Gene loci information

Transcript annotation

  • This transcript has been annotated as Alpha-soluble NSF attachment protein.

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 g10858 g10858.t1 TSS g10858.t1 12305462 12305462
chr_1 g10858 g10858.t1 isoform g10858.t1 12305534 12306781
chr_1 g10858 g10858.t1 exon g10858.t1.exon1 12305534 12305625
chr_1 g10858 g10858.t1 cds g10858.t1.CDS1 12305534 12305625
chr_1 g10858 g10858.t1 exon g10858.t1.exon2 12305764 12305950
chr_1 g10858 g10858.t1 cds g10858.t1.CDS2 12305764 12305950
chr_1 g10858 g10858.t1 exon g10858.t1.exon3 12306008 12306139
chr_1 g10858 g10858.t1 cds g10858.t1.CDS3 12306008 12306139
chr_1 g10858 g10858.t1 exon g10858.t1.exon4 12306252 12306572
chr_1 g10858 g10858.t1 cds g10858.t1.CDS4 12306252 12306572
chr_1 g10858 g10858.t1 exon g10858.t1.exon5 12306632 12306781
chr_1 g10858 g10858.t1 cds g10858.t1.CDS5 12306632 12306781
chr_1 g10858 g10858.t1 TTS g10858.t1 12307710 12307710

Sequences

>g10858.t1 Gene=g10858 Length=882
ATGGCCGATAATGAGCAAAAAGCATTACAACTTATAGCTGAGGCCGAGAAGAAACTCAAT
TCGTCAAAAGGATTTCTTGGGTCTCTTTTTGGTAGTGGCGCTAATAAAGTTGACGATGCC
ATAGAATGTTATCACCGTGCTGCGAATATGTTTAAAATGGCCAAAAAATGGCAACAAGCA
GGATCTGCTTTTTGTGAAGCAGCAAATTTACATGCGAAAGCTGGAAGTCGTCATGATGCA
GCAACGAATTATGTTGATGCATCAAATTGCTACAAAAAGGTTGATCCAAATGAAGCAGTG
GCATGTTTGCTCAAAGCAATTGATATTTACACAGATATGGGTCGGTTTACAATGGCTGCA
AAACATCATCAAACAATAGCTGAAATGTTTGAAAATGAAGCAAATGATTTGCATCGTGCA
GTGCAACATTACGAGCAAGCAGCTGATTATTTCAAGGGCGAAGAGTCAACAAGTTCGGCA
AACAAATGCATGCTAAAAGTTGCACAGTATGCAGCACAATTAGAAGATTATGAAAAGGCA
ATCCAAATTTACGAATCTGTAGCCGGTTCATGTCTTGATAGCTCTCTACTCAAGTACAGC
GCAAAAGAGTACTTCTTCCGTGCTTCATTGTGTCATTTGAGTGTAGATTTGCTTAATGCT
CAACACGCATTAGACAAGTATGCATCACAATATCCAGCATTTCAAGATTCACGTGAATTT
AAATTGGTCAAGACTCTAATTGAGCACTTAGAAGAGCAAAACATCGATGGTTATACAGAA
GCTGTAAAAGATTATGACAGCATTTCTCGTTTAGATCAGTGGTACACTACAATTTTATTG
CGTATCAAAAAGCAACATAATGATAATCCAGATTTACGATAA

>g10858.t1 Gene=g10858 Length=293
MADNEQKALQLIAEAEKKLNSSKGFLGSLFGSGANKVDDAIECYHRAANMFKMAKKWQQA
GSAFCEAANLHAKAGSRHDAATNYVDASNCYKKVDPNEAVACLLKAIDIYTDMGRFTMAA
KHHQTIAEMFENEANDLHRAVQHYEQAADYFKGEESTSSANKCMLKVAQYAAQLEDYEKA
IQIYESVAGSCLDSSLLKYSAKEYFFRASLCHLSVDLLNAQHALDKYASQYPAFQDSREF
KLVKTLIEHLEEQNIDGYTEAVKDYDSISRLDQWYTTILLRIKKQHNDNPDLR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g10858.t1 CDD cd15832 SNAP 7 284 5.16174E-133
14 g10858.t1 Coils Coil Coil 127 147 -
13 g10858.t1 Coils Coil Coil 167 187 -
12 g10858.t1 Gene3D G3DSA:1.25.40.10 - 6 292 4.3E-120
2 g10858.t1 PANTHER PTHR13768 SOLUBLE NSF ATTACHMENT PROTEIN SNAP 4 292 5.0E-129
3 g10858.t1 PANTHER PTHR13768:SF23 ALPHA-SOLUBLE NSF ATTACHMENT PROTEIN 4 292 5.0E-129
10 g10858.t1 PRINTS PR00448 NSF attachment protein signature 36 55 4.2E-69
7 g10858.t1 PRINTS PR00448 NSF attachment protein signature 99 116 4.2E-69
4 g10858.t1 PRINTS PR00448 NSF attachment protein signature 128 145 4.2E-69
9 g10858.t1 PRINTS PR00448 NSF attachment protein signature 161 184 4.2E-69
8 g10858.t1 PRINTS PR00448 NSF attachment protein signature 192 211 4.2E-69
6 g10858.t1 PRINTS PR00448 NSF attachment protein signature 232 252 4.2E-69
5 g10858.t1 PRINTS PR00448 NSF attachment protein signature 263 283 4.2E-69
1 g10858.t1 Pfam PF14938 Soluble NSF attachment protein, SNAP 7 285 6.1E-110
11 g10858.t1 SUPERFAMILY SSF48452 TPR-like 6 289 2.37E-76

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:0006886 intracellular protein transport BP
GO:0005515 protein binding MF

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