General information for g5245.t3
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.t3 | isoform | g5245.t3 | 8107997 | 8109445 |
| chr_2 | g5245 | g5245.t3 | exon | g5245.t3.exon1 | 8107997 | 8109129 |
| chr_2 | g5245 | g5245.t3 | TTS | g5245.t3 | 8107998 | 8107998 |
| chr_2 | g5245 | g5245.t3 | cds | g5245.t3.CDS1 | 8108623 | 8109129 |
| chr_2 | g5245 | g5245.t3 | exon | g5245.t3.exon2 | 8109196 | 8109445 |
| chr_2 | g5245 | g5245.t3 | cds | g5245.t3.CDS2 | 8109196 | 8109270 |
| chr_2 | g5245 | g5245.t3 | TSS | g5245.t3 | 8109801 | 8109801 |
Sequences
>g5245.t3 Gene=g5245 Length=1383
ATGACAAGTTTACTTCTCGAATATGAACAACAATATTCAGTTATCACTGCAGAAATTACT
TCTAATATTGGTCGCCTTGGTGCTGTCTCAATTGGTAAGAAATGACATCAAGTACTTTTT
AAATGAAATTTAGCTGGAAATTAATTTCAATTTATATGCTATAATCGCCACTTGTATGTT
GATGTTTTCAGATGATCGAAGAAACTTAATTGTTGAGATAAATAGAGGCATCGATGAAGC
ACAAGAGCTTCTGGAGCAAATTGGTCTTGAAATTAATCAAAATGTCGATTCAACGCAAAG
AGCGAGTCAACAAACACGATTAAAATCTTATCATGCCGAGTTAAAACGATTAGAAGAAGA
CTATAATAAGGCAAAGATAAAACCGAATCCGCTACTAGTTGATGATTCGTCGTCAATTGA
CGATTTTGATATTGGAATAAGTGAAGATCAGAAACGTAGGCTGTTAGATAATTCTGAACG
ATTAGAAAGAACTGGCAATCAATTGCAAGAAGGATATAGAATTGCAATTGAAACAGAAGA
AATTGGTACGCAAGTACTTCAAAATTTACATAATCAAAGAGAAACAATTCAACGCTCGAG
AAATCGTTTAAGAGAAACAAATGCAGATCTCGGTAGATCTTCACGCTTAATGAACATGAT
GATAATGAGAGGATTAAGAGATAAATTTGCACTATACATTATTGCAGTAGTTTTTGTAAT
CGCGATTACATTAACAATATATTTTTCTATAAAATAAACAAAAGATTATGTTAATTGTTA
AAAGAGAAAATTAGACAGAAACATATGCCGGTATGAAGAATGATTGAATAATTTATGAAC
ACATGACAAGGTATTAATGATATAATGAGACGATAATTGACACGTCTTGAAAGCAACCTG
TGAACTTAAATGCTTATACAATTATTCCGGGAAAATCCTTTGATTCATAACGATATTGAA
TTCAATACAAAACATGAAATGTTCAATCATTCTTCTCCAATTTGATTTATATGCTGTTAA
TTAATAATAAATATGTTTAATCAAGATATAATAGAACATTTTGTACTCGACTTCTAATGA
AAGCACTTCAAAATAATGTCTTTATAGAAAAATTGTATTATTTCTTAATCTTCTCAAAAT
GAAACATGCAAGACATACACGAAAAAAGAAAATACATGTATTAAAAAGTAATGAATGAAT
CAAGTCATTCTCACACCCCACAGTCGTAATATTATTTAATTGATAAATTAACAATAAAAA
TAATGAACATTTTTTTGATGTGTTGATCTTTATAAGCTTTAATGTTAATAAATGGATCAA
TTCAACGTAGCATACACATCAGAATAATTTATATGATAATAAAGAGAAAATAATTAACAA
GTA
>g5245.t3 Gene=g5245 Length=193
MLMFSDDRRNLIVEINRGIDEAQELLEQIGLEINQNVDSTQRASQQTRLKSYHAELKRLE
EDYNKAKIKPNPLLVDDSSSIDDFDIGISEDQKRRLLDNSERLERTGNQLQEGYRIAIET
EEIGTQVLQNLHNQRETIQRSRNRLRETNADLGRSSRLMNMMIMRGLRDKFALYIIAVVF
VIAITLTIYFSIK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g5245.t3 | CDD | cd15891 | SNARE_Vti1a | 100 | 160 | 1.06711E-27 |
| 9 | g5245.t3 | Coils | Coil | Coil | 42 | 69 | - |
| 10 | g5245.t3 | Coils | Coil | Coil | 128 | 151 | - |
| 7 | g5245.t3 | Gene3D | G3DSA:1.20.58.400 | - | 3 | 72 | 8.5E-15 |
| 8 | g5245.t3 | Gene3D | G3DSA:1.20.5.110 | - | 90 | 170 | 2.7E-25 |
| 3 | g5245.t3 | PANTHER | PTHR21230 | VESICLE TRANSPORT V-SNARE PROTEIN VTI1-RELATED | 5 | 185 | 3.6E-51 |
| 4 | g5245.t3 | PANTHER | PTHR21230:SF62 | VESICLE TRANSPORT THROUGH INTERACTION WITH T-SNARES HOMOLOG 1A | 5 | 185 | 3.6E-51 |
| 14 | g5245.t3 | PIRSF | PIRSF028865 | Membrin-2 | 4 | 192 | 2.9E-11 |
| 2 | g5245.t3 | Pfam | PF05008 | Vesicle transport v-SNARE protein N-terminus | 6 | 64 | 8.7E-13 |
| 1 | g5245.t3 | Pfam | PF12352 | Snare region anchored in the vesicle membrane C-terminus | 101 | 165 | 7.4E-18 |
| 11 | g5245.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 170 | - |
| 13 | g5245.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 171 | 192 | - |
| 12 | g5245.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 193 | 193 | - |
| 17 | g5245.t3 | SMART | SM00397 | tSNARE_6 | 95 | 162 | 6.7E-4 |
| 6 | g5245.t3 | SUPERFAMILY | SSF47661 | t-snare proteins | 6 | 66 | 1.41E-10 |
| 5 | g5245.t3 | SUPERFAMILY | SSF58038 | SNARE fusion complex | 103 | 162 | 1.22E-15 |
| 16 | g5245.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 170 | 192 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5245/g5245.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5245.t3.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.
