Gene loci information

Transcript annotation

  • This transcript has been annotated as GTP-binding protein SAR1.

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 g1978 g1978.t57 TSS g1978.t57 14174170 14174170
chr_3 g1978 g1978.t57 isoform g1978.t57 14174227 14175479
chr_3 g1978 g1978.t57 exon g1978.t57.exon1 14174227 14174834
chr_3 g1978 g1978.t57 cds g1978.t57.CDS1 14174792 14174834
chr_3 g1978 g1978.t57 exon g1978.t57.exon2 14175073 14175479
chr_3 g1978 g1978.t57 cds g1978.t57.CDS2 14175073 14175479
chr_3 g1978 g1978.t57 TTS g1978.t57 14176066 14176066

Sequences

>g1978.t57 Gene=g1978 Length=1015
ACTGCGTTAATTGATAAGTTAGCTