General information for g5245.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Vesicle transport through interaction with t-SNAREs homolog 1A.
Parent gene
- The parent gene g5245 is located on chr_2: 8108623..8109802 (- 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 | g5245 | g5245.t1 | TTS | g5245.t1 | 8107998 | 8107998 |
| chr_2 | g5245 | g5245.t1 | isoform | g5245.t1 | 8108623 | 8109445 |
| chr_2 | g5245 | g5245.t1 | exon | g5245.t1.exon1 | 8108623 | 8109129 |
| chr_2 | g5245 | g5245.t1 | cds | g5245.t1.CDS1 | 8108623 | 8109129 |
| chr_2 | g5245 | g5245.t1 | exon | g5245.t1.exon2 | 8109196 | 8109254 |
| chr_2 | g5245 | g5245.t1 | cds | g5245.t1.CDS2 | 8109196 | 8109254 |
| chr_2 | g5245 | g5245.t1 | exon | g5245.t1.exon3 | 8109352 | 8109445 |
| chr_2 | g5245 | g5245.t1 | cds | g5245.t1.CDS3 | 8109352 | 8109445 |
| chr_2 | g5245 | g5245.t1 | TSS | g5245.t1 | 8109801 | 8109801 |
Sequences
>g5245.t1 Gene=g5245 Length=660
ATGACAAGTTTACTTCTCGAATATGAACAACAATATTCAGTTATCACTGCAGAAATTACT
TCTAATATTGGTCGCCTTGGTGCTGTCTCAATTGATGATCGAAGAAACTTAATTGTTGAG
ATAAATAGAGGCATCGATGAAGCACAAGAGCTTCTGGAGCAAATTGGTCTTGAAATTAAT
CAAAATGTCGATTCAACGCAAAGAGCGAGTCAACAAACACGATTAAAATCTTATCATGCC
GAGTTAAAACGATTAGAAGAAGACTATAATAAGGCAAAGATAAAACCGAATCCGCTACTA
GTTGATGATTCGTCGTCAATTGACGATTTTGATATTGGAATAAGTGAAGATCAGAAACGT
AGGCTGTTAGATAATTCTGAACGATTAGAAAGAACTGGCAATCAATTGCAAGAAGGATAT
AGAATTGCAATTGAAACAGAAGAAATTGGTACGCAAGTACTTCAAAATTTACATAATCAA
AGAGAAACAATTCAACGCTCGAGAAATCGTTTAAGAGAAACAAATGCAGATCTCGGTAGA
TCTTCACGCTTAATGAACATGATGATAATGAGAGGATTAAGAGATAAATTTGCACTATAC
ATTATTGCAGTAGTTTTTGTAATCGCGATTACATTAACAATATATTTTTCTATAAAATAA
>g5245.t1 Gene=g5245 Length=219
MTSLLLEYEQQYSVITAEITSNIGRLGAVSIDDRRNLIVEINRGIDEAQELLEQIGLEIN
QNVDSTQRASQQTRLKSYHAELKRLEEDYNKAKIKPNPLLVDDSSSIDDFDIGISEDQKR
RLLDNSERLERTGNQLQEGYRIAIETEEIGTQVLQNLHNQRETIQRSRNRLRETNADLGR
SSRLMNMMIMRGLRDKFALYIIAVVFVIAITLTIYFSIK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g5245.t1 | CDD | cd15891 | SNARE_Vti1a | 126 | 186 | 1.81548E-27 |
| 9 | g5245.t1 | Coils | Coil | Coil | 68 | 95 | - |
| 10 | g5245.t1 | Coils | Coil | Coil | 154 | 177 | - |
| 7 | g5245.t1 | Gene3D | G3DSA:1.20.58.400 | - | 2 | 98 | 1.4E-25 |
| 8 | g5245.t1 | Gene3D | G3DSA:1.20.5.110 | - | 116 | 196 | 3.6E-25 |
| 3 | g5245.t1 | PANTHER | PTHR21230 | VESICLE TRANSPORT V-SNARE PROTEIN VTI1-RELATED | 1 | 211 | 1.1E-62 |
| 4 | g5245.t1 | PANTHER | PTHR21230:SF62 | VESICLE TRANSPORT THROUGH INTERACTION WITH T-SNARES HOMOLOG 1A | 1 | 211 | 1.1E-62 |
| 14 | g5245.t1 | PIRSF | PIRSF028865 | Membrin-2 | 8 | 218 | 1.8E-12 |
| 2 | g5245.t1 | Pfam | PF05008 | Vesicle transport v-SNARE protein N-terminus | 12 | 90 | 2.6E-16 |
| 1 | g5245.t1 | Pfam | PF12352 | Snare region anchored in the vesicle membrane C-terminus | 127 | 191 | 9.6E-18 |
| 11 | g5245.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 196 | - |
| 13 | g5245.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 197 | 218 | - |
| 12 | g5245.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 219 | 219 | - |
| 17 | g5245.t1 | SMART | SM00397 | tSNARE_6 | 121 | 188 | 6.7E-4 |
| 6 | g5245.t1 | SUPERFAMILY | SSF47661 | t-snare proteins | 8 | 92 | 3.61E-17 |
| 5 | g5245.t1 | SUPERFAMILY | SSF58038 | SNARE fusion complex | 129 | 188 | 1.57E-15 |
| 16 | g5245.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 197 | 218 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5245/g5245.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5245.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016020 | membrane | CC |
| GO:0006886 | intracellular protein transport | BP |
| GO:0005484 | SNAP receptor activity | MF |
| GO:0005794 | Golgi apparatus | CC |
| GO:0016192 | vesicle-mediated transport | BP |
KEGG
Orthology
- This transcript has been annotated with K08493 (vesicle transport through interaction with t-SNAREs 1)
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.
