General information for g959.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Syntaxin-1A.
Parent gene
- The parent gene g959 is located on chr_3: 7052529..7062065 (+ 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 | g959 | g959.t4 | isoform | g959.t4 | 7041650 | 7056627 |
| chr_3 | g959 | g959.t4 | exon | g959.t4.exon1 | 7041650 | 7042295 |
| chr_3 | g959 | g959.t4 | exon | g959.t4.exon2 | 7051815 | 7051995 |
| chr_3 | g959 | g959.t4 | exon | g959.t4.exon3 | 7052074 | 7052128 |
| chr_3 | g959 | g959.t4 | exon | g959.t4.exon4 | 7052336 | 7052530 |
| chr_3 | g959 | g959.t4 | cds | g959.t4.CDS1 | 7052455 | 7052530 |
| chr_3 | g959 | g959.t4 | exon | g959.t4.exon5 | 7052601 | 7052674 |
| chr_3 | g959 | g959.t4 | cds | g959.t4.CDS2 | 7052601 | 7052674 |
| chr_3 | g959 | g959.t4 | exon | g959.t4.exon6 | 7052753 | 7052890 |
| chr_3 | g959 | g959.t4 | cds | g959.t4.CDS3 | 7052753 | 7052890 |
| chr_3 | g959 | g959.t4 | exon | g959.t4.exon7 | 7053118 | 7053228 |
| chr_3 | g959 | g959.t4 | cds | g959.t4.CDS4 | 7053118 | 7053228 |
| chr_3 | g959 | g959.t4 | exon | g959.t4.exon8 | 7056281 | 7056627 |
| chr_3 | g959 | g959.t4 | cds | g959.t4.CDS5 | 7056281 | 7056379 |
| chr_3 | g959 | g959.t4 | TTS | g959.t4 | 7056612 | 7056612 |
| chr_3 | g959 | g959.t4 | TSS | g959.t4 | NA | NA |
Sequences
>g959.t4 Gene=g959 Length=1747
TTCTTAACAGTCTAGTATATTTTCAAAGTTCAATTGTATATTAGTATCTCAAAAGTAATG
TTTATACTTGCTTATACTCTTATGTATGGGAGAAGACTTAGTGTTGTGATTAATCGTGTA
AAATGATAATTTTCAGAGACTTTCTATAGTGAAAAATTAATTATTTCTAATTTTTGATTA
CTCTTAACTATCTAAGAATGAGTGATTGAGTGACAAGCATTCTACTGCATATAGTGATTT
GATAAAACATCGTGTTGCTCTTAACTTAAGAATTTGTTCATGCGCAAATAGTCGAAAAGA
AAATCAATAAAATCGTGAAAAAAACCTTCGCGATTTGTGGAGAATTTGTGCTGAAATTAA
TGTTTTAGCGTGAATAAATCATAAATAAAAATCAATGGAAGCCTAGTGAATACTAAATAG
TATTTAAATATCATAAGGGTTTTAGTGAAAAGTGTGTAAATTCTGAAATTTGGAAAGTTT
TCATTTCTGTAAGGCTGCTTGAAGAAAAGAAGAGAGTGCGAGAGAACGAAAAAATTGCAA
AATCCCAAAGTTGATTTTCAAAGCATCAAACGACTGCCTCAACAAATATTGAAATACAAC
ATTAAAAAGCATCATGACGAAGGATAGATTAGCAGCATTGCATGCGGCTCAAAGTGATGA
CGAGGATGCGGGGATGGATGAAGTTGCCATCAACGTCGATGGCTTCATGGAGGAGTTTTT
CACTGAGGTGGAAGAAGTTAGAGAGATGATAGATAAAATACAATATAATGTGGAAGAGGT
TAAGAAAAAACACAGTTCCATCTTATCCGCTCCTCAAACGGATGAAAAAACCAAGCAAGA
GTTAGAGGATCTGATGGCAGATATTAAGAAAAATGCCAATAGAATAAATATAGAATATCG
AACAAAGTATCGAGCAAGAAGAGCAGAGTAAATCAGCAAGTGCCGATTTACGAATACGTA
AGACACAACATTCGACATTATCACGAAAATTTGTCGAAGTAATGACAGAATATAATCGAA
