General information for g5609.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Phosphoribosylformylglycinamidine synthase.
Parent gene
- The parent gene g5609 is located on chr_2: 10597946..10598677 (+ 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_2 | g5609 | g5609.t1 | TSS | g5609.t1 | 10594203 | 10594203 |
| chr_2 | g5609 | g5609.t1 | isoform | g5609.t1 | 10594228 | 10598617 |
| chr_2 | g5609 | g5609.t1 | exon | g5609.t1.exon1 | 10594228 | 10594305 |
| chr_2 | g5609 | g5609.t1 | cds | g5609.t1.CDS1 | 10594228 | 10594305 |
| chr_2 | g5609 | g5609.t1 | exon | g5609.t1.exon2 | 10594513 | 10595431 |
| chr_2 | g5609 | g5609.t1 | cds | g5609.t1.CDS2 | 10594513 | 10595431 |
| chr_2 | g5609 | g5609.t1 | exon | g5609.t1.exon3 | 10595506 | 10597886 |
| chr_2 | g5609 | g5609.t1 | cds | g5609.t1.CDS3 | 10595506 | 10597886 |
| chr_2 | g5609 | g5609.t1 | exon | g5609.t1.exon4 | 10597946 | 10598617 |
| chr_2 | g5609 | g5609.t1 | cds | g5609.t1.CDS4 | 10597946 | 10598617 |
| chr_2 | g5609 | g5609.t1 | TTS | g5609.t1 | 10598682 | 10598682 |
Sequences
>g5609.t1 Gene=g5609 Length=4050
ATGCCGATCAGTCGTTTTTATAATTTGATCGCCTTTGATGAGGCTAAAATTAATACTATC
TTAAAGGATTTAAGAAAGATCTATGACAATATCAGCTGCGTGAAAACAGAAAAATCATTT
CATGTTGAACTCATCGAGGGACATTCGTTATCAAATGAGGACGAGAAAAAGCTAAGATGG
ATTTTGAAAAACACACAGGAAAAAGATAATCTCACTAAAGAGCCGTCTCTAAAAGCATCA
AAGAAAAACCATATTCTTATTGAAATTGGACCACGCTTTAACTTTTCAACGGCTGAATCA
ACGAATTCTGTTAGCATTTGTCACTCGATACATTTGACATCAATAATTCGAATTGAAACA
AGCATCCGCTATTTAATAGAATTAGATGAAAATTCCAAACTGTTAACAGCTGAAGATGAA
CTTATACTAGTTGATCATTTGAGTGATAGAATGACACAGTGTCGTTATACTGATGAAAAC
ATTCCACATGATTCTTTCGATGAACGCTTGCCAAAAGAAAAAGAATCTTGGTTCTATGTC
CCTGTTTTGACTCAAGGACGAAAAGCTTTACAAGAAGTTAATTCAAAAATGGGCCTCGCA
TTTGATAATTGGGATCTTGATTATTATACTGATTTATTTACAAATGTGTTAAAGCGAGAT
CCAACAAGTACTGAATTATTTGATTGTGCTCAATCAAATTCGGAACATTCTCGTCATTGG
TTCTTTAAAGGTCGCATGATAATTGATGGAAAGGAAGAAGAAAAATCACTTATTAAAATG
ATTATTGACACACAAAATTATTCAAATCAAAACAATACAATCAAATTTAGTGACAATTCA
AGTGCCATTAAAGGATTTAAGTGTAAAACATTACATCCTACTTCATTTATTGAGCCTGGA
AAAATGGAAACTAAAGAAGTTGATTTGGATTTAATTTTTACTGCAGAAACACACAATATG
CCTACAACTGTGGCTCCTTTTCCCGGTGCAACTACAGGCACAGGAGGACGAATTAGAGAT
GTTCAAGGTGTTGGTAGAGGTGGTCATACAATTGCAGGTACTGCTGGATATTGTGTTGGA
GTTTTAAACATTCCTGACTATCATTTGCCATACGAAACTCAAAATCAACTCTATCCACCA
TCATTTGCTAGTCCTTTAAAGATCATAATCGAAGCTAGTAATGGTGCATCAGATTATGGC
AATAAATTTGGTGAGCCTGTGCTTTCTGGTTTTGCAATTTCTTATGGCCTAACAAATGCA
