General information for g13092.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Argininosuccinate synthase.
Parent gene
- The parent gene g13092 is located on chr_1: 27920798..27921607 (+ 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 | g13092 | g13092.t4 | TSS | g13092.t4 | 27919610 | 27919610 |
| chr_1 | g13092 | g13092.t4 | isoform | g13092.t4 | 27919647 | 27921607 |
| chr_1 | g13092 | g13092.t4 | exon | g13092.t4.exon1 | 27919647 | 27919799 |
| chr_1 | g13092 | g13092.t4 | cds | g13092.t4.CDS1 | 27919647 | 27919799 |
| chr_1 | g13092 | g13092.t4 | exon | g13092.t4.exon2 | 27919871 | 27920030 |
| chr_1 | g13092 | g13092.t4 | cds | g13092.t4.CDS2 | 27919871 | 27920030 |
| chr_1 | g13092 | g13092.t4 | exon | g13092.t4.exon3 | 27920115 | 27920224 |
| chr_1 | g13092 | g13092.t4 | cds | g13092.t4.CDS3 | 27920115 | 27920224 |
| chr_1 | g13092 | g13092.t4 | exon | g13092.t4.exon4 | 27920345 | 27920696 |
| chr_1 | g13092 | g13092.t4 | cds | g13092.t4.CDS4 | 27920345 | 27920696 |
| chr_1 | g13092 | g13092.t4 | exon | g13092.t4.exon5 | 27920790 | 27921607 |
| chr_1 | g13092 | g13092.t4 | cds | g13092.t4.CDS5 | 27920790 | 27921298 |
| chr_1 | g13092 | g13092.t4 | TTS | g13092.t4 | 27921600 | 27921600 |
Sequences
>g13092.t4 Gene=g13092 Length=1593
ATGGAAAAGGAGAATAAAAAAGTTTTGCTGGCATATTCAGGTGGATTGGATACTAGTTGC
ATACTAAAATGGCTTCTCGAAAAAGGCTATGAGGTAATTTGTTTCATGGCAGACGTTGGA
CAAGATGAAGATTTTCAGCAAGCACGAGATAAAGCACTTAAAATTGGTGCAAGTGATTGT
GTTGTCAAGGATGTTAAATTTCACTTCGTTGAAAATTTTGTTTGGCCAGCCATAAAAATG
GGACTGATTTACGAGAAGCGATATTTAATGGGAACTTCATTGGCTAGGCCTTGCATTACA
TTGGCTTTGATAGAGACTGCAAAAGAGCATAATTGTGCATACATTTCTCATGGTGCTACT
GGAAAAGGCAACGATCAAATACGTTTTGAATTATCTGCCTATGCTTTGAATCCCGCTATT
AAGGTCATTGCTGTTTGGCGATTGCCAGAATTTTGCGAGAGATTCCAAGGGCGAAACGAT
TTGCTCGAATATGCAAAAGAAAATTCAATTCCTGTAGCTGCTACTTTGAAGAAACCGTGG
AGTATGGATGCAAATATCATGCATATAAGCTATGAATCGGGAATTCTAGAAGATCCCTCA
CAATCAGCACCTGATGATCTTTACACTATGACCAAAAATCCTCAACATGCACCCAACAAT
CCAACTCGAATTGACATTGTTTTCAATCACGGCATACCTGTGCGTTGCACTAACTTGACA
ACGGGAAATACTTATGAAATTCCGACACATATTCTGCAATATTTGAATCAAATTGGTGAA
CACGGAATCGGACGCGTAGATCTAGTTGAAAATCGATTTGTTGGTCTAAAGTCACGTGGC
ATATATGAAACTCCTGGCTGTAAAATTCTCTATGAAGCACACCTTGATTTAGAGGTCTAT
TGTCTAGATCGAGAAATTTTTCGCGTGAAGAGCTTTTTGGCGGACAAGATGGCTGAATAT
GTGTACAATGGATTTTGGTTCTCGCCTGAAGCCGAATATGTTAGAAAATGTTTGGATGAG
TCGCAACGATCTGTTAATGGACGTGTTACAATAGAGCTTTTTAAAGGAAATGTTTCAATT
ATTGGACGTGAATCAATAAGCTCATTGTACAATCAAGAACTAGTTTCAATGAATGTCCAT
GGACAGCTCGATTATACTGCTGCAACAGGCTTCATAGAAATCAACGCTATTCGTCTAAAA
