PPVKL..ALGRY.L
Retrocopy FDLAAILIGAYEPRWFMKWQHIEP*EVVRIHTDVQAKKTVAIHWGTFVLENEHYLEPPVKLHQALGRYRL

Parental  TTEDFFVLKHGESRYLNSDDKNVE
          .T.DFFVLKHGESRYLNSDDKN.E
Retrocopy MTKDFFVLKHGESRYLNSDDKNFE

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_2178 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,