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 summary: | ||
| Parental gene symbol: | PFKP | ||
| Ensembl ID: | ENSCJAG00000020417 | ||
| Aliases: | None | ||
| Description: | phosphofructokinase, platelet [Source:HGNC Symbol;Acc:8878] |
Retrocopy-Parental alignment summary:
>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
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 |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
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 |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3223 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3223 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3223 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000010287 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000020417 | 1 retrocopy |
retro_cjac_3223 ,
|