RetrogeneDB ID: retro_cjac_3223

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:60720363..60722633(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PFKP
• Ensembl ID: ENSCJAG00000020417
• Aliases: None
• Description: phosphofructokinase, platelet [Source:HGNC Symbol;Acc:8878]

Sequence

>retro_cjac_3223
GGGATTGGCAAAGCCATCGCTGTCTTAACTTCTGGTGGAGATGCCCAAGGTATGAATGCTGCTGTCTGGGCAGTGGTTCA
AGTTGGTATTTTCACCGGTGCCCATGTCTTGTTTGTCCATGAGGGTTATCAAGGCCTGGTGGATGGTGGTCACACCAGGG
AAGCCACCTGGGAGAGCGTTTCGATGATGCTTCAGCTGGGAGGCACAGTGATTGGAAGTGCCCGGTGCAAGGACTTTCGG
GAACAAGAAGGACGACTCCAAGTTGCCTACAACCTGGTGAAACGTGGGATCACCAATCTCTGTGTCATTGGGGGTGATGG
CAGCTCACTGGGGCTGACACCTTCTGTTCTGAGTGTAGTGACTTATTGAGTGACCTCCAGAAAGCAGGTAAGATCACAGA
TGAGGAGGCTATGAAGTCCAGCTACCTGAACATTGTGGGCCTGGTTGGGTCAATTGACAATGACCTCTGTGGCACTGATA
TGACCATTGGCACTGACTCTGCCCTGCACCGGATCATAGAAATTGTAGATGCCATCACTACCACTGCTCAGAGCCACCAG
AGGACATTTGTGTTAGAAGTGATGGGCCGCCACTATGGATATCTGGCCCTTGTTACCTCTCTGTCCTGTGGGGCCGACTG
GGTTTTTATTCCTGAATGTCCACCAGATGATGACTGGGAGGAACACCTTTGTCACCAACTCAGCGAGACAAGGACCCGTG
GTTCTCATCTCAACATCATCATTTTGGCTGAGGGTGCAATTGACAAGAATGGAAAACCAATCACCTCAGAAGACATCAAG
AATCTGGTGGCAACACGTTTGGGATAGGACACCCGGGTCACTGTCTTGGGGCATGTGCAGAGGGGTGAGACGCCATTGGC
CTTTGACAGAATTCTGGGCAGCAGTATGGGTGTCAAAGCAGTGATGGCACTTTTGGAGGGGACTCTAGATACCCCAGCCT
GTGTACTGAGCCTCTCTGGGAACTAGGCTGTGCGCCTGCCCCTCATGGAAAGTGTCCAGGTGACTAAAGATGTGACCAAG
GCTATGGATGACAAGAAATTTGATGAAGCCATGAAGCTGAGAGGCCGGAGCTTCATGAACAACTGGGAGGTGTACAAGCT
TCTAGCTCATGTCAGACCGCCAGTATCTAAGAGTGGTTCACACACAGTGGCTGTGATGAACGTGGGGGCCCCGGCTGCAG
GCCTGAATGCTGCTGTTCACTCCACTGTGAGGATTGGCCTCATCCAGGGCAACCGAGTACTTGTTGTCTGTGATGGTTTC
AAGGGCTGGCCAACGGGCAGATAGAGGAAGCCGGCTGGAGCTATGTTGGGGGCTGGACTGGCCAAGGTGGTTCTAAACTT
GGGACTAAAAGGACTCTACTCAAGAAGAGCTTTGAGCAGATCAGGGCCAATATAACTAAGTTTAACATCCAGGGCCTCAT
CATCACTGGGGGCTTTGAGGCATACACAGGGGGTCTGGAGCTAATGGAGGGCAGGAAGCAGTTTGATGAGCTCTGCATCC
CATTTGTGGTCATTTCTGCTACAGTCTCCAACAACGTCCCTGGCTCAGACTTTAGCACTGGGGCTGACACAGCACTCAAT
ACTATCTGTACGACCTGTGACCACATCAAGCAGTCAGGAGCTGGCACCAAGCGTCGGGTGTTTATCATCGAGACCATGGG
TGGCTACTGTGGCTACCTGGCCACCATGGCTGGACTGGCAGCTGGGGCTGATGCTGCCTACATTTTTGAGGAGCCCTTCA
CCATTTGAGACCTGCAGGCAAATGTTGAACATCTGGTGCAAAAGATGAAAACAACTGTGAAAAGGAGCTTGGTGTTAAGG
AATGAAAAGTGCAATAAGAACTATACCACTGACTTCATTTTCAACCTGTACTCCGAGGAGGGAAAGGGCATCTTCGACAG
CAGAAAGAATGTGCTTGGTCACATGCAGCAGGGTGGGAGCCCAACTCCATTTGATAGGAATTTTGCCACTAAGATGGGCG
CCAACGCTATGAACTAGATGTCTGGGAAAAATCAAAGAGAGTTACCGTAATGGGCAGATTTTTGCCAATACTCAGGACTC
TGGCTGTGTTCTGGGGATGCGTAAGAGGGCTCTGGTCTTCCAACCAGTGACTGAGCTAAAGGACCAAACGAATTTTGAGC
ATCAAATCCCCAAGGAGCAGTGGTGGCTGAAACTGAGGCCCATCCTCAAAATCCTGGCCAAGTGTGAGACTGACTTGGAC
ACCTCAGACCATGCCCACCTGGGGCACATC

