Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Synaptosomal-associated protein 29.

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 g10276 g10276.t1 TSS g10276.t1 8609520 8609520
chr_1 g10276 g10276.t1 isoform g10276.t1 8609924 8610664
chr_1 g10276 g10276.t1 exon g10276.t1.exon1 8609924 8610664
chr_1 g10276 g10276.t1 cds g10276.t1.CDS1 8609924 8610664
chr_1 g10276 g10276.t1 TTS g10276.t1 8610743 8610743

Sequences

>g10276.t1 Gene=g10276 Length=741
ATGTCAGGCCATCAGTATTTACAAAACGGAAACAGTCTATTTTGCGACGATGATGTTGAT
GACGACACATTCCTTAAAAATTCTCGTGTAAATAATAGCAGTAGCAAGCAGGATGAATAT
TTAGAACAAAGGCAAATGTATGAACAGAAAAGAAAAGAAATTGAAAGTCGAACTCTTAAT
TCATCACAAAGAAGTATAGGTTTGCTTAGAGAAACTGAACAAGTAGGTATTGCGACAGCA
ACCGAATTAGCTAAACAACGTGAGCAACTCGAAAAGACGCGAGATCAGTTAGATACGATT
AATACCAGTTTGAAATTTAGTCAACGCCATTTGAATGGGATTAAGAGTATGTTTGGTGGC
CTCAAAAATTACCTCTCTGGAAAATCAGATCTTGAACCATCTAAAACATCACCATCGTCC
TCCAATAGCTCATCAATAGCATCTCCTCAACTTTCTGCTGACGAACGTTATTCATCACAT
CCTACCACTCGACTTCGTAATGATCCTATTCAACAACAGCAACAAATTCCTGGTAATGTG
AACTTCAATAAGCAACTCGATCGCAATTTAGATGAAATGTGTGACAGTTTGTCGCGCTTG
AAAGGCTTAGCAATCGATCTTAATGGTGAAATTGAGTCTCAAAACGATCTAATTGATGAA
ATTGGTGACAAAGTGGAGAATGTTGATGCTAAGATTAACAAACAAAATAGAGAAATGTTT
AAAATATTGGGCAAAAAGTAA

>g10276.t1 Gene=g10276 Length=246
MSGHQYLQNGNSLFCDDDVDDDTFLKNSRVNNSSSKQDEYLEQRQMYEQKRKEIESRTLN
SSQRSIGLLRETEQVGIATATELAKQREQLEKTRDQLDTINTSLKFSQRHLNGIKSMFGG
LKNYLSGKSDLEPSKTSPSSSNSSSIASPQLSADERYSSHPTTRLRNDPIQQQQQIPGNV
NFNKQLDRNLDEMCDSLSRLKGLAIDLNGEIESQNDLIDEIGDKVENVDAKINKQNREMF
KILGKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g10276.t1 CDD cd15887 SNARE_SNAP29N 49 113 4.62315E-23
11 g10276.t1 CDD cd15856 SNARE_SNAP29C 183 239 1.77192E-20
9 g10276.t1 Coils Coil Coil 37 57 -
10 g10276.t1 Coils Coil Coil 80 103 -
8 g10276.t1 Coils Coil Coil 218 238 -
7 g10276.t1 Gene3D G3DSA:1.20.5.110 - 41 118 7.2E-26
6 g10276.t1 Gene3D G3DSA:1.20.5.110 - 181 241 3.2E-21
15 g10276.t1 MobiDBLite mobidb-lite consensus disorder prediction 129 179 -
2 g10276.t1 PANTHER PTHR19305:SF9 SYNAPTOSOMAL-ASSOCIATED PROTEIN 29 29 245 9.0E-44
3 g10276.t1 PANTHER PTHR19305 SYNAPTOSOMAL ASSOCIATED PROTEIN 29 245 9.0E-44
1 g10276.t1 Pfam PF12352 Snare region anchored in the vesicle membrane C-terminus 57 115 1.2E-7
16 g10276.t1 ProSiteProfiles PS50192 t-SNARE coiled-coil homology domain profile. 180 242 15.691
14 g10276.t1 SMART SM00397 tSNARE_6 43 114 0.1
13 g10276.t1 SMART SM00397 tSNARE_6 175 242 1.5E-8
5 g10276.t1 SUPERFAMILY SSF58038 SNARE fusion complex 44 115 3.27E-16
4 g10276.t1 SUPERFAMILY SSF58038 SNARE fusion complex 182 243 7.1E-16

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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