CAAAACGAGCGTGATGAATATGTCAAATCAATAATGTTTAGTGGAGGTTTAGGTACAATG
GATGGTACATATCATAGAAAAAAGATAGATCCAGAACGTGGCATGTTGTTAGCTAAAATT
GGTGGTCCTGTTTACAGAATTGGAGTTGGGGGAGGTGCAGCAAGTTCAGTTGAAGTTCAA
GGTGATAATAAATGTGAACTTGATTTTAATGCAGTGCAACGAGGTGATGCAGAAATGGAA
AATAAATTAAATCGAGTTGTGCGAGCATGCATTGAAATGGGAGATGAAAATCCAATTCTT
GCTATTCATGATCAAGGTGCTGGCGGAAATGGAAATGTCTTAAAAGAGTTAGTTGAACCA
AATTATGCCGGAGCAGTGATTTTTTCAAAAGAATTTCAATTAGGTGATCCCACTATCAAT
GCTTTAGAATTGTGGGCAGCAGAATATCAGGAAAACAACGCTATTTTATGCAAACCAGAA
GATAGAAAACTTCTTACCGATATTTGTGAACGTGAACGTTGTCCAATCAATTTTGTAGGA
GTTGTTACAGGTAATGGATATGTAACACTCATTGAAGAAAAAGCTGATTTCAAAAAATAT
CTCGATCGTGAAAATATTCCGAGTGATGTGCCTTTCGATATGAATTTAAAATATGTGTTA
GGTGAAATGCCACGCAAAGTTTTTGATCTTGAAAGAAAAAAGAAATCTCTTATGCCTTTG
AAATTTTTGGATGATGATTGTCATTATCAAAATTATTTAGATCGAGTACTTAGTATTCTT
GCAGTAGGAAGTAAGAGATTTCTCACAAATAAAGTTGATCGATGTGTCACTGGTTTAATT
GTGCAACAACAATGTGTTGGTCCACTTCATACACCACTTGCTGATTATGCATTAACTCTA
ACTTCACATTTCGAGAAAAATGGCATTGCAACTTCAATTGGTACACAGCCTATTAAAGGA
TTAATTAATGCAGAAGCTGGTGCAAGAATGTCAATTGCTGAAGCAATTTCAAATTTAGTG
TTTGTTAAAATTACTGAGCTTGCAGATGTCAAATGTTCTGGTAATTGGATGTGGGCAGCT
AAACTACCAGGTGAAGGCGCAAAAATGTATGATGCATGTAAAGCAATGTGTGAAATGATG
AAAGAATTGAATATAGCAGTTGATGGTGGCAAAGATTCTCTCTCAATGGCAGCTAGAGTT
AGTGGAGAAACTGTAAAATCGCCAGGAACTTTAGTAATTTCAACATACGCTCCTTGTCCT
GATGTCACTCTAAGAATCACTCCTGATTTAAAAGCTCCTTCAGAAAATAAAGTTGGTGAA
TTAATTTGGATTAATATTGATGGAAAATTCCGATTAGGTGCTAGTGCTTTAGCTCAATCA
TTGAAACAACAAGGAAATGATTCACCAGATATAGAAAATGTTATTGCATTGAAGAATGCT
TTTAATGTGACTCAAAAACTTCTTGAGAAAAAACTACTCTTATCTGGTCATGATATAAGT
GATGGAGGTTTGATCGTTTGCCTAATTGAAATGGCAATTGGAGGAATGTGTGGAATCAGT
GTAGATTTGAAAAATGCTATGAAAATTTTTAAACTCGAAGAGACATCGATTGAAAATGTT
CTGAAAATTCTCTTTGCTGAAGAATGTGGATGGATTTTGGAATGCAAAAGTGAACATTTA
AAAACAATTCTCGATGAATATAAAAACTCTAATGTGAATGCAATTCATATTGGAAAATCT
AAAGATTTTGGAATGCAATCTCGAATTAAAATTATGTTTGAAAATTTTTCAATAATTGAC
ATGACTACACTAGAAGCAATTAAAAAATGGGAACGTACAAGTTTTGAATTTGAAAAACTT
CAAATGAATCTAAAATGTGCAGAGGAAGAATATAATTCATATGATTTAAGATCTGGTCCC
AAATATTTTCTTTCATTTAATCCTGATGATGCTATAAAATTGCTTAAAAAACCATCTGAT
CCTTGGCGTGTTGCAGTTATACGTGAAGAAGGCGTGAATGGAGATCGAGAAATGATTGCA
GCTTTATTAAAGGCTAATTTTGAAGTTTATGATGTTACTATGAGTGACTTGCTTGACAGA
AAAGCTTTTCTTGAAAATTATCGTGGAATAATTTTCCCTGGAGGTTTCAGTTATGCCGAC
ACACTTGGTTCAGCAAAAGGATGGGCTGCAAGCATACGATTTAGTGACTTATTACAACCA
CAGTTTGAAAACTTTAAGATTCGAAAAGACACATTTTCACTTGGTGTATGCAATGGTTGT
CAATTGATGAGCTTGATAGGATGGATTGATTATGAAGAAAATTCTACAAATGATGATGTT
CCTTCGATCGCTCTATTGCATAATAAATCTGGTAGATTTGAATGTCGTTGGAGCACATTG
