General information for g1978.t16
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Adenylosuccinate synthetase.
Parent gene
- The parent gene g1978 is located on chr_3: 14175617..14176064 (+ 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_3 | g1978 | g1978.t16 | TSS | g1978.t16 | 14170301 | 14170301 |
| chr_3 | g1978 | g1978.t16 | isoform | g1978.t16 | 14170363 | 14174042 |
| chr_3 | g1978 | g1978.t16 | exon | g1978.t16.exon1 | 14170363 | 14170572 |
| chr_3 | g1978 | g1978.t16 | cds | g1978.t16.CDS1 | 14170363 | 14170572 |
| chr_3 | g1978 | g1978.t16 | exon | g1978.t16.exon2 | 14171681 | 14171783 |
| chr_3 | g1978 | g1978.t16 | cds | g1978.t16.CDS2 | 14171681 | 14171783 |
| chr_3 | g1978 | g1978.t16 | exon | g1978.t16.exon3 | 14172083 | 14172368 |
| chr_3 | g1978 | g1978.t16 | cds | g1978.t16.CDS3 | 14172083 | 14172368 |
| chr_3 | g1978 | g1978.t16 | exon | g1978.t16.exon4 | 14172471 | 14172636 |
| chr_3 | g1978 | g1978.t16 | cds | g1978.t16.CDS4 | 14172471 | 14172636 |
| chr_3 | g1978 | g1978.t16 | exon | g1978.t16.exon5 | 14172807 | 14172973 |
| chr_3 | g1978 | g1978.t16 | cds | g1978.t16.CDS5 | 14172807 | 14172836 |
| chr_3 | g1978 | g1978.t16 | exon | g1978.t16.exon6 | 14173051 | 14173235 |
| chr_3 | g1978 | g1978.t16 | exon | g1978.t16.exon7 | 14173296 | 14174042 |
| chr_3 | g1978 | g1978.t16 | TTS | g1978.t16 | 14174000 | 14174000 |
Sequences
>g1978.t16 Gene=g1978 Length=1864
ATGGCATCATCAACGCTAAATGGAGAAATCAATAATATAAACTACACAGATGATGTTATT
TCCCGTAATCGTTCTGGATCTTTAACTGGATCAGTTAGTAGTTATTCAAACAAGGTTTTA
GTAGTACTCGGTGCACAATGGGGAGATGAAGGGAAGGGAAAAGTCGTGGATATGCTTTCA
GTCAACGCTGACGTTGTTTGTAGATGTCAAGGCGGTAATAATGCAGGACATACAGTTGTC
GTTGATGGAAAGGAATTTGATTTTCATCTTTTGCCGAGTGGAATAATCAATGAAAAAAGC
ATATCTATAATTGGCAATGGAGTTGTTGTACATCTTCCTGGCTTATTTGAGGAATTGGCA
AAGAATGAGGCAAAAGGCTTATCAGATTGGCAAAATCGTTTGATTGTCTCTGACAGAGCT
CATTTGGTTTTTGATTTTCATCAACAAGTTGATGGATTGCAAGAGGCAGAAAAATGTAGA
GAAGGAAAATCACTTGGCACAACGAAAAAGGGCATTGGTCCAGCCTATTCTTCGAAAGCC
ACACGTAATGGCATTCGAGTTGGAGACTTGCTTGGTGATTTCAACACATTTAGTGACAAA
TTTCGTTCAATTGTTGCTACTCATCAACGTTTGTTTCCTGGCTGTGTCGTTGATGTTGAA
GCAGAACTCACTCGATATCAACAGTATGCTGAAAAATTACGACCTTATGTGAAAGACACC
ATCTTTTATCTTCATTCTGGTAATTTTAAAAACCAAACAAGCATCATATCGATTTTGGAA
CATATCCTTATGTGACGAGTAGTAATTGCTCAATCGGTGGCGTTTTAACAGGTCTCGGTT
TGCCGCCAAAAGTTATTGGAGAAGTCATTGGTGTTGTTAAGTCATATACGACAAGAGTCG
GTGATGGACCATTCCCCACAGAATTAAAAGATGACATTGGTGAACTTTTACAAACGCGTG
GTGGAGAAATTGGTGTCACAACAAAACGAAAACGTCGTTGTGGTTGGTTGGATTTACCTG
