General information for g5733.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Septin-1.
Parent gene
- The parent gene g5733 is located on chr_2: 11449716..11450411 (+ 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 | g5733 | g5733.t4 | TSS | g5733.t4 | 11447475 | 11447475 |
| chr_2 | g5733 | g5733.t4 | isoform | g5733.t4 | 11447678 | 11450411 |
| chr_2 | g5733 | g5733.t4 | exon | g5733.t4.exon1 | 11447678 | 11447695 |
| chr_2 | g5733 | g5733.t4 | cds | g5733.t4.CDS1 | 11447678 | 11447695 |
| chr_2 | g5733 | g5733.t4 | exon | g5733.t4.exon2 | 11448708 | 11449512 |
| chr_2 | g5733 | g5733.t4 | cds | g5733.t4.CDS2 | 11448708 | 11449512 |
| chr_2 | g5733 | g5733.t4 | exon | g5733.t4.exon3 | 11449634 | 11450411 |
| chr_2 | g5733 | g5733.t4 | cds | g5733.t4.CDS3 | 11449634 | 11449662 |
| chr_2 | g5733 | g5733.t4 | TTS | g5733.t4 | NA | NA |
Sequences
>g5733.t4 Gene=g5733 Length=1601
ATGTCTGCTGACAAACAATTTTCTGCAATGGATACATCAGGTTATGTTGGTTTTGCTAAT
TTGCCAAATCAAGTACATCGAAAGTCAGTGAAAAAAGGATTCGAGTTCACATTGATGATT
GTTGGCGAAAGTGGACTAGGCAAATCAACCTTAGTCAACTCTCTATTTTTAACAGACTTG
TATCCAGAGAGAGTTGTTCCTGATGCCGTTGAGAGACAAAAACAAACTTTAAAATTGGAT
GCTTCTACAGTTGAGATTGAAGAACGTGGTGTTAAACTTCGTTTGACAGTAGTTGATGTG
CCAGGTTTTGGTGATGCCATTGATAATTCAAATAGTTTCAACTCAATTTTGGAGTATATT
GATGAGCAATATGAGAGATATTTAAGAGATGAAAGTGGTTTGAATCGTAGAAATATCGTT
GATAATCGTGTTCATTGCTGCTTCTATTTTATATCACCCTTTGGTCATGGGCTAAAACCA
CTTGACATTGAGTTTATGAAAAAGTTACATCTTAAAGTGAATATTGTTCCCGTGATTGCA
AAAGCAGATATGTTGACTAAGAAAGAAGTCAGTCGTTTAAAGATGAGAATTCTTGAAGAA
ATCAAAGAGAATGGTATTAAAATTTATCCATTACCCGATTGTGACTCAGACGAGGATGAA
GATTACAAAGAACAAGTTAGACAATTGAAAGAAGCCGTCCCTTTTGCAGTTTGTGGTTCA
ACTACCTTACTAGAAGTAAAAGGAAAAAAAGTCAGAGGTCGTTTATATCCATGGGGCGTA
GTTGAGGTGAAATTTATATTTTTTAACCTTATAAAAATTTTATTACTCATATGCAAGATT
TGCAAGAAGTAACACAAGAAGTTCATTATGAAAATTATCGTTCTGAGAGATTAGCAAAGG
CAAGTCGATCAAATGGAAAAGTGACAAATGGAACTAATGGACATCTCGCTAAAGAGGAAG
TCTTTGAGGATGATGCAGCAGAAAAGGATAGAATCCTAAAGGAAAAAGAAGCAGAATTAA
AAAGAATGCAGGAAATGTTAGCACAAATGCAAGCAAAAATTCAAGCGCAACAACAATAAT
TTATTTTAAAATTTTTATCTCATAAAAGAATACATTTCAAACAAGAAATATTTTAATGAC
AAGATCTTATTTAAAGAGATTTTATTTCATCCTAAAATTATATTATTGATTGTCATTATC
CCGCTTATATTTTATATGTTTTATATCAGCAATGCTATTCATCATATATTTTAATTAATT
TAGTATTTTTTTGTGCCAATATGTTTCTATATTACTTAATTCTAATATAGTCGAGCAGAA
TTTATGTAACTTCCGATTATATTTTATTGAGACAACTCACTCTTTGAAGACATTTCGAAA
ACAAATTTTCTATAGAAATGTACTTATGGACAAAAAAAATATTTCGATTATTTCCTCGAT
TTTAGCTTTTAAGAAAAAAGTTTAGAGATTTTAAGAGCATGCATTTGCTAAGCATTATAT
TTTTTCACTATATACATACAAAAATAAAGAATATCCACTTTCTTGAAAAATAATTTATTA
ATAATTTCAATTTAAAGTTTAATCTACATTATGTGATAAAT
>g5733.t4 Gene=g5733 Length=283
MSADKQFSAMDTSGYVGFANLPNQVHRKSVKKGFEFTLMIVGESGLGKSTLVNSLFLTDL
YPERVVPDAVERQKQTLKLDASTVEIEERGVKLRLTVVDVPGFGDAIDNSNSFNSILEYI
DEQYERYLRDESGLNRRNIVDNRVHCCFYFISPFGHGLKPLDIEFMKKLHLKVNIVPVIA
KADMLTKKEVSRLKMRILEEIKENGIKIYPLPDCDSDEDEDYKEQVRQLKEAVPFAVCGS
TTLLEVKGKKVRGRLYPWGVVEVKFIFFNLIKILLLICKICKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g5733.t4 | CDD | cd01850 | CDC_Septin | 32 | 263 | 3.33142E-132 |
| 5 | g5733.t4 | Gene3D | G3DSA:3.40.50.300 | - | 11 | 272 | 1.3E-94 |
| 2 | g5733.t4 | PANTHER | PTHR18884:SF71 | SEPTIN-4 | 11 | 263 | 1.8E-159 |
| 3 | g5733.t4 | PANTHER | PTHR18884 | SEPTIN | 11 | 263 | 1.8E-159 |
| 9 | g5733.t4 | PIRSF | PIRSF006698 | Septin | 1 | 269 | 5.6E-116 |
| 1 | g5733.t4 | Pfam | PF00735 | Septin | 32 | 264 | 6.8E-106 |
| 7 | g5733.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 254 | - |
| 8 | g5733.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 255 | 278 | - |
| 6 | g5733.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 279 | 283 | - |
| 12 | g5733.t4 | ProSiteProfiles | PS51719 | Septin-type guanine nucleotide-binding (G) domain profile. | 32 | 283 | 89.359 |
| 4 | g5733.t4 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 12 | 262 | 9.77E-27 |
| 11 | g5733.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 255 | 277 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5733/g5733.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5733.t4.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005525 | GTP binding | 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.
