General information for g11988.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Trifunctional purine biosynthetic protein adenosine-3.
Parent gene
- The parent gene g11988 is located on chr_1: 20151772..20153547 (+ strand)
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.t4 | TSS | g11988.t4 | 20147282 | 20147282 |
| chr_1 | g11988 | g11988.t4 | isoform | g11988.t4 | 20148126 | 20150244 |
| chr_1 | g11988 | g11988.t4 | exon | g11988.t4.exon1 | 20148126 | 20148894 |
| chr_1 | g11988 | g11988.t4 | cds | g11988.t4.CDS1 | 20148299 | 20148894 |
| chr_1 | g11988 | g11988.t4 | exon | g11988.t4.exon2 | 20148958 | 20150244 |
| chr_1 | g11988 | g11988.t4 | cds | g11988.t4.CDS2 | 20148958 | 20150242 |
| chr_1 | g11988 | g11988.t4 | TTS | g11988.t4 | NA | NA |
Sequences
>g11988.t4 Gene=g11988 Length=2056
TAGGAGATCATAAATTTGGATCAGCTGGAGATGTAGTTGTTGTTGAAGAAAAACTTTCTG
GTCAAGAAATTTCCGTTTTGGCATTTGTTGATTCTAATTCCGTAAGATTGCTATTGCCAG
CACAAGATCACAAACGTTTATTAGATAACGATGAAGGTCTTAATACTGGCGGAATGGGTG
CTTATTGTCCATGTCCATTGATTAGTCAGCAAGAATTAGATATTGTTAAAACACAAGTTT
TACAGCGTGCTGTCGATGGATTACGTGTTGAAGGCATATCGTATAATGGAATTTTATATG
CAGGAATGATGCTCACTCCTGATGGACCTAAAACTTTAGAATTCAATTGTCGTTTTGGCG
ATCCTGAAACTCAAGTTATTTTGCCACTCTTAGAAAATGATTTGTTTGATTTAATGACTG
CAACATGCTCGAATCAACTCTGTAATGTACCAGAATTAGAATTCAAATCAAATATAAATG
CTGTTGGTGTTGTAATGGCATCAAAAGGATATCCGCAAACATCAACCAAGGGTTGTGTAA
TTGAAGGTATTGAACAAGTCAATGCTAAAGAAAATCACATTGTTTTCCATAGTGGAACAA
CTAAAAATGATAAAAATCAATGGGTTACAAACGGTGGCCGTGTTCTTATTAATGTTGCTT
TAGCAAATGATTTAAAATCAGCAGCAGATTTAGCAACACAAGCTTCTGACGTTATTAAAT
TTGAAGGAGCTCAATATCGTCGTGATATTGCAAAGAAAGCAATAAAAATACAACCAATTT
CATATAAAAACAGTGGTGTGGATATAGAAGCTGGTGAATCTCTAGTACAAAGAATCAAGC
CGCTTGCTCGAGGAACAAATCGAAGTGGCGTTATTGGTGAAATAGGCAGCTTTGGTGGAT
TAATCAAATTAAACGACATTAAATATATCGATAAAAATGGTTTGGAGACAAATTATAAAG
ATCCTGTTTTAGTTCAGGGAACAGATGGGGTAGGAACTAAATTGAAAATTGCAGAAGCAC
TCAATATTTGGGATACAATTGGAATTGATCTTGTCGCTATGTGTGTCAACGATGTATTAT
GTAATGGAGCAGAACCTGTTGCATTTCTCGATTATATAGCTTGTGGCCTCCTCGATGTTC
CATCTGCTGCAATGATTGTTAAAGGAATATCAGAAGCATGTCGTGAATCAAATTGTGCAC
TAATAGGTGGTGAAACTGCAGAAATGCCTTCCATGTATGAAAAAGGAAAATATGATTTGG
CAGGTTATTGCGTCGGAATTGTTGAATATGAAGATATTTTACCTAAAATGAATGAAGTTC
GTGAAGGTGATATTGTTGTTGCTTTACCATCAAGTGGTATTCATAGCAATGGTTTCTCAC
TTGTCAATAAAATTCTTGAAAAATTGGATTTTAAATTGACTGATATTGCACCATTCAGTG
ATGATGGCAACTCATTTGGAAAAGAATTTTTGACACCAACAAAATTATATGTTTCTAATG
TAATGCCATTGTTGAGAAAAGGAAATGTTAAATCACTTGCTCACATTACAGGTGGAGGAT
TATATGAAAATATTCCAAGAGCTCTACCATCAAATGTTTGTGTACAACTCGATGCAGTTA
CATGGAAGTTACCAAAAGTGTTTGGTTGGTTAGCAGCACAAGGCAATATTGATGAAAATG
AAATGCTAAGAACTTTTAATTGTGGCATTGGAATGATCATTATTTTACCACGAAATAATA
TTGAATGGCAGTCGATTTCAGAAGCAAAATTGATTGGAAATGTTACAAAACGAGAAACAT
CAGATTCACCACAAGTAATTGTGAAAAATTTCAAAGAAGTGCTCGAAAAAGAAATTTCAC
CATGGAAAAATGCATCAAACTCTACCACAATCAGTTATAAAGATAGTGGTGTGGATATTA
TTGCTGGAAATGCTCTTGTCGATAATATCAAGCCCTTTGCAAAATCAACCAATCGCAAAG
GAGTTCTAGGTGGTCTTGGTTCTTTTGGAGGTTTATTTAGATTAAAAGAACTTGAGCAAG
TTTACACTGATCCTGT
>g11988.t4 Gene=g11988 Length=627
MGAYCPCPLISQQELDIVKTQVLQRAVDGLRVEGISYNGILYAGMMLTPDGPKTLEFNCR
