Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Synaptosomal-associated protein 25.

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_3 g1584 g1584.t9 TTS g1584.t9 12007092 12007092
chr_3 g1584 g1584.t9 isoform g1584.t9 12008033 12018808
chr_3 g1584 g1584.t9 exon g1584.t9.exon1 12008033 12008109
chr_3 g1584 g1584.t9 cds g1584.t9.CDS1 12008034 12008109
chr_3 g1584 g1584.t9 exon g1584.t9.exon2 12008169 12008286
chr_3 g1584 g1584.t9 cds g1584.t9.CDS2 12008169 12008286
chr_3 g1584 g1584.t9 exon g1584.t9.exon3 12010908 12010956
chr_3 g1584 g1584.t9 cds g1584.t9.CDS3 12010908 12010956
chr_3 g1584 g1584.t9 exon g1584.t9.exon4 12016106 12016147
chr_3 g1584 g1584.t9 cds g1584.t9.CDS4 12016106 12016147
chr_3 g1584 g1584.t9 exon g1584.t9.exon5 12016216 12016300
chr_3 g1584 g1584.t9 cds g1584.t9.CDS5 12016216 12016299
chr_3 g1584 g1584.t9 exon g1584.t9.exon6 12018411 12018459
chr_3 g1584 g1584.t9 exon g1584.t9.exon7 12018759 12018808
chr_3 g1584 g1584.t9 TSS g1584.t9 12018999 12018999

Sequences

>g1584.t9 Gene=g1584 Length=470
CAAATAAGTAAATAACACAGTTGTTTAAGCGTTGATAAAAAATATTAAAGCTTTCCCTCA
AGTAATTGTATCGGATTAATTAAAAACTATATCTATCAGAATGCCGGCACCAACTGCAGA
ACCAGCACCTCCACGAACTGAACTGCAAGAATTGCAATTAAAGGCACAAGAAAAGACCGA
TGAGTCTCTTGAGTCAACACGTCGAATGTTGGCACTTTGCGAAGAGAGTGAAGATGTTGG
TGCGAAAACTCTGAATAATTTAGTTAGTCAAGGCGAACAATTGGATCGAATTGAGGAGGG
TATGGACCAGATTAATGCTGACATGCGTGAAGCTGAAAAAAATTTGAGTGGAATGGAAAA
ATGCTGCGGTATTTGTGTTTTGCCATGTAATAAGAGTGCGTCATTTAAAGAGGATGATGG
AACATGGAAGGGTAATGATGATGGAAAAGTTGTAAACAATCAGCCACAAC

>g1584.t9 Gene=g1584 Length=123
MPAPTAEPAPPRTELQELQLKAQEKTDESLESTRRMLALCEESEDVGAKTLNNLVSQGEQ
LDRIEEGMDQINADMREAEKNLSGMEKCCGICVLPCNKSASFKEDDGTWKGNDDGKVVNN
QPQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g1584.t9 CDD cd15889 SNARE_SNAP25N_23N 20 84 6.60698E-30
6 g1584.t9 Coils Coil Coil 61 88 -
5 g1584.t9 Gene3D G3DSA:1.20.5.110 - 5 85 2.8E-36
9 g1584.t9 MobiDBLite mobidb-lite consensus disorder prediction 103 123 -
2 g1584.t9 PANTHER PTHR19305:SF14 SYNAPTOSOMAL-ASSOCIATED PROTEIN-RELATED 9 122 7.4E-47
3 g1584.t9 PANTHER PTHR19305 SYNAPTOSOMAL ASSOCIATED PROTEIN 9 122 7.4E-47
1 g1584.t9 Pfam PF00835 SNAP-25 family 95 123 2.9E-7
10 g1584.t9 ProSiteProfiles PS50192 t-SNARE coiled-coil homology domain profile. 23 85 12.598
8 g1584.t9 SMART SM00397 tSNARE_6 18 85 3.2E-11
4 g1584.t9 SUPERFAMILY SSF58038 SNARE fusion complex 13 83 5.02E-22

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

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