Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Vesicle transport through interaction with t-SNAREs homolog 1A.

Parent gene

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.t5 TTS g5245.t5 8107998 8107998
chr_2 g5245 g5245.t5 isoform g5245.t5 8108623 8109802
chr_2 g5245 g5245.t5 exon g5245.t5.exon1 8108623 8109129
chr_2 g5245 g5245.t5 cds g5245.t5.CDS1 8108623 8109129
chr_2 g5245 g5245.t5 exon g5245.t5.exon2 8109196 8109254
chr_2 g5245 g5245.t5 cds g5245.t5.CDS2 8109196 8109254
chr_2 g5245 g5245.t5 exon g5245.t5.exon3 8109352 8109508
chr_2 g5245 g5245.t5 cds g5245.t5.CDS3 8109352 8109445
chr_2 g5245 g5245.t5 exon g5245.t5.exon4 8109647 8109802
chr_2 g5245 g5245.t5 TSS g5245.t5 8109801 8109801

Sequences

>g5245.t5 Gene=g5245 Length=879
TTTTGACATTTCTCTGTTTATGAAATTTTCGTCATTCTTTTTCTCTTTAATTAATATTGA
TAGAATTGGCCAGTTTGAGAAAGTTAAATTGACCTTAAAGTGAAAAGAAGAAAAGCACTA
ATTTAATTCAATAGTTTAAACAGGCAAATTTTGAAATATAAAAAATTTGTAAAAGTTACT
TCAAGAACATTCTGTACAATAAAATCTGGCATTTCAACAATGACAAGTTTACTTCTCGAA
TATGAACAACAATATTCAGTTATCACTGCAGAAATTACTTCTAATATTGGTCGCCTTGGT
GCTGTCTCAATTGATGATCGAAGAAACTTAATTGTTGAGATAAATAGAGGCATCGATGAA
GCACAAGAGCTTCTGGAGCAAATTGGTCTTGAAATTAATCAAAATGTCGATTCAACGCAA
AGAGCGAGTCAACAAACACGATTAAAATCTTATCATGCCGAGTTAAAACGATTAGAAGAA
GACTATAATAAGGCAAAGATAAAACCGAATCCGCTACTAGTTGATGATTCGTCGTCAATT
GACGATTTTGATATTGGAATAAGTGAAGATCAGAAACGTAGGCTGTTAGATAATTCTGAA
CGATTAGAAAGAACTGGCAATCAATTGCAAGAAGGATATAGAATTGCAATTGAAACAGAA
GAAATTGGTACGCAAGTACTTCAAAATTTACATAATCAAAGAGAAACAATTCAACGCTCG
AGAAATCGTTTAAGAGAAACAAATGCAGATCTCGGTAGATCTTCACGCTTAATGAACATG
ATGATAATGAGAGGATTAAGAGATAAATTTGCACTATACATTATTGCAGTAGTTTTTGTA
ATCGCGATTACATTAACAATATATTTTTCTATAAAATAA

>g5245.t5 Gene=g5245 Length=219
MTSLLLEYEQQYSVITAEITSNIGRLGAVSIDDRRNLIVEINRGIDEAQELLEQIGLEIN
QNVDSTQRASQQTRLKSYHAELKRLEEDYNKAKIKPNPLLVDDSSSIDDFDIGISEDQKR
RLLDNSERLERTGNQLQEGYRIAIETEEIGTQVLQNLHNQRETIQRSRNRLRETNADLGR
SSRLMNMMIMRGLRDKFALYIIAVVFVIAITLTIYFSIK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g5245.t5 CDD cd15891 SNARE_Vti1a 126 186 1.81548E-27
9 g5245.t5 Coils Coil Coil 68 95 -
10 g5245.t5 Coils Coil Coil 154 177 -
7 g5245.t5 Gene3D G3DSA:1.20.58.400 - 2 98 1.4E-25
8 g5245.t5 Gene3D G3DSA:1.20.5.110 - 116 196 3.6E-25
3 g5245.t5 PANTHER PTHR21230 VESICLE TRANSPORT V-SNARE PROTEIN VTI1-RELATED 1 211 1.1E-62
4 g5245.t5 PANTHER PTHR21230:SF62 VESICLE TRANSPORT THROUGH INTERACTION WITH T-SNARES HOMOLOG 1A 1 211 1.1E-62
14 g5245.t5 PIRSF PIRSF028865 Membrin-2 8 218 1.9E-12
2 g5245.t5 Pfam PF05008 Vesicle transport v-SNARE protein N-terminus 12 90 2.6E-16
1 g5245.t5 Pfam PF12352 Snare region anchored in the vesicle membrane C-terminus 127 191 9.6E-18
11 g5245.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 196 -
13 g5245.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 197 218 -
12 g5245.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 219 219 -
17 g5245.t5 SMART SM00397 tSNARE_6 121 188 6.7E-4
6 g5245.t5 SUPERFAMILY SSF47661 t-snare proteins 8 92 3.61E-17
5 g5245.t5 SUPERFAMILY SSF58038 SNARE fusion complex 129 188 1.57E-15
16 g5245.t5 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.t5; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5245.t5.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

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.

Raw TPM values