Gene loci information

Transcript annotation

  • This transcript has been annotated as hypothetical.

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 g6817 g6817.t2 TSS g6817.t2 18881398 18881398
chr_2 g6817 g6817.t2 isoform g6817.t2 18881607 18882437
chr_2 g6817 g6817.t2 exon g6817.t2.exon1 18881607 18881916
chr_2 g6817 g6817.t2 cds g6817.t2.CDS1 18881607 18881916
chr_2 g6817 g6817.t2 exon g6817.t2.exon2 18881983 18882145
chr_2 g6817 g6817.t2 cds g6817.t2.CDS2 18881983 18882145
chr_2 g6817 g6817.t2 exon g6817.t2.exon3 18882212 18882437
chr_2 g6817 g6817.t2 cds g6817.t2.CDS3 18882212 18882437
chr_2 g6817 g6817.t2 TTS g6817.t2 18882836 18882836

Sequences

>g6817.t2 Gene=g6817 Length=699
ATGAATCAAACAAAAATTCCTATAAAAGTTGCAGAAATTTCCATAAATAAATTCAATGAA
CAAATTTTTCAAAAAGTCACACAATTAAGAACCTTTCGAATTTCTCAATCAAACACAACG
TCCTTGAGTGATCTAGAGAAATTACGGAAAGATGCAATCAATTGTTTACGCGTTGTGAAA
CAACTTAAGCAGCTCCTAATCGAAATAGATCACCTAAAATCACAAACAAGAGAAGAAGAT
CATGAAAAATTTGATGAATTAACATCACGGAGACGACAAGATGCACTAAAAGAAATTCAA
TTATATCAAGATATGAAACCTATAGATAAACTTAACGAATTATCACATCATGCGACAACT
AATATTGATAATGAAATGCCAGCAATTGATACAAAGAAAGAAAACATTCACATACAGCTT
CAAGTAGATGATCGAGAAATCAGAAAACGCGAATTGGAATCAAGAGAAGCATTATTGAGG
GAATTTGAGAATTTACAAACTGAATGTGAATCAATTGCAAATTTATTTCAAAATGTCAGT
GAACTGGTAGCAGAGCAGGCACCTATGGTTGATAAGATTGAAGAAAATGTTGAAGAAACA
GAACATAATGTTGAAGAAGGTACAAAACATTTACAGCAAGCATTAAGTTATAAGAAAACT
ATGTATCCACTTCTTGGTGGACTTGTAGGAGCTGCCATG

>g6817.t2 Gene=g6817 Length=233
MNQTKIPIKVAEISINKFNEQIFQKVTQLRTFRISQSNTTSLSDLEKLRKDAINCLRVVK
QLKQLLIEIDHLKSQTREEDHEKFDELTSRRRQDALKEIQLYQDMKPIDKLNELSHHATT
NIDNEMPAIDTKKENIHIQLQVDDREIRKRELESREALLREFENLQTECESIANLFQNVS
ELVAEQAPMVDKIEENVEETEHNVEEGTKHLQQALSYKKTMYPLLGGLVGAAM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g6817.t2 Coils Coil Coil 148 175 -
8 g6817.t2 Coils Coil Coil 190 210 -
7 g6817.t2 Gene3D G3DSA:1.20.5.110 - 159 222 4.9E-14
2 g6817.t2 PANTHER PTHR19957 SYNTAXIN 2 229 5.1E-33
3 g6817.t2 PANTHER PTHR19957:SF139 SYNTAXIN-17 2 229 5.1E-33
1 g6817.t2 Pfam PF05739 SNARE domain 189 219 1.3E-8
10 g6817.t2 ProSiteProfiles PS50192 t-SNARE coiled-coil homology domain profile. 171 214 12.8
6 g6817.t2 SMART SM00397 tSNARE_6 147 214 1.4E-6
5 g6817.t2 SUPERFAMILY SSF47661 t-snare proteins 15 207 2.2E-11
4 g6817.t2 SUPERFAMILY SSF58038 SNARE fusion complex 152 219 4.19E-13

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:0000149 SNARE binding MF
GO:0097352 autophagosome maturation BP
GO:0097111 endoplasmic reticulum-Golgi intermediate compartment organization BP
GO:0006888 endoplasmic reticulum to Golgi vesicle-mediated transport BP
GO:0016192 vesicle-mediated transport BP

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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