AAAGTTGCTTCAAGTAATGCAATAATGTTAAGACGAATGCAAGGAAGCGTTTTGGGATGT
TGGGTCGCACATGGAGAAGGTCGATTCTCATTCAAAAATCAACAGGTGCTGAAAAATCTC
AAAGCATCAAATTCAATTGCTCTTCATTATGTAGATGACGATATGAAACCTACTGAAAAA
TATCCATTAAATCCAAACGGTAGTGTTGAAGGAATTGCTGCAATTTGCTCAAAAGATGGT
CGTCATTTGGCTATGATGCCTCATCCAGAGAGATGTTGTGAAATGTTCCAATGGCCATTT
TTACCATCAGATTTTAAAACTGAAAATTGCCCATGGCAATCAATGTTCAATGAAGCAAAT
ATTTGGTGTTGCGAAAACAAACAAAACTAA
>g5609.t1 Gene=g5609 Length=1349
MPISRFYNLIAFDEAKINTILKDLRKIYDNISCVKTEKSFHVELIEGHSLSNEDEKKLRW
ILKNTQEKDNLTKEPSLKASKKNHILIEIGPRFNFSTAESTNSVSICHSIHLTSIIRIET
SIRYLIELDENSKLLTAEDELILVDHLSDRMTQCRYTDENIPHDSFDERLPKEKESWFYV
PVLTQGRKALQEVNSKMGLAFDNWDLDYYTDLFTNVLKRDPTSTELFDCAQSNSEHSRHW
FFKGRMIIDGKEEEKSLIKMIIDTQNYSNQNNTIKFSDNSSAIKGFKCKTLHPTSFIEPG
KMETKEVDLDLIFTAETHNMPTTVAPFPGATTGTGGRIRDVQGVGRGGHTIAGTAGYCVG
VLNIPDYHLPYETQNQLYPPSFASPLKIIIEASNGASDYGNKFGEPVLSGFAISYGLTNA
QNERDEYVKSIMFSGGLGTMDGTYHRKKIDPERGMLLAKIGGPVYRIGVGGGAASSVEVQ
GDNKCELDFNAVQRGDAEMENKLNRVVRACIEMGDENPILAIHDQGAGGNGNVLKELVEP
NYAGAVIFSKEFQLGDPTINALELWAAEYQENNAILCKPEDRKLLTDICERERCPINFVG
VVTGNGYVTLIEEKADFKKYLDRENIPSDVPFDMNLKYVLGEMPRKVFDLERKKKSLMPL
KFLDDDCHYQNYLDRVLSILAVGSKRFLTNKVDRCVTGLIVQQQCVGPLHTPLADYALTL
TSHFEKNGIATSIGTQPIKGLINAEAGARMSIAEAISNLVFVKITELADVKCSGNWMWAA
KLPGEGAKMYDACKAMCEMMKELNIAVDGGKDSLSMAARVSGETVKSPGTLVISTYAPCP
DVTLRITPDLKAPSENKVGELIWINIDGKFRLGASALAQSLKQQGNDSPDIENVIALKNA
FNVTQKLLEKKLLLSGHDISDGGLIVCLIEMAIGGMCGISVDLKNAMKIFKLEETSIENV
LKILFAEECGWILECKSEHLKTILDEYKNSNVNAIHIGKSKDFGMQSRIKIMFENFSIID
MTTLEAIKKWERTSFEFEKLQMNLKCAEEEYNSYDLRSGPKYFLSFNPDDAIKLLKKPSD
PWRVAVIREEGVNGDREMIAALLKANFEVYDVTMSDLLDRKAFLENYRGIIFPGGFSYAD
TLGSAKGWAASIRFSDLLQPQFENFKIRKDTFSLGVCNGCQLMSLIGWIDYEENSTNDDV
PSIALLHNKSGRFECRWSTLKVASSNAIMLRRMQGSVLGCWVAHGEGRFSFKNQQVLKNL
KASNSIALHYVDDDMKPTEKYPLNPNGSVEGIAAICSKDGRHLAMMPHPERCCEMFQWPF
LPSDFKTENCPWQSMFNEANIWCCENKQN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 24 | g5609.t1 | CDD | cd02203 | PurL_repeat1 | 225 | 610 | 9.74233E-111 |
| 22 | g5609.t1 | CDD | cd02204 | PurL_repeat2 | 715 | 999 | 3.16827E-73 |
| 23 | g5609.t1 | CDD | cd01740 | GATase1_FGAR_AT | 1084 | 1336 | 3.73532E-98 |
| 21 | g5609.t1 | Coils | Coil | Coil | 1037 | 1057 | - |
| 18 | g5609.t1 | Gene3D | G3DSA:1.10.8.750 | - | 172 | 233 | 2.0E-19 |
| 19 | g5609.t1 | Gene3D | G3DSA:3.30.1330.10 | - | 234 | 442 | 1.4E-34 |
| 16 | g5609.t1 | Gene3D | G3DSA:3.90.650.10 | - | 443 | 619 | 1.2E-44 |