FGDPETQVILPLLENDLFDLMTATCSNQLCNVPELEFKSNINAVGVVMASKGYPQTSTKG
CVIEGIEQVNAKENHIVFHSGTTKNDKNQWVTNGGRVLINVALANDLKSAADLATQASDV
IKFEGAQYRRDIAKKAIKIQPISYKNSGVDIEAGESLVQRIKPLARGTNRSGVIGEIGSF
GGLIKLNDIKYIDKNGLETNYKDPVLVQGTDGVGTKLKIAEALNIWDTIGIDLVAMCVND
VLCNGAEPVAFLDYIACGLLDVPSAAMIVKGISEACRESNCALIGGETAEMPSMYEKGKY
DLAGYCVGIVEYEDILPKMNEVREGDIVVALPSSGIHSNGFSLVNKILEKLDFKLTDIAP
FSDDGNSFGKEFLTPTKLYVSNVMPLLRKGNVKSLAHITGGGLYENIPRALPSNVCVQLD
AVTWKLPKVFGWLAAQGNIDENEMLRTFNCGIGMIIILPRNNIEWQSISEAKLIGNVTKR
ETSDSPQVIVKNFKEVLEKEISPWKNASNSTTISYKDSGVDIIAGNALVDNIKPFAKSTN
RKGVLGGLGSFGGLFRLKELEQVYTDP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g11988.t4 | CDD | cd02196 | PurM | 235 | 522 | 6.39863E-155 |
| 13 | g11988.t4 | Gene3D | G3DSA:3.30.470.20 | - | 1 | 98 | 2.5E-32 |
| 14 | g11988.t4 | Gene3D | G3DSA:3.90.600.10 | Glycinamide Ribonucleotide Synthetase; Chain A | 102 | 204 | 6.0E-31 |
| 16 | g11988.t4 | Gene3D | G3DSA:3.30.1330.10 | - | 205 | 376 | 9.4E-68 |
| 12 | g11988.t4 | Gene3D | G3DSA:3.90.650.10 | - | 377 | 566 | 7.9E-66 |
| 15 | g11988.t4 | Gene3D | G3DSA:3.30.1330.10 | - | 572 | 627 | 3.4E-11 |
| 7 | g11988.t4 | Hamap | MF_00741 | Phosphoribosylformylglycinamidine cyclo-ligase [purM]. | 202 | 553 | 41.314709 |
| 6 | g11988.t4 | PANTHER | PTHR10520 | TRIFUNCTIONAL PURINE BIOSYNTHETIC PROTEIN ADENOSINE-3-RELATED | 1 | 555 | 3.7E-228 |
| 5 | g11988.t4 | PANTHER | PTHR10520 | TRIFUNCTIONAL PURINE BIOSYNTHETIC PROTEIN ADENOSINE-3-RELATED | 569 | 618 | 3.7E-228 |
| 1 | g11988.t4 | Pfam | PF01071 | Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain | 1 | 66 | 8.2E-23 |
| 3 | g11988.t4 | Pfam | PF02843 | Phosphoribosylglycinamide synthetase, C domain | 103 | 195 | 2.8E-26 |
| 4 | g11988.t4 | Pfam | PF00586 | AIR synthase related protein, N-terminal domain | 265 | 370 | 9.3E-16 |
| 2 | g11988.t4 | Pfam | PF02769 | AIR synthase related protein, C-terminal domain | 383 | 541 | 2.6E-25 |
| 18 | g11988.t4 | ProSitePatterns | PS00184 | Phosphoribosylglycinamide synthetase signature. | 60 | 67 | - |
| 22 | g11988.t4 | ProSiteProfiles | PS50975 | ATP-grasp fold profile. | 21 | 86 | 9.836 |
| 20 | g11988.t4 | SMART | SM01209 | GARS_A_3 | 1 | 66 | 7.6E-7 |
| 19 | g11988.t4 | SMART | SM01210 | GARS_C_2 | 102 | 197 | 2.0E-42 |
| 11 | g11988.t4 | SUPERFAMILY | SSF56059 | Glutathione synthetase ATP-binding domain-like | 1 | 90 | 4.89E-16 |
| 8 | g11988.t4 | SUPERFAMILY | SSF51246 | Rudiment single hybrid motif | 103 | 197 | 3.45E-26 |
| 10 | g11988.t4 | SUPERFAMILY | SSF55326 | PurM N-terminal domain-like | 202 | 375 | 1.64E-44 |
| 9 | g11988.t4 | SUPERFAMILY | SSF56042 | PurM C-terminal domain-like | 380 | 541 | 1.24E-49 |
| 21 | g11988.t4 | TIGRFAM | TIGR00878 | purM: phosphoribosylformylglycinamidine cyclo-ligase | 202 | 525 | 1.7E-121 |
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
- This transcript has been annotated with K01933 (phosphoribosylformylglycinamidine cyclo-ligase)
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