General information for g1858.t4
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.t4 | isoform | g1858.t4 | 13423863 | 13434668 |
| chr_3 | g1858 | g1858.t4 | exon | g1858.t4.exon1 | 13423863 | 13424529 |
| chr_3 | g1858 | g1858.t4 | cds | g1858.t4.CDS1 | 13424456 | 13424529 |
| chr_3 | g1858 | g1858.t4 | exon | g1858.t4.exon2 | 13426552 | 13426684 |
| chr_3 | g1858 | g1858.t4 | cds | g1858.t4.CDS2 | 13426552 | 13426684 |
| chr_3 | g1858 | g1858.t4 | exon | g1858.t4.exon3 | 13434505 | 13434668 |
| chr_3 | g1858 | g1858.t4 | cds | g1858.t4.CDS3 | 13434505 | 13434549 |
| chr_3 | g1858 | g1858.t4 | TSS | g1858.t4 | NA | NA |
| chr_3 | g1858 | g1858.t4 | TTS | g1858.t4 | NA | NA |
Sequences
>g1858.t4 Gene=g1858 Length=964
GAGCTGTTGGTGGTGATGATCAGACTGATGAAGATAAGGAGAAGGCCGAGGAAGAAGAAA
GAGAGCGACTTGAAGCAATCCGAGAAGCTGAAGAGCGCCGAAAAGAGAAGCATCGCAAAA
TGGAAGAGGAACGTGAAAAGATGCGTCAAGAGATAAGAGACAAATACAACATTAAGAAGA
AGGAAGAAATTGTGGAGCAACCTCCTCAAGAGGAACCCAATCCACTTATGAGGAAGAAAA
AGACGCCGGAAGAGTTGGCCGCTGAAGCTGAGGCTGAAGATCTTGACGATTTTACTAAAT
TGAAAAATTCAATAGAAACACAAGTGAACGAATTAAAAACACAAATCGAAAGCAAATGTG
TTATGCAGTGATATGTTAATTGTTATTCATTCATATTATAATATTTTTAACAATGATGAT
GAGATAAAATGTTCATTGAAAGAAAATAATAAATATTAATAATGAGTTTAATTCACATTA
AAAAATATGCAAAAAAATTCACATAAAAAAAGAAGTTGATTGAATTATGAAAAGAAAAAA
AAGTAATGCAAAAAAAGAAAATAAAAAAATTCATTAGCAATTAAATTAATTGATTGAGTA
GAGTTGATTATTATATACACATATATGAGAATGATAAATAATATTATTAAAAAATTATTA
TATTTTCAAAAAAAGAAAAAAAAACAGAAATAATAATTGGTTGAGGAAATTTACATTTAC
ATTAATTCATAAGAGTGCATCTGTAGTTGAAACTAACAATGAAAAAAAAAATAAATTAAA
TAAAAAGTTGAAAATTTGAAAAAACCACCAAAAACAAATTGAAAAAGTCTTGCTAAGATT
GCTGAAAATGCAATGCTGCGTTTTACTCGTCCAGTAAACGATTCATTCGAAAAATTGCCT
TTTTCCTCGTTCGAAAATATTACTGGACGCGAGAGACAGAGGGAAAATGAAGATTGGCGC
TAGT
>g1858.t4 Gene=g1858 Length=83
MEEEREKMRQEIRDKYNIKKKEEIVEQPPQEEPNPLMRKKKTPEELAAEAEAEDLDDFTK
LKNSIETQVNELKTQIESKCVMQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g1858.t4 | Coils | Coil | Coil | 55 | 75 | - |
| 6 | g1858.t4 | Gene3D | G3DSA:1.20.5.580 | Single Helix bin | 1 | 28 | 2.0E-10 |
| 5 | g1858.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 22 | 55 | - |
| 2 | g1858.t4 | PANTHER | PTHR16705:SF4 | COMPLEXIN | 1 | 83 | 1.2E-24 |
| 3 | g1858.t4 | PANTHER | PTHR16705 | COMPLEXIN | 1 | 83 | 1.2E-24 |
| 1 | g1858.t4 | Pfam | PF05835 | Synaphin protein | 1 | 73 | 2.2E-18 |
| 4 | g1858.t4 | SUPERFAMILY | SSF58038 | SNARE fusion complex | 1 | 19 | 4.97E-6 |
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 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.