| 20 | g5609.t1 | Gene3D | G3DSA:3.30.1330.10 | - | 652 | 839 | 5.4E-26 |
| 15 | g5609.t1 | Gene3D | G3DSA:3.90.650.10 | - | 849 | 1024 | 2.6E-25 |
| 17 | g5609.t1 | Gene3D | G3DSA:3.40.50.880 | - | 1025 | 1344 | 4.5E-116 |
| 7 | g5609.t1 | Hamap | MF_00419 | Phosphoribosylformylglycinamidine synthase [purL]. | 3 | 1344 | 19.026009 |
| 6 | g5609.t1 | PANTHER | PTHR10099 | PHOSPHORIBOSYLFORMYLGLYCINAMIDINE SYNTHASE | 10 | 1343 | 0.0 |
| 1 | g5609.t1 | Pfam | PF18076 | Formylglycinamide ribonucleotide amidotransferase N-terminal | 47 | 165 | 3.3E-13 |
| 3 | g5609.t1 | Pfam | PF18072 | Formylglycinamide ribonucleotide amidotransferase linker domain | 190 | 239 | 1.7E-9 |
| 4 | g5609.t1 | Pfam | PF02769 | AIR synthase related protein, C-terminal domain | 455 | 609 | 1.8E-21 |
| 5 | g5609.t1 | Pfam | PF02769 | AIR synthase related protein, C-terminal domain | 873 | 999 | 1.1E-12 |
| 2 | g5609.t1 | Pfam | PF13507 | CobB/CobQ-like glutamine amidotransferase domain | 1083 | 1343 | 2.4E-100 |
| 27 | g5609.t1 | ProSiteProfiles | PS51273 | Glutamine amidotransferase type 1 domain profile. | 1084 | 1335 | 13.371 |
| 25 | g5609.t1 | SMART | SM01211 | GATase_5_2 | 1081 | 1343 | 6.3E-128 |
| 8 | g5609.t1 | SUPERFAMILY | SSF82697 | PurS-like | 4 | 167 | 1.2E-28 |
| 14 | g5609.t1 | SUPERFAMILY | SSF109736 | FGAM synthase PurL, linker domain | 175 | 240 | 4.58E-16 |
| 12 | g5609.t1 | SUPERFAMILY | SSF55326 | PurM N-terminal domain-like | 241 | 443 | 1.12E-42 |
| 9 | g5609.t1 | SUPERFAMILY | SSF56042 | PurM C-terminal domain-like | 452 | 690 | 2.84E-34 |
| 11 | g5609.t1 | SUPERFAMILY | SSF55326 | PurM N-terminal domain-like | 665 | 847 | 2.62E-55 |
| 10 | g5609.t1 | SUPERFAMILY | SSF56042 | PurM C-terminal domain-like | 861 | 1054 | 2.24E-36 |
| 13 | g5609.t1 | SUPERFAMILY | SSF52317 | Class I glutamine amidotransferase-like | 1079 | 1343 | 4.42E-90 |
| 26 | g5609.t1 | TIGRFAM | TIGR01735 | FGAM_synt: phosphoribosylformylglycinamidine synthase | 11 | 1342 | 0.0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5609/g5609.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5609.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0004642 | phosphoribosylformylglycinamidine synthase activity | MF |
| GO:0006189 | ‘de novo’ IMP biosynthetic process | BP |
KEGG
Orthology
- This transcript has been annotated with K01952 (phosphoribosylformylglycinamidine synthase)
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.
