General information for g5733.t1
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.t1 | TSS | g5733.t1 | 11447475 | 11447475 |
| chr_2 | g5733 | g5733.t1 | isoform | g5733.t1 | 11447678 | 11449889 |
| chr_2 | g5733 | g5733.t1 | exon | g5733.t1.exon1 | 11447678 | 11447695 |
| chr_2 | g5733 | g5733.t1 | cds | g5733.t1.CDS1 | 11447678 | 11447695 |
| chr_2 | g5733 | g5733.t1 | exon | g5733.t1.exon2 | 11448708 | 11449475 |
| chr_2 | g5733 | g5733.t1 | cds | g5733.t1.CDS2 | 11448708 | 11449475 |
| chr_2 | g5733 | g5733.t1 | exon | g5733.t1.exon3 | 11449530 | 11449579 |
| chr_2 | g5733 | g5733.t1 | cds | g5733.t1.CDS3 | 11449530 | 11449579 |
| chr_2 | g5733 | g5733.t1 | exon | g5733.t1.exon4 | 11449634 | 11449889 |
| chr_2 | g5733 | g5733.t1 | cds | g5733.t1.CDS4 | 11449634 | 11449889 |
| chr_2 | g5733 | g5733.t1 | TTS | g5733.t1 | 11450361 | 11450361 |
Sequences
>g5733.t1 Gene=g5733 Length=1092
ATGTCTGCTGACAAACAATTTTCTGCAATGGATACATCAGGTTATGTTGGTTTTGCTAAT
TTGCCAAATCAAGTACATCGAAAGTCAGTGAAAAAAGGATTCGAGTTCACATTGATGATT
GTTGGCGAAAGTGGACTAGGCAAATCAACCTTAGTCAACTCTCTATTTTTAACAGACTTG
TATCCAGAGAGAGTTGTTCCTGATGCCGTTGAGAGACAAAAACAAACTTTAAAATTGGAT
GCTTCTACAGTTGAGATTGAAGAACGTGGTGTTAAACTTCGTTTGACAGTAGTTGATGTG
CCAGGTTTTGGTGATGCCATTGATAATTCAAATAGTTTCAACTCAATTTTGGAGTATATT
GATGAGCAATATGAGAGATATTTAAGAGATGAAAGTGGTTTGAATCGTAGAAATATCGTT
GATAATCGTGTTCATTGCTGCTTCTATTTTATATCACCCTTTGGTCATGGGCTAAAACCA
CTTGACATTGAGTTTATGAAAAAGTTACATCTTAAAGTGAATATTGTTCCCGTGATTGCA
AAAGCAGATATGTTGACTAAGAAAGAAGTCAGTCGTTTAAAGATGAGAATTCTTGAAGAA
ATCAAAGAGAATGGTATTAAAATTTATCCATTACCCGATTGTGACTCAGACGAGGATGAA
GATTACAAAGAACAAGTTAGACAATTGAAAGAAGCCGTCCCTTTTGCAGTTTGTGGTTCA
ACTACCTTACTAGAAGTAAAAGGAAAAAAAGTCAGAGGTCGTTTATATCCATGGGGCGTA
GTTGAGGTTGAAAATCCTGAGCATTGCGATTTTATTAAACTTCGCACTATGTTGATTACT
CATATGCAAGATTTGCAAGAAGTAACACAAGAAGTTCATTATGAAAATTATCGTTCTGAG
AGATTAGCAAAGGCAAGTCGATCAAATGGAAAAGTGACAAATGGAACTAATGGACATCTC
GCTAAAGAGGAAGTCTTTGAGGATGATGCAGCAGAAAAGGATAGAATCCTAAAGGAAAAA
GAAGCAGAATTAAAAAGAATGCAGGAAATGTTAGCACAAATGCAAGCAAAAATTCAAGCG
CAACAACAATAA
>g5733.t1 Gene=g5733 Length=363
MSADKQFSAMDTSGYVGFANLPNQVHRKSVKKGFEFTLMIVGESGLGKSTLVNSLFLTDL
YPERVVPDAVERQKQTLKLDASTVEIEERGVKLRLTVVDVPGFGDAIDNSNSFNSILEYI
DEQYERYLRDESGLNRRNIVDNRVHCCFYFISPFGHGLKPLDIEFMKKLHLKVNIVPVIA
KADMLTKKEVSRLKMRILEEIKENGIKIYPLPDCDSDEDEDYKEQVRQLKEAVPFAVCGS
TTLLEVKGKKVRGRLYPWGVVEVENPEHCDFIKLRTMLITHMQDLQEVTQEVHYENYRSE
RLAKASRSNGKVTNGTNGHLAKEEVFEDDAAEKDRILKEKEAELKRMQEMLAQMQAKIQA
QQQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g5733.t1 | CDD | cd01850 | CDC_Septin | 32 | 302 | 1.30849E-163 |
| 6 | g5733.t1 | Coils | Coil | Coil | 330 | 363 | - |
| 5 | g5733.t1 | Gene3D | G3DSA:3.40.50.300 | - | 35 | 315 | 1.4E-117 |
| 2 | g5733.t1 | PANTHER | PTHR18884:SF71 | SEPTIN-4 | 11 | 359 | 8.0E-197 |
| 3 | g5733.t1 | PANTHER | PTHR18884 | SEPTIN | 11 | 359 | 8.0E-197 |
| 7 | g5733.t1 | PIRSF | PIRSF006698 | Septin | 1 | 363 | 4.3E-142 |
| 1 | g5733.t1 | Pfam | PF00735 | Septin | 32 | 308 | 1.5E-128 |
| 9 | g5733.t1 | ProSiteProfiles | PS51719 | Septin-type guanine nucleotide-binding (G) domain profile. | 32 | 304 | 112.387 |
| 4 | g5733.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 12 | 278 | 2.05E-28 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5733/g5733.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5733.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005525 | GTP binding | MF |
KEGG
Orthology
- This transcript has been annotated with K16942 (septin 2)
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.