Alignment

ORF - retro_cjac_3223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.84 %
• Parental protein coverage: 96.68 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GAGKAIGVLTSGGDAQGMNAAVRAVVRMGIYVGAKVYFIYEGYQGMVDGGSNIVEADWESVSSILQVGGT
          G.GKAI.VLTSGGDAQGMNAAV.AVV..GI..GA.V.F..EGYQG.VDGG....EA.WESVS..LQ.GGT
Retrocopy GIGKAIAVLTSGGDAQGMNAAVWAVVQVGIFTGAHVLFVHEGYQGLVDGG-HTREATWESVSMMLQLGGT

Parental  IIGSARCQAFRTRDGRLK-ARNLVQRGITNLCVIGGDGS-LTGANLFRKEWSGLLEELAKNGQIEKEAVQ
          .IGSARC..FR...GRL..A.NLV.RGITNLCVIGGDGS.LTGA..F..E.S.LL..L.K.G.I..E...
Retrocopy VIGSARCKDFREQEGRLQVAYNLVKRGITNLCVIGGDGS<LTGADTFCSECSDLLSDLQKAGKITDEEAM

Parental  RYAHLNVVGMVGSIDNDFCGTDMTIGTDSALHRIIEVVDAIMTTAQSHQRTFVLEVMGRHCGYLALVSAL
          ....LN.VG.VGSIDND.CGTDMTIGTDSALHRIIE.VDAI.TTAQSHQRTFVLEVMGRH.GYLALV..L
Retrocopy KSSYLNIVGLVGSIDNDLCGTDMTIGTDSALHRIIEIVDAITTTAQSHQRTFVLEVMGRHYGYLALVTSL

Parental  ACGADWVFLPESPPEEGWEEQMCVKLSENRARKKRLNIIIVAEGAIDTQNKPITSEKIKDLVVTQLGYDT
          .CGADWVF.PE.PP...WEE..C..LSE.R.R...LNIII.AEGAID...KPITSE.IK.LV.T.LG.DT
Retrocopy SCGADWVFIPECPPDDDWEEHLCHQLSETRTRGSHLNIIILAEGAIDKNGKPITSEDIKNLVATRLG*DT

