RetrogeneDB ID: retro_chof_2660

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_95056:1..1091(+)
• 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_2660
CAGAATTCTGGAGGAATGATTCTTCTAGGTTTTCAAGGAAAAGCTTCAAATTGGATTACAGATTAGAGGAATATATAACT
AAATCAAAGAAAGGAAAAAATGGGAGCTTTGTTAACCCTTGGCCAACATGGAGGAATCCCTCTATTCCAAATGCCCTCAG
ATTGTTGATCATAGAAAAAGATCACAGCAATAATCCACATTCCAAAGAGGAACTTGATAAAGAACTCTCAGTGCTTAAGC
CCTATTTCAGCAATGACTCTGTAGTGAAGGAAGCTGGCTTAAGGGTCACATGGCTGAGACATGCAACAGTAATGGTAGAA
ACTGATGAGCTCATAATTCTCATGAATCCCATTTTTAGCGATCATGCTTCACCACCACAGTACATGGATCTAAAATGCTT
TTGTTAGCCTCCATGCACAATAAGCAAGCTGCCTCCAATAGATGTGGTCCTTATCAGTCAAAACCACTGTGATCACCTGG
ACTACAATTCTGTCATTGCTCTGAATGGGTGATTCAGTAATGCATTGAGATGATTTGTGCCTTTGGGTCTCCTTGACTGC
ATGCAGAAATACAGCTAAGAGAATATGATTGAGCTGGACCAGTGGGAGGAGAATTGTGTTTCCAGACATGATAAGGTCAC
CTTTGTCTATCCACCATCCCAGCACTGCTGCAGAGGACTCTAACGGATGACAATAAGGTTCTGTGGGGTGACTGGTCTGT
CTTGAGACCTTGGAATAGATTCTTTTTTTTTGCAGGAGATACTGGTTATTGCCCTGCTTTTGAATAGATGGGAAAAAGAT
TTGGACCTTTTGGTCTTGCAGCTATTCTTATTGGAGCTTATGAACCCAGGTGGCATATGAAATGGCAGCACATAGACCCA
GAAGAAGCTGTAAGGTTTCACACTTATGTCCAAGCAGAGAAATCTGTGGCAATTCACTGGTGAACTTTTGTCTTAGCAAA
TGAGCACTACTTAGACCCTCCAGTGAAACTGCATGAAGCTCTAGGAAGATACAGACTTATGACTGAAGATTTTTTTGTCT
TGAAGCATGGAGAATCAAGATACCAAAATAATAATGATAAAAACTTTGAA

Alignment

ORF - retro_chof_2660 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.24 %
• Parental protein coverage: 92.88 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RNSGG-SDSSRFSRKSFKLDYRLEEDVTKSKKGKDGRFVNPWPTWKNPSIPNALRWLIMEKDHSNVPRSK
          .NSGG..DSSRFSRKSFKLDYRLEE..TKSKKGK.G.FVNPWPTW.NPSIPNALR.LI.EKDHSN.P.SK
Retrocopy QNSGG<NDSSRFSRKSFKLDYRLEEYITKSKKGKNGSFVNPWPTWRNPSIPNALRLLIIEKDHSNNPHSK

Parental  EELDKELPVLKPYFINDPEKAGVKEAGLRVKWLGHATVMLEMGEILFLTDPIFSQCVSPSQ-VGLKYFCC
          EELDKEL.VLKPYF.ND.....VKEAGLRV.WL.HATVM.E..E...L..PIFS...SP.Q...LK.FC.
Retrocopy EELDKELSVLKPYFSND---SVVKEAGLRVTWLRHATVMVETDELIILMNPIFSDHASPPQYMDLKCFC*

Parental  PPCTIFELPPADVVLISHNHYDHLDYNSVIALNERFGNELRWFVPLGLLDWMQKCGCENVIELDWWEENC
          PPCTI..LPP.DVVLIS.NH.DHLDYNSVIALN..F.N.LR.FVPLGLLD.MQK...EN.IELD.WEENC
Retrocopy PPCTISKLPPIDVVLISQNHCDHLDYNSVIALNG*FSNALR*FVPLGLLDCMQKYS*ENMIELDQWEENC

Parental  VPRHDKVTFVFTPSQHWCK-RTLMDDNKVLWGSWSVLGPWNRFFF-AGDTGYCPAFEEIGKRFGPFDLAA
          V.RHDKVTFV..PSQH.C..RTL.DDNKVLWG.WSVL.PWNRF...AGDTGYCPAFE..GKRFGPF.LAA
Retrocopy VSRHDKVTFVYPPSQHCCR<RTLTDDNKVLWGDWSVLRPWNRFXXXAGDTGYCPAFE*MGKRFGPFGLAA

Parental  IPVGAYEPRWFMKWQHIDPEEAVRIHIDVQAKKSVAIHWGTFVLANEHYLDPPVKLREALGRYGLTTEDF
          I..GAYEPRW.MKWQHIDPEEAVR.H..VQA.KSVAIHW.TFVLANEHYLDPPVKL.EALGRY.L.TEDF
Retrocopy ILIGAYEPRWHMKWQHIDPEEAVRFHTYVQAEKSVAIHW*TFVLANEHYLDPPVKLHEALGRYRLMTEDF

Parental  FVLKHGESRYLNSDDKNVE
          FVLKHGESRY.N..DKN.E
Retrocopy FVLKHGESRYQNNNDKNFE

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_2660 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 ,