CACAAACTGATTATCGAGAGAGATGTAAAGCGAGAATACAACGTCAATTGGAAATCACTG
GTAAAGCCACAACAAATGAAGAACTCGAAGAAATGTTGGAGCAAGGAAATTCGGCAGTGT
TTACACAAGGAATTATTATGGAAACACAACAAGCAAAACAGACCCTGGCAGATATCGAAG
CACGACATGCTGATATCATTAAACTTGAAAACTCAATTCGAGAATTGCACGATATGTTCA
TGGATATGGCAATGTTGGTCGAGAGTCAGGGTGAAATGATTGATCGTATAGAGTATCATG
TTGAGCATGCAATGGATTATGTCCAAACAGCTACACAAGATACCAAAAAAGCACTCAAAT
ACCAAAGTAAAGCTCGTCGGAAAAAGATATTGATTATAGCATGTTTGACTATAGCGGCAG
TGATTTTATTGATAATTTTAATCTTATACCTTATGAGTTTATTTGGAGCGACAAATTAAA
CTCGACAAACAAATATAATATTAACAATTCTATACTAATCGCCATATCAACAAAAATTCA
AATTATATCAATTAAACAATGTCATGGACGTCAACACCTTTGGACTAGAGCAAATAACTT
ATATGCACATGGAGGAGGATGTTAAATTAGAATTAATTGTTGTAATTATAATTTAAATAA
GGCAATAGTTGGTGCGCATAAAATATGGATTATTAAATAAATTTTTCCTGCCACTTTTAT
TCGATTA
>g959.t4 Gene=g959 Length=165
MTEYNRTQTDYRERCKARIQRQLEITGKATTNEELEEMLEQGNSAVFTQGIIMETQQAKQ
TLADIEARHADIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYHVEHAMDYVQTATQD
TKKALKYQSKARRKKILIIACLTIAAVILLIILILYLMSLFGATN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g959.t4 | CDD | cd15880 | SNARE_syntaxin1 | 61 | 129 | 3.44602E-39 |
| 6 | g959.t4 | Gene3D | G3DSA:1.20.58.70 | - | 1 | 117 | 2.0E-55 |
| 3 | g959.t4 | PANTHER | PTHR19957:SF231 | SYNTAXIN-1A HOMOLOG | 1 | 154 | 1.5E-75 |
| 4 | g959.t4 | PANTHER | PTHR19957 | SYNTAXIN | 1 | 154 | 1.5E-75 |
| 1 | g959.t4 | Pfam | PF00804 | Syntaxin | 1 | 97 | 1.7E-37 |
| 2 | g959.t4 | Pfam | PF05739 | SNARE domain | 98 | 150 | 1.2E-15 |
| 7 | g959.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 135 | - |
| 9 | g959.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 136 | 158 | - |
| 8 | g959.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 159 | 165 | - |
| 12 | g959.t4 | ProSitePatterns | PS00914 | Syntaxin / epimorphin family signature. | 68 | 107 | - |
| 14 | g959.t4 | ProSiteProfiles | PS50192 | t-SNARE coiled-coil homology domain profile. | 62 | 124 | 20.749 |
| 13 | g959.t4 | SMART | SM00397 | tSNARE_6 | 57 | 124 | 4.3E-21 |
| 5 | g959.t4 | SUPERFAMILY | SSF47661 | t-snare proteins | 1 | 117 | 3.92E-41 |
| 11 | g959.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 136 | 158 | - |
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:0016020 | membrane | CC |
| GO:0006886 | intracellular protein transport | BP |
| GO:0005484 | SNAP receptor activity | MF |
| GO:0016192 | vesicle-mediated 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.