Parental  RVTILGHVQRGGTPSAFDRILASRMGVEAVIALLEATPDTPACVVSLSGNHAVRLPLMECVQMTQDVQKA
          RVT.LGHVQRG.TP.AFDRIL.S.MGV.AV.ALLE.T.DTPACV.SLSGN.AVRLPLME.VQ.T.DV.KA
Retrocopy RVTVLGHVQRGETPLAFDRILGSSMGVKAVMALLEGTLDTPACVLSLSGN*AVRLPLMESVQVTKDVTKA

Parental  MDERRFQDAVQLRGKSFEGNLNTYKRLAIKLPDDQIPKTNCNVAVI-NVGAPAAGMNAAVRSAVRMGIAD
          MD...F..A..LRG.SF..N...YK.LA...P.....K.........NVGAPAAG.NAAV.S.VR.G...
Retrocopy MDDKKFDEAMKLRGRSFMNNWEVYKLLAHVRP--PVSKSGSHTVAVMNVGAPAAGLNAAVHSTVRIGLIQ

Parental  GHRMLAIYDG-FDGFAKGQIKEIGWTDVGGWTGQGGSILGTKRVLPGKYLEEIATQMRMHSINALLIIGG
          G.R.L...DG.F.G.A.GQI.E.GW..VGGWTGQGGS.LGTKR.L..K..E.I........I..L.I.GG
Retrocopy GNRVLVVCDG<FQGLANGQIEEAGWSYVGGWTGQGGSKLGTKRTLLKKSFEQIRANITKFNIQGLIITGG

Parental  FEAYLGLLELSAAREKHEEFCVPMVMVPATVSNNVPGSDFSIGADTALNTITDTCDRIKQSASGTKRRVF
          FEAY.G.LEL...R....E.C.P.V...ATVSNNVPGSDFS.GADTALNTI..TCD.IKQS..GTKRRVF
Retrocopy FEAYTGGLELMEGRKQFDELCIPFVVISATVSNNVPGSDFSTGADTALNTICTTCDHIKQSGAGTKRRVF

Parental  IIETMGGYCGYLANMGGLAAGADAAYIFEEPFDIRDLQSNVEHLTEKMKTTIQRGLVLRNESCSENYTTD
          IIETMGGYCGYLA.M.GLAAGADAAYIFEEPF.I.DLQ.NVEHL..KMKTT..R.LVLRNE.C..NYTTD
Retrocopy IIETMGGYCGYLATMAGLAAGADAAYIFEEPFTI*DLQANVEHLVQKMKTTVKRSLVLRNEKCNKNYTTD

Parental  FIYQLYSEEGKGVFDCRKNVLGHMQQGGAPSPFDRNFGTKISARAMEWIT-AKLKAARGRGKKF-TTDDS
          FI..LYSEEGKG.FD.RKNVLGHMQQGG.P.PFDRNF.TK..A.AM......K.K.....G..F..T.DS
Retrocopy FIFNLYSEEGKGIFDSRKNVLGHMQQGGSPTPFDRNFATKMGANAMN*MS>GKIKESYRNGQIFANTQDS

Parental  VCVLGISKRNVIFQPVAELKKETDFEHRIPKEQWWLKLRPLMKILAKYKASYDVSDSGQLEHV
          .CVLG..KR...FQPV.ELK..T.FEH.IPKEQWWLKLRP..KILAK.....D.SD...L.H.
Retrocopy GCVLGMRKRALVFQPVTELKDQTNFEHQIPKEQWWLKLRPILKILAKCETDLDTSDHAHLGHI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.42 RPM	54.63 RPM
SRP051959_heart	9.58 RPM	54.60 RPM
SRP051959_kidney	1.24 RPM	25.65 RPM
SRP051959_liver	0.26 RPM	8.23 RPM
SRP051959_lung	0.57 RPM	36.31 RPM
SRP051959_lymph_node	0.37 RPM	58.06 RPM
SRP051959_skeletal_muscle	90.41 RPM	8.54 RPM
SRP051959_spleen	0.48 RPM	49.90 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3223 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3223 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3223 has 0 orthologous retrocopies within eutheria group .

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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 ,