TGTTACGATATACCTCACTTGTCAATGGTTATTCAGCAATTTGCTTAACGAAACTTGATA
TCCTTGATACTTTGCCTACAATTAAAATTGGCATCAATTATAAATTACATAACAAAACGA
TCTACAATTTTCCTGGATCTATTTCTGATTTGGCTCAAGTTGAGGTCGAATATGTTACAC
TCCCTGGTTGGCAACAATCGACTGCAAATATTCGCGACTTTCGTGACCTACCCGAAAATG
CACAAAACTATGTGCGATTTATTGAGAAGGATTTGGATGTTCCAATTAAGTGGATTGGAG
TTGGAAAAGGGCGAGAATCAATTATTAAAGTATATTAAAAACATGTGCAGTATTGCACTT
AAAATTACTTATTTTTTTAACTTGATAAATTCTTCAGAAACCAAATGAGATATAGCCCTT
TCCTATTTTGTTAAAACACTCTCTTTTATAAAAGAGCCTTAAATATTTTTTTTATAAAAT
TAAATTGTAAATGATCATTTTGATTGTGAACAAGAATTAACATTTTGAGGGAGCTTAATG
GCTTTTAAATACTTAAATTTTTATCTTAATAGTAATAATTTAGCCAAGAACAGTAATCGC
ACATGCACACAACAAACACTATACTTAAATTGCTATTACTTATAATTAGCATATGATACA
CTTTAAATAATCAATTCCAATGTGAAAAAAAATTTGAATGTTAAGAAAATATCTTTGTTT
GATGCAATGAACAGAAACTTATAGAGACGAGATATGCTAAACTTGCTATATTTTAAATAA
ATTTTTAATTGTCCTTTAAAACAAAAAAAACTTTTATTTTAATTTAGAAAATATAATTAA
CAGT
>g1978.t16 Gene=g1978 Length=264
MASSTLNGEINNINYTDDVISRNRSGSLTGSVSSYSNKVLVVLGAQWGDEGKGKVVDMLS
VNADVVCRCQGGNNAGHTVVVDGKEFDFHLLPSGIINEKSISIIGNGVVVHLPGLFEELA
KNEAKGLSDWQNRLIVSDRAHLVFDFHQQVDGLQEAEKCREGKSLGTTKKGIGPAYSSKA
TRNGIRVGDLLGDFNTFSDKFRSIVATHQRLFPGCVVDVEAELTRYQQYAEKLRPYVKDT
IFYLHSGNFKNQTSIISILEHILM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g1978.t16 | Gene3D | G3DSA:3.40.440.10 | Adenylosuccinate Synthetase | 41 | 255 | 2.8E-85 |
| 10 | g1978.t16 | Gene3D | G3DSA:1.10.300.10 | Adenylosuccinate Synthetase | 138 | 236 | 2.8E-85 |
| 4 | g1978.t16 | Hamap | MF_00011 | Adenylosuccinate synthetase [purA]. | 1 | 264 | 80.9235 |
| 2 | g1978.t16 | PANTHER | PTHR11846 | ADENYLOSUCCINATE SYNTHETASE | 28 | 246 | 7.4E-100 |
| 3 | g1978.t16 | PANTHER | PTHR11846:SF2 | ADENYLOSUCCINATE SYNTHETASE ISOZYME 1 | 28 | 246 | 7.4E-100 |
| 1 | g1978.t16 | Pfam | PF00709 | Adenylosuccinate synthetase | 41 | 248 | 1.7E-78 |
| 7 | g1978.t16 | ProSitePatterns | PS01266 | Adenylosuccinate synthetase GTP-binding site. | 46 | 53 | - |
| 8 | g1978.t16 | ProSitePatterns | PS00513 | Adenylosuccinate synthetase active site. | 171 | 182 | - |
| 6 | g1978.t16 | SMART | SM00788 | adenylsucc_synt | 39 | 264 | 3.5E-44 |
| 5 | g1978.t16 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 37 | 255 | 5.42E-69 |
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:0006164 | purine nucleotide biosynthetic process | BP |
| GO:0005525 | GTP binding | MF |
| GO:0004019 | adenylosuccinate synthase activity | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
