RetrogeneDB ID: retro_chof_782

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_14779:18337..19660(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PFKP
• Ensembl ID: ENSCHOG00000010287
• Aliases: None
• Description: phosphofructokinase, platelet [Source:HGNC Symbol;Acc:8878]

Sequence

>retro_chof_782
ATGAATGCTGCTGTCAGGGCTGTGGTTCGAGTTGGTATCTTTATCAGTGTCCATGTCTTCTTTGTCCATGAGGATTATGA
AGGCCTGGTGGATGGTGGAGATAGCATCAGGGAAGCCACCTGGGAGAGTGTTTCGATGATGTTTCAGCTGGGAGGCACAG
TGATTGGAAGTGCTCGGTGCAAGGACTTTCGCGAGCGAGAGGGACGACTCCAAGCTGCCCTCAACCTGGTGAAGCGTGGG
ATCACCAACCTGTGTGTCATTGGGGGTGATGGCAGCCTCACTGGGGCTGACACCTTCCTTTCTGAGTGGAGTGACTTGTT
GAGTGAACTCCAGAAAGCGGGTAAGATCACAGCTGAGGAAGTTAAGAATTCCAGGTACCTGAACATCGTGGGCCTGGTTG
GCTCTATTGACAATGACTTCTGCGGCACCGATATGACCATTGGCACTGACTCTGCCCTGCACCGGATCATAGAGATTGTA
GATGCCATCACAACCACTTCTCAGAGCCACCAGAGGATATTTGTGTTAGAAGTGATGGGCCGGCACTGTGGATACCTGGC
CCTTGTTACCTCTCTCTCCTGTGGGGCCGACTGAGTTTTTATTCCTGAATGTCCACCAGGTGATGACTGGGAGGAACACC
TTTGCTGTCGGCTCACTGAGACAAGGACCCGTGGTTCTCGTCTCAACATCATCATTGTGGCTGAGGGTGCAATTGATAGG
AATGGGAAACCAATCACCTCAGAAGACATGAAGAATCTGGTGGTAAAGCGTCTGGGATATGACACCCGGGTCACTGTCTT
GGGGCATGTGCAGCGGGGTGGGACGCCGTCAGCTTTTGACCAAATCCTGGGCAGCAGGATGGGTGTGGAAGCAGTGATGG
CACTTTTAGAAGGGACCCCAGACACCCCAGCCTGTGTGGTGAGCCTCTCGGGTAACCAGGCAGTGCGACTGCCCCTCATG
GAGTGTGTCCAAGTGACCAAAGATGTGACCAAGGCCATGAGCGAGAAGAAATTTGATGAAGCCCTGAAGCTAAGAAGCTG
GAGCTTCATGAACAACTGGGAAGTATACAAGCTTCTAGCTCATGTCCAACCCCCAGTGGCTAAGACTGATTCACGTACAG
TGGCTATGATGAACGTGGGTGCCCCAGCTGCAGGCATGAATGCTGCTGTCCGCTCCACTGTGAGGATTGGTGTCATCCAG
GGCAACCGAATGCTGGTTGTGCATGAGGGCTTCGAGGGCCTGGCCAAGGGTCAGGTTGAGGAAGCTGGCTGGAGCTATGT
TGGGGGCTGGACTGGGCAAGGTGGTTCTAAACTTGGAACTAAA

Alignment

ORF - retro_chof_782 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.16 %
• Parental protein coverage: 59.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNAAVRAVVRMGIYVGAKVYFIYEGYQGMVDGGSNIVEASWESVSSILQVGGTIIGSARCQAFRTREGRL
          MNAAVRAVVR.GI.....V.F..E.Y.G.VDGG..I.EA.WESVS...Q.GGT.IGSARC..FR.REGRL
Retrocopy MNAAVRAVVRVGIFISVHVFFVHEDYEGLVDGGDSIREATWESVSMMFQLGGTVIGSARCKDFREREGRL

Parental  KAAHNLVQLRITNLCVIGGDGSLTGANIFRKEWSGLLEELAENGKIDADTMKEYSYLNVVGMVGSIDNDF
          .AA.NLV...ITNLCVIGGDGSLTGA..F..EWS.LL.EL...GKI.A...K...YLN.VG.VGSIDNDF
Retrocopy QAALNLVKRGITNLCVIGGDGSLTGADTFLSEWSDLLSELQKAGKITAEEVKNSRYLNIVGLVGSIDNDF

Parental  CGTDMTIGTDSALHRIIEVVDAIMTTAQSHQRTFVLEVMGRHCGYLAVVSALACGADWVFLPEYPPKEGW
          CGTDMTIGTDSALHRIIE.VDAI.TT.QSHQR.FVLEVMGRHCGYLA.V..L.CGAD.VF.PE.PP...W
Retrocopy CGTDMTIGTDSALHRIIEIVDAITTTSQSHQRIFVLEVMGRHCGYLALVTSLSCGAD*VFIPECPPGDDW

Parental  EEEMCLKLSENRARKKRLNIIIVAEGAIDTQNRPITSEEVKELVVKQLGYDTRVTILGHVQRGGTPSAFD
          EE..C..L.E.R.R..RLNIIIVAEGAID....PITSE..K.LVVK.LGYDTRVT.LGHVQRGGTPSAFD
Retrocopy EEHLCCRLTETRTRGSRLNIIIVAEGAIDRNGKPITSEDMKNLVVKRLGYDTRVTVLGHVQRGGTPSAFD

Parental  RILASRMGVEAVIALLEATPETPACVVSLSGNHAMRLPLMECVQMTQEVQKAMDERRFQAAVQLRGRNFE
          .IL.SRMGVEAV.ALLE.TP.TPACVVSLSGN.A.RLPLMECVQ.T..V.KAM.E..F..A..LR...F.
Retrocopy QILGSRMGVEAVMALLEGTPDTPACVVSLSGNQAVRLPLMECVQVTKDVTKAMSEKKFDEALKLRSWSFM

Parental  SNLNTYKQLSSKLPDDQIVKSNCNVAIINVGAPAAGMNAAVRSAVRVGISNGHKMFAVYDSFEGFSQGHX
          .N...YK.L....P......S...VA..NVGAPAAGMNAAVRS.VR.G...G..M..V...FEG...G..
Retrocopy NNWEVYKLLAHVQPPVAKTDSR-TVAMMNVGAPAAGMNAAVRSTVRIGVIQGNRMLVVHEGFEGLAKGQV

Parental  XXXXXXXXXXXXAQGGCS-GTK
          .............QGG...GTK
Retrocopy EEAGWSYVGGWTGQGGSKLGTK

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_782 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010287	1 retrocopy	retro_chof_782 ,
Callithrix jacchus	ENSCJAG00000020417	1 retrocopy	retro_cjac_3223,