General information for g1858.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Complexin.
Parent gene
- The parent gene g1858 is located on chr_3: 13456758..13459140 (- 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 | g1858 | g1858.t1 | TTS | g1858.t1 | 13424018 | 13424018 |
| chr_3 | g1858 | g1858.t1 | isoform | g1858.t1 | 13424456 | 13457148 |
| chr_3 | g1858 | g1858.t1 | exon | g1858.t1.exon1 | 13424456 | 13424529 |
| chr_3 | g1858 | g1858.t1 | cds | g1858.t1.CDS1 | 13424456 | 13424529 |
| chr_3 | g1858 | g1858.t1 | exon | g1858.t1.exon2 | 13426552 | 13426684 |
| chr_3 | g1858 | g1858.t1 | cds | g1858.t1.CDS2 | 13426552 | 13426684 |
| chr_3 | g1858 | g1858.t1 | exon | g1858.t1.exon3 | 13434505 | 13434668 |
| chr_3 | g1858 | g1858.t1 | cds | g1858.t1.CDS3 | 13434505 | 13434668 |
| chr_3 | g1858 | g1858.t1 | exon | g1858.t1.exon4 | 13457094 | 13457148 |
| chr_3 | g1858 | g1858.t1 | cds | g1858.t1.CDS4 | 13457094 | 13457148 |
| chr_3 | g1858 | g1858.t1 | TSS | g1858.t1 | NA | NA |
Sequences
>g1858.t1 Gene=g1858 Length=426
ATGGCAGCATTCGTGGCTAAACAAATGGTTGGAAACAAGCTCAGCGCTGTTAAAGGAGCT
GTTGGTGGTGATGATCAGACTGATGAAGATAAGGAGAAGGCCGAGGAAGAAGAAAGAGAG
CGACTTGAAGCAATCCGAGAAGCTGAAGAGCGCCGAAAAGAGAAGCATCGCAAAATGGAA
GAGGAACGTGAAAAGATGCGTCAAGAGATAAGAGACAAATACAACATTAAGAAGAAGGAA
GAAATTGTGGAGCAACCTCCTCAAGAGGAACCCAATCCACTTATGAGGAAGAAAAAGACG
CCGGAAGAGTTGGCCGCTGAAGCTGAGGCTGAAGATCTTGACGATTTTACTAAATTGAAA
AATTCAATAGAAACACAAGTGAACGAATTAAAAACACAAATCGAAAGCAAATGTGTTATG
CAGTGA
>g1858.t1 Gene=g1858 Length=141
MAAFVAKQMVGNKLSAVKGAVGGDDQTDEDKEKAEEEERERLEAIREAEERRKEKHRKME
EEREKMRQEIRDKYNIKKKEEIVEQPPQEEPNPLMRKKKTPEELAAEAEAEDLDDFTKLK
NSIETQVNELKTQIESKCVMQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g1858.t1 | Coils | Coil | Coil | 27 | 76 | - |
| 8 | g1858.t1 | Coils | Coil | Coil | 113 | 133 | - |
| 7 | g1858.t1 | Gene3D | G3DSA:1.20.5.580 | Single Helix bin | 26 | 86 | 5.2E-19 |
| 5 | g1858.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 113 | - |
| 6 | g1858.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 23 | 113 | - |
| 2 | g1858.t1 | PANTHER | PTHR16705:SF4 | COMPLEXIN | 1 | 141 | 1.3E-46 |
| 3 | g1858.t1 | PANTHER | PTHR16705 | COMPLEXIN | 1 | 141 | 1.3E-46 |
| 1 | g1858.t1 | Pfam | PF05835 | Synaphin protein | 2 | 131 | 1.7E-41 |
| 4 | g1858.t1 | SUPERFAMILY | SSF58038 | SNARE fusion complex | 37 | 76 | 3.79E-12 |
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:0019905 | syntaxin binding | MF |
| GO:0006836 | neurotransmitter transport | BP |
KEGG
Orthology
- This transcript has been annotated with K15294 (complexin-1/2)
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.
