General information for g5423.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Syntaxin-5.
Parent gene
- The parent gene g5423 is located on chr_2: 9516352..9517140 (+ 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 | g5423 | g5423.t1 | TSS | g5423.t1 | 9515742 | 9515742 |
| chr_2 | g5423 | g5423.t1 | isoform | g5423.t1 | 9515824 | 9517048 |
| chr_2 | g5423 | g5423.t1 | exon | g5423.t1.exon1 | 9515824 | 9516259 |
| chr_2 | g5423 | g5423.t1 | cds | g5423.t1.CDS1 | 9515824 | 9516259 |
| chr_2 | g5423 | g5423.t1 | exon | g5423.t1.exon2 | 9516321 | 9517048 |
| chr_2 | g5423 | g5423.t1 | cds | g5423.t1.CDS2 | 9516321 | 9517048 |
| chr_2 | g5423 | g5423.t1 | TTS | g5423.t1 | 9517147 | 9517147 |
Sequences
>g5423.t1 Gene=g5423 Length=1164
ATGCGAAAAAGATTCAATTCAGAGTCTGAAAATTCAGTGACCCAAATTATTGTCGAAGAA
GATAATAAATATAAGGATAAAGCACTAGGAGCTGAAAATTTAGCAACAAAATTATTTAAG
ACATTTTACAAAAGTGAAAATAATTATCCAAATTCTGCTTTAAACAGCAGCAAATTAAAT
ACAACAGTAAACGAAGATTATTTATTGCCTGATCCGGAAACAGAAGAAATTTTCGTCATG
ACAGCTCGCGATAGAACAGTTGAATTCTCAAATACGATTCGCAGTCTACAAGGTCGAAAT
ATTAATCGTGTAGTGAATTTAAGAGACCCTAAGAAAGTCAAGCAAATGCAAAGTTATTCA
GAGTTTATGAGCATTGCGAAAAACATAGGAAAAAATATTGCGAGTACATATGCAAAGTTA
GAGAAATTAACTCTATTGGCAAAGAAAAAATCTCTTTTTGATGATAGGCCAGCTGAAATT
CAAGAGTTGACGTATATAATCAAAAGTGATCTGAATTCTTTGAATCAACAGATAGGACAG
TTGCAAGAGATATCACGAAATCAAGGAAGAACAAGTGGCAAGCATTTGCATTCACATTCC
TCAAATATGGTCATGGCATTGCAAACACGTCTTGCAAGCATGAGCTCAAATTTTCAGCAA
GTTCTTGAAGTACGAACTGAGAATTTAAAGCAACAAAAAACACGTCGTGAACAATTTTCT
CAAGCACCGGTCACAACTACACTTCCGCCTAAACGTGATAATCATCATGGAAGCTTATTA
TACAGTGAAAACGATGACCATGTAAATATTGATATGTCATCGCAACCGTTGTTGCCTAAA
AATCAAATTCAACAACAGCAAATGCTTCTTTATGATGATACCGATCAGTATGTGCAACAA
AGAGCTGAAACAATGCAAAATATTGAAAGCACGATTGTTGAACTTGGAGGAATTTTTCAG
CAATTAGCACACATGGTGAAAGAGCAAGAAGAAACTGTAGGCAGAATCGATTCAAATATT
CAAGATGTAGAGATGAATGTAGAAGCTGCTCATGGAGAAATTTTAAAATATTTTCAATCC
GTTTCTAAAAATCGCTGGCTTATGATAAAAATATTCGGTGTCCTTATTTTCTTCTTTATA
TTTTTTGTCTTATTTGTTGCCTAA
>g5423.t1 Gene=g5423 Length=387
MRKRFNSESENSVTQIIVEEDNKYKDKALGAENLATKLFKTFYKSENNYPNSALNSSKLN
TTVNEDYLLPDPETEEIFVMTARDRTVEFSNTIRSLQGRNINRVVNLRDPKKVKQMQSYS
EFMSIAKNIGKNIASTYAKLEKLTLLAKKKSLFDDRPAEIQELTYIIKSDLNSLNQQIGQ
LQEISRNQGRTSGKHLHSHSSNMVMALQTRLASMSSNFQQVLEVRTENLKQQKTRREQFS
QAPVTTTLPPKRDNHHGSLLYSENDDHVNIDMSSQPLLPKNQIQQQQMLLYDDTDQYVQQ
RAETMQNIESTIVELGGIFQQLAHMVKEQEETVGRIDSNIQDVEMNVEAAHGEILKYFQS
VSKNRWLMIKIFGVLIFFFIFFVLFVA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g5423.t1 | CDD | cd15844 | SNARE_syntaxin5 | 299 | 370 | 1.0944E-37 |
| 5 | g5423.t1 | Gene3D | G3DSA:1.20.58.70 | - | 113 | 350 | 1.9E-19 |
| 2 | g5423.t1 | PANTHER | PTHR19957 | SYNTAXIN | 82 | 386 | 1.5E-94 |
| 3 | g5423.t1 | PANTHER | PTHR19957:SF3 | SYNTAXIN-5 | 82 | 386 | 1.5E-94 |
| 1 | g5423.t1 | Pfam | PF05739 | SNARE domain | 332 | 383 | 4.5E-14 |
| 6 | g5423.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 365 | - |
| 8 | g5423.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 366 | 386 | - |
| 7 | g5423.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 387 | 387 | - |
| 12 | g5423.t1 | ProSiteProfiles | PS50192 | t-SNARE coiled-coil homology domain profile. | 295 | 357 | 18.206 |
| 11 | g5423.t1 | SMART | SM00397 | tSNARE_6 | 290 | 357 | 5.5E-15 |
| 4 | g5423.t1 | SUPERFAMILY | SSF47661 | t-snare proteins | 119 | 350 | 1.22E-42 |
| 10 | g5423.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 364 | 386 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5423/g5423.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5423.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016020 | membrane | CC |
| GO:0016192 | vesicle-mediated transport | BP |
KEGG
Orthology
- This transcript has been annotated with K08490 (syntaxin 5)
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.
