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.t16 TSS g10858.t16 12305462 12305462
chr_1 g10858 g10858.t16 isoform g10858.t16 12306107 12307276
chr_1 g10858 g10858.t16 exon g10858.t16.exon1 12306107 12306139
chr_1 g10858 g10858.t16 cds g10858.t16.CDS1 12306113 12306139
chr_1 g10858 g10858.t16 exon g10858.t16.exon2 12306252 12306572
chr_1 g10858 g10858.t16 cds g10858.t16.CDS2 12306252 12306572
chr_1 g10858 g10858.t16 exon g10858.t16.exon3 12306632 12307276
chr_1 g10858 g10858.t16 cds g10858.t16.CDS3 12306632 12306781
chr_1 g10858 g10858.t16 TTS g10858.t16 12307710 12307710

Sequences

>g10858.t16 Gene=g10858 Length=999
GCTGAAATGTTTGAAAATGAAGCAAATGATTTGCATCGTGCAGTGCAACATTACGAGCAA
GCAGCTGATTATTTCAAGGGCGAAGAGTCAACAAGTTCGGCAAACAAATGCATGCTAAAA
GTTGCACAGTATGCAGCACAATTAGAAGATTATGAAAAGGCAATCCAAATTTACGAATCT
GTAGCCGGTTCATGTCTTGATAGCTCTCTACTCAAGTACAGCGCAAAAGAGTACTTCTTC
CGTGCTTCATTGTGTCATTTGAGTGTAGATTTGCTTAATGCTCAACACGCATTAGACAAG
TATGCATCACAATATCCAGCATTTCAAGATTCACGTGAATTTAAATTGGTCAAGACTCTA
ATTGAGCACTTAGAAGAGCAAAACATCGATGGTTATACAGAAGCTGTAAAAGATTATGAC
AGCATTTCTCGTTTAGATCAGTGGTACACTACAATTTTATTGCGTATCAAAAAGCAACAT
AATGATAATCCAGATTTACGATAAATTGTCAATACTTGCTCTAGTTCTCCCATTGCGAAA
CTCAATGATGCAAAAGATGAAGAAGGTGAAAGAATTCCATTTTATGTCGTTTTTTTAAAA
TTTAGCATAAAAGAGTAAAATTCCTAATCGTTTTTAGGAGTAAATTTTTGTCCATCAATA
ACTTACTTACACATTATTATTATTTTTTTGTTGTAAACTATAAACGCATGCAAAAAAATT
AAAAAAAAACTAACGAAAAAATAAAATTATTACAATGATACATTTCTGATATATCTCTAG
TGATAAGAACTCTTTAAAAAGAAGAAATTGAAAAATATTTAAATATAATATGATGTTATA
GCTTATTTGATGCTGTTATTTTTTTATTTGATCATTAAAAGTTTTAAGTTAAAAATGAGT
CATGGGTTTTCTCACTTTTTTATTCATATTTTTTGTAACTAAAACGTTGCATTTTGTTTA
TCTCGAATGTGTACATACACATAGTCGTTGTGCATAAAT

>g10858.t16 Gene=g10858 Length=165
MFENEANDLHRAVQHYEQAADYFKGEESTSSANKCMLKVAQYAAQLEDYEKAIQIYESVA
GSCLDSSLLKYSAKEYFFRASLCHLSVDLLNAQHALDKYASQYPAFQDSREFKLVKTLIE
HLEEQNIDGYTEAVKDYDSISRLDQWYTTILLRIKKQHNDNPDLR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g10858.t16 CDD cd15832 SNAP 1 156 2.41465E-72
6 g10858.t16 Coils Coil Coil 39 59 -
5 g10858.t16 Gene3D G3DSA:1.25.40.10 - 1 164 6.4E-66
2 g10858.t16 PANTHER PTHR13768 SOLUBLE NSF ATTACHMENT PROTEIN SNAP 2 164 9.1E-72
3 g10858.t16 PANTHER PTHR13768:SF23 ALPHA-SOLUBLE NSF ATTACHMENT PROTEIN 2 164 9.1E-72
1 g10858.t16 Pfam PF14938 Soluble NSF attachment protein, SNAP 2 157 2.5E-59
4 g10858.t16 SUPERFAMILY SSF48452 TPR-like 3 161 2.18E-40

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

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