GAGCATTATCGTGCATATGGTTCAACTCCAAATAATAATATGCATAGCTTGAATCGTAAA
TTTTCACGTGTCAAATTAAATTGATGTTTACACCTTTTTCTCAGTTCATCACCATTAAAT
ACTGCTGCAATTAAGAACATGAGCAAATACAAAAAATTTCATAATTCAACGAGCTTTAAT
CTGTCTGTCGTCTCGTTAGTACTAAATAAAATGTAAAATATGAGTAATATGCATCATGAA
AAGAGGATTATTAAGTGTAAAAGACCAATGTGGGAATCACTCTTAACATCTTCATCGCAT
GGGTCTCCTCTTCAAGCAGCGTGTGCTTTGTAATTAATGATGTAAAAATGAACTATGAAT
AAAGATGTTTAAAACATATAAATTATAATTCTA
>g13092.t4 Gene=g13092 Length=427
MEKENKKVLLAYSGGLDTSCILKWLLEKGYEVICFMADVGQDEDFQQARDKALKIGASDC
VVKDVKFHFVENFVWPAIKMGLIYEKRYLMGTSLARPCITLALIETAKEHNCAYISHGAT
GKGNDQIRFELSAYALNPAIKVIAVWRLPEFCERFQGRNDLLEYAKENSIPVAATLKKPW
SMDANIMHISYESGILEDPSQSAPDDLYTMTKNPQHAPNNPTRIDIVFNHGIPVRCTNLT
TGNTYEIPTHILQYLNQIGEHGIGRVDLVENRFVGLKSRGIYETPGCKILYEAHLDLEVY
CLDREIFRVKSFLADKMAEYVYNGFWFSPEAEYVRKCLDESQRSVNGRVTIELFKGNVSI
IGRESISSLYNQELVSMNVHGQLDYTAATGFIEINAIRLKEHYRAYGSTPNNNMHSLNRK
FSRVKLN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g13092.t4 | CDD | cd01999 | Argininosuccinate_Synthase | 8 | 398 | 0.0 |
| 7 | g13092.t4 | Gene3D | G3DSA:3.40.50.620 | HUPs | 1 | 180 | 6.0E-69 |
| 8 | g13092.t4 | Gene3D | G3DSA:3.90.1260.10 | Argininosuccinate synthetase | 181 | 371 | 1.3E-75 |
| 9 | g13092.t4 | Gene3D | G3DSA:1.20.5.470 | Single helix bin | 372 | 407 | 2.2E-12 |
| 4 | g13092.t4 | Hamap | MF_00005 | Argininosuccinate synthase [argG]. | 5 | 407 | 43.127075 |
| 2 | g13092.t4 | PANTHER | PTHR11587 | ARGININOSUCCINATE SYNTHASE | 4 | 405 | 3.6E-170 |
| 3 | g13092.t4 | PANTHER | PTHR11587:SF2 | ARGININOSUCCINATE SYNTHASE | 4 | 405 | 3.6E-170 |
| 1 | g13092.t4 | Pfam | PF00764 | Arginosuccinate synthase | 10 | 401 | 3.6E-146 |
| 12 | g13092.t4 | ProSitePatterns | PS00564 | Argininosuccinate synthase signature 1. | 11 | 19 | - |
| 11 | g13092.t4 | ProSitePatterns | PS00565 | Argininosuccinate synthase signature 2. | 118 | 129 | - |
| 6 | g13092.t4 | SUPERFAMILY | SSF52402 | Adenine nucleotide alpha hydrolases-like | 3 | 176 | 1.85E-45 |
| 5 | g13092.t4 | SUPERFAMILY | SSF69864 | Argininosuccinate synthetase, C-terminal domain | 177 | 405 | 1.83E-80 |
| 13 | g13092.t4 | TIGRFAM | TIGR00032 | argG: argininosuccinate synthase | 7 | 402 | 1.9E-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:0005524 | ATP binding | MF |
| GO:0004055 | argininosuccinate synthase activity | MF |
| GO:0006526 | arginine biosynthetic process | BP |
KEGG
Orthology
- This transcript has been annotated with K01940 (argininosuccinate 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. There were no conditions that were differentially expressed