General information for g1978.t39
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t39 | isoform | g1978.t39 | 14172372 | 14174449 |
| chr_3 | g1978 | g1978.t39 | exon | g1978.t39.exon1 | 14172372 | 14173208 |
| chr_3 | g1978 | g1978.t39 | cds | g1978.t39.CDS1 | 14172653 | 14173186 |
| chr_3 | g1978 | g1978.t39 | exon | g1978.t39.exon2 | 14174162 | 14174253 |
| chr_3 | g1978 | g1978.t39 | exon | g1978.t39.exon3 | 14174329 | 14174449 |
| chr_3 | g1978 | g1978.t39 | TSS | g1978.t39 | NA | NA |
| chr_3 | g1978 | g1978.t39 | TTS | g1978.t39 | NA | NA |
Sequences
>g1978.t39 Gene=g1978 Length=1050
ATTTTTCATGATTAATTATTTATCATTTTCCTTGACAATTTGAAAAATGTTCAATTATTT
ACATACAAAAATACCTTTTCTTTTTATATCTATGCATAGATTTCGTTCAATTGTTGCTAC
TCATCAACGTTTGTTTCCTGGCTGTGTCGTTGATGTTGAAGCAGAACTCACTCGATATCA
ACAGTATGCTGAAAAATTACGACCTTATGTGAAAGACACCATCTTTTATCTTCATTCTGG
TAATTTTAAAAACCAAACAAGCATCGTCAATTTCATTCTAAATGTGTAAACATTTAACTC
GTTTAGCATTGCGAAATGGCAAGACTGTTTTGGTCGAAGGAGCAAATGCGGCAATGTTGG
GTGAGTATATTCATTCATTTTCAATTTGCATGCATAAAGGAATTGTCAAAACAAATTATC
ATTGTCTTTTTTTAGATATCGATTTTGGAACATATCCTTATGTGACGAGTAGTAATTGCT
CAATCGGTGGCGTTTTAACAGGTCTCGGTTTGCCGCCAAAAGTTATTGGAGAAGTCATTG
GTGTTGTTAAGTCATATACGACAAGAGTCGGTGATGGACCATTCCCCACAGAATTAAAAG
ATGTAATTACCACCTTATTAAATTTATTTTTAGTGGTCTATTTTTATGAATTCATCACGT
ATGCTTCTTTTTTTCATAGGACATTGGTGAACTTTTACAAACGCGTGGTGGAGAAATTGG
TGTCACAACAAAACGAAAACGTCGTTGTGGTTGGTTGGATTTACCTGTGTTACGATATAC
CTCACTTGTCAATGGTTATTCAGCAATTTGCTTAACGAAACTTGATATCCTTGATACTCT
CACCAAAGTGAATAAAAATTGTCAAAAAGTTCCAGGTTGGAATTTTTTCATTATTTTAAA
ATACTGCGTTAATTGATAAGTTAGCTAAGTTATTGAGAAACAGTCAATTTGTTATTTTGG
TGAAAATGTTCGAGAGTTGAAGATATGCTGGCCCTGAAAATTAGTCTCTCATATGTAGTG
TATAGCCACTATACTGCTTTATATTTTAAA
>g1978.t39 Gene=g1978 Length=177
MCKHLTRLALRNGKTVLVEGANAAMLGEYIHSFSICMHKGIVKTNYHCLFLDIDFGTYPY
VTSSNCSIGGVLTGLGLPPKVIGEVIGVVKSYTTRVGDGPFPTELKDVITTLLNLFLVVY
FYEFITYASFFHRTLVNFYKRVVEKLVSQQNENVVVVGWIYLCYDIPHLSMVIQQFA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g1978.t39 | Gene3D | G3DSA:3.40.440.10 | Adenylosuccinate Synthetase | 34 | 126 | 3.5E-26 |
| 2 | g1978.t39 | PANTHER | PTHR11846 | ADENYLOSUCCINATE SYNTHETASE | 48 | 113 | 2.2E-28 |
| 1 | g1978.t39 | Pfam | PF00709 | Adenylosuccinate synthetase | 49 | 111 | 1.1E-26 |
| 9 | g1978.t39 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 107 | - |
| 10 | g1978.t39 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 108 | 131 | - |
| 8 | g1978.t39 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 132 | 177 | - |
| 6 | g1978.t39 | SMART | SM00788 | adenylsucc_synt | 8 | 156 | 4.4E-8 |
| 5 | g1978.t39 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 39 | 114 | 2.34E-25 |
| 3 | g1978.t39 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 67 | 89 | - |
| 4 | g1978.t39 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 109 | 131 | - |
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.
