Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Syntaxin-7.

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_1 g10529 g10529.t5 isoform g10529.t5 10357904 10359148
chr_1 g10529 g10529.t5 exon g10529.t5.exon1 10357904 10358075
chr_1 g10529 g10529.t5 TSS g10529.t5 10357918 10357918
chr_1 g10529 g10529.t5 exon g10529.t5.exon2 10358191 10358276
chr_1 g10529 g10529.t5 cds g10529.t5.CDS1 10358192 10358276
chr_1 g10529 g10529.t5 exon g10529.t5.exon3 10358340 10358409
chr_1 g10529 g10529.t5 cds g10529.t5.CDS2 10358340 10358409
chr_1 g10529 g10529.t5 exon g10529.t5.exon4 10358464 10358998
chr_1 g10529 g10529.t5 cds g10529.t5.CDS3 10358464 10358998
chr_1 g10529 g10529.t5 exon g10529.t5.exon5 10359059 10359148
chr_1 g10529 g10529.t5 cds g10529.t5.CDS4 10359059 10359148
chr_1 g10529 g10529.t5 TTS g10529.t5 10359575 10359575

Sequences

>g10529.t5 Gene=g10529 Length=953
TGAAATTTAAATTGAAGATTCACCAACCCTGATCAACACAACAAAAGTAACAAAAATAAT
TGAAATATAAAATTTTGATAGATTTTAACAACTTAAACTAATAAAATTAGTAACAATTGA
AGAATAAAGTTGTACTTGATTCAGTGATACTGAAATAAAATTGTTATTCAAAAATGAGTT
CCTTCGATAATAGTGATGCAGAATTTCAAAAGCATTCACAATTCATTAGTACCAGCGTCC
AAAAAATTTACCAAAATGTTTCATCTATGAATCGTATGGTCAGTCAAGTTGGAACAGCTC
AAGAGACACCAGAAATAAGACAGCAATTACATCAAATTCGCACTTATACTCAACAATTAA
TAAAAGATACTGACTCTTCATTCAAAGATATTGTAAATTGTAAAGATCGTCATCTTAAAA
TCCAAAGAGATCGGTTAGTTGATGAGTTTACAGCAGCACTTACTGCATTTCAAGCTGTTC
AAAAGAGAACAGTTGATTTGGAGAAAAATGCCATTCGTCAAGCAAAAGCAAATGTCACAT
TACCTAAACCACCATCGTCTAACAAATCAACCAGTAATAGCTTTTCCGAGTCACAATTTG
AAAATAATTTTGTTGATAATAGAGGCCCAACACAAGCACAATTACAACAAGAAGAGATTG
ATTTGCAAGCATTAGAAGAACAAGAAAGAACAATTCGAGAATTAGAAGAAAATATTGTGG
GTGTAAATGAAATTTATAAGAAATTAGGTGCATTAGTATATGAACAAGGCCAGACAGTCG
ATTCAATTGAGGCTTCTGTTGAAAACGCAAGCGTTTTTGTTCAAGATGGAACAGAGCAAT
TACGACGCGCAAGTCATTATAGCAATCAAGCACGAAAGAAAAAATTGATATTAGCCCTCA
TTCTTGGTGGTATACTGGCAGTGATTATTCTACTTTTCATCATAAGAAACTAA

>g10529.t5 Gene=g10529 Length=259
MSSFDNSDAEFQKHSQFISTSVQKIYQNVSSMNRMVSQVGTAQETPEIRQQLHQIRTYTQ
QLIKDTDSSFKDIVNCKDRHLKIQRDRLVDEFTAALTAFQAVQKRTVDLEKNAIRQAKAN
VTLPKPPSSNKSTSNSFSESQFENNFVDNRGPTQAQLQQEEIDLQALEEQERTIRELEEN
IVGVNEIYKKLGALVYEQGQTVDSIEASVENASVFVQDGTEQLRRASHYSNQARKKKLIL
ALILGGILAVIILLFIIRN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g10529.t5 Coils Coil Coil 157 187 -
6 g10529.t5 Gene3D G3DSA:1.20.58.70 - 2 122 3.1E-31
7 g10529.t5 Gene3D G3DSA:1.20.5.110 - 153 258 2.3E-23
15 g10529.t5 MobiDBLite mobidb-lite consensus disorder prediction 119 141 -
16 g10529.t5 MobiDBLite mobidb-lite consensus disorder prediction 122 141 -
3 g10529.t5 PANTHER PTHR19957:SF90 SYNTAXIN-7 8 254 1.2E-53
4 g10529.t5 PANTHER PTHR19957 SYNTAXIN 8 254 1.2E-53
1 g10529.t5 Pfam PF14523 Syntaxin-like protein 18 112 3.6E-25
2 g10529.t5 Pfam PF05739 SNARE domain 201 251 6.0E-13
9 g10529.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 237 -
11 g10529.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 238 257 -
10 g10529.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 258 259 -
17 g10529.t5 ProSiteProfiles PS50192 t-SNARE coiled-coil homology domain profile. 164 226 15.17
13 g10529.t5 SMART SM00503 SynN_4 3 111 1.0E-5
14 g10529.t5 SMART SM00397 tSNARE_6 159 226 4.8E-9
5 g10529.t5 SUPERFAMILY SSF47661 t-snare proteins 6 219 5.49E-34
12 g10529.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 238 257 -

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: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