Gene loci information

Transcript annotation

  • This transcript has been annotated as Trifunctional purine biosynthetic protein adenosine-3.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_1 g11988 g11988.t3 TSS g11988.t3 20147282 20147282
chr_1 g11988 g11988.t3 isoform g11988.t3 20147416 20148958
chr_1 g11988 g11988.t3 exon g11988.t3.exon1 20147416 20147452
chr_1 g11988 g11988.t3 cds g11988.t3.CDS1 20147416 20147452
chr_1 g11988 g11988.t3 exon g11988.t3.exon2 20147513 20147655
chr_1 g11988 g11988.t3 cds g11988.t3.CDS2 20147513 20147655
chr_1 g11988 g11988.t3 exon g11988.t3.exon3 20147774 20148958
chr_1 g11988 g11988.t3 cds g11988.t3.CDS3 20147774 20148898
chr_1 g11988 g11988.t3 TTS g11988.t3 NA NA

Sequences

>g11988.t3 Gene=g11988 Length=1365
ATGGAGAAGAAGAATGTTTTGTTAATTGGAAGTGGAGGACGTGAGCACGCATTAGCTTGG
AAACTTCAACAGAGCAAACATGTAGCTCATATTTTTACATTTCCTGGATCATTTGCCATA
TCGCAGCTTGAAAAAGCAAAGATAGTGAGCAGCAATGAGATGAATCTCAAAGATTTCACG
GGGATAGCTGCATGGTGCAAAAACAATATTATTGATCTTGTCGTTGTTGGGCCAGAAGAT
CCTCTTGCTGAGGGAATCGCCGATGTTCTCAAGAAAAATGGCATACCATGCTTTGGACCA
TCAAAAGCAGGTGCGAGAATTGAATCTGACAAGAGTTGGTCAAAGGAATTCATGATTAAA
CATAACATTCCGACTGCACGCTATGGATCTTTTACTGATGCAAATAAAGCAAAAGAATAC
ATTAAAAATACAAGAAATGCACTCGTGGTCAAAGCGAGTGGACTAGCTGCTGGAAAAGGA
GTTATCGTTGCAGAAACAATTGACGAGGCATGTGCAGCTGTTGATGAAATATTAGGAGAT
CATAAATTTGGATCAGCTGGAGATGTAGTTGTTGTTGAAGAAAAACTTTCTGGTCAAGAA
ATTTCCGTTTTGGCATTTGTTGATTCTAATTCCGTAAGATTGCTATTGCCAGCACAAGAT
CACAAACGTTTATTAGATAACGATGAAGGTCTTAATACTGGCGGAATGGGTGCTTATTGT
CCATGTCCATTGATTAGTCAGCAAGAATTAGATATTGTTAAAACACAAGTTTTACAGCGT
GCTGTCGATGGATTACGTGTTGAAGGCATATCGTATAATGGAATTTTATATGCAGGAATG
ATGCTCACTCCTGATGGACCTAAAACTTTAGAATTCAATTGTCGTTTTGGCGATCCTGAA
ACTCAAGTTATTTTGCCACTCTTAGAAAATGATTTGTTTGATTTAATGACTGCAACATGC
TCGAATCAACTCTGTAATGTACCAGAATTAGAATTCAAATCAAATATAAATGCTGTTGGT
GTTGTAATGGCATCAAAAGGATATCCGCAAACATCAACCAAGGGTTGTGTAATTGAAGGT
ATTGAACAAGTCAATGCTAAAGAAAATCACATTGTTTTCCATAGTGGAACAACTAAAAAT
GATAAAAATCAATGGGTTACAAACGGTGGCCGTGTTCTTATTAATGTTGCTTTAGCAAAT
GATTTAAAATCAGCAGCAGATTTAGCAACACAAGCTTCTGACGTTATTAAATTTGAAGGA
GCTCAATATCGTCGTGATATTGCAAAGAAAGCAATAAAAATGTAATTGATTATTTTAATT
TTAATAAATCATAACTCATCTGAAATATCTCTTTCATTTCTCAGA

>g11988.t3 Gene=g11988 Length=434
MEKKNVLLIGSGGREHALAWKLQQSKHVAHIFTFPGSFAISQLEKAKIVSSNEMNLKDFT
GIAAWCKNNIIDLVVVGPEDPLAEGIADVLKKNGIPCFGPSKAGARIESDKSWSKEFMIK
HNIPTARYGSFTDANKAKEYIKNTRNALVVKASGLAAGKGVIVAETIDEACAAVDEILGD
HKFGSAGDVVVVEEKLSGQEISVLAFVDSNSVRLLLPAQDHKRLLDNDEGLNTGGMGAYC
PCPLISQQELDIVKTQVLQRAVDGLRVEGISYNGILYAGMMLTPDGPKTLEFNCRFGDPE
TQVILPLLENDLFDLMTATCSNQLCNVPELEFKSNINAVGVVMASKGYPQTSTKGCVIEG
IEQVNAKENHIVFHSGTTKNDKNQWVTNGGRVLINVALANDLKSAADLATQASDVIKFEG
AQYRRDIAKKAIKM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g11988.t3 Gene3D G3DSA:3.40.50.20 - 5 101 9.8E-34
11 g11988.t3 Gene3D G3DSA:3.30.1490.20 - 127 196 2.8E-26
10 g11988.t3 Gene3D G3DSA:3.30.470.20 - 197 333 4.0E-53
12 g11988.t3 Gene3D G3DSA:3.90.600.10 Glycinamide Ribonucleotide Synthetase; Chain A 337 434 7.3E-31
6 g11988.t3 Hamap MF_00138 Phosphoribosylamine–glycine ligase [purD]. 4 432 38.318745
4 g11988.t3 PANTHER PTHR10520 TRIFUNCTIONAL PURINE BIOSYNTHETIC PROTEIN ADENOSINE-3-RELATED 5 428 5.0E-166
5 g11988.t3 PANTHER PTHR10520:SF12 TRIFUNCTIONAL PURINE BIOSYNTHETIC PROTEIN ADENOSINE-3 5 428 5.0E-166
2 g11988.t3 Pfam PF02844 Phosphoribosylglycinamide synthetase, N domain 5 108 1.9E-32
1 g11988.t3 Pfam PF01071 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain 110 301 8.8E-81
3 g11988.t3 Pfam PF02843 Phosphoribosylglycinamide synthetase, C domain 338 430 1.6E-26
14 g11988.t3 ProSitePatterns PS00184 Phosphoribosylglycinamide synthetase signature. 295 302 -
18 g11988.t3 ProSiteProfiles PS50975 ATP-grasp fold profile. 115 321 32.991
16 g11988.t3 SMART SM01209 GARS_A_3 109 301 4.5E-121
15 g11988.t3 SMART SM01210 GARS_C_2 337 432 2.0E-42
7 g11988.t3 SUPERFAMILY SSF52440 PreATP-grasp domain 4 109 7.19E-31
9 g11988.t3 SUPERFAMILY SSF56059 Glutathione synthetase ATP-binding domain-like 110 325 1.73E-57
8 g11988.t3 SUPERFAMILY SSF51246 Rudiment single hybrid motif 338 432 1.88E-26
17 g11988.t3 TIGRFAM TIGR00877 purD: phosphoribosylamine–glycine ligase 5 432 4.1E-154

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0046872 metal ion binding MF
GO:0005524 ATP binding MF
GO:0009113 purine nucleobase biosynthetic process BP
GO:0004641 phosphoribosylformylglycinamidine cyclo-ligase activity MF
GO:0004637 phosphoribosylamine-glycine ligase activity MF
GO:0006189 ‘de novo’ IMP biosynthetic process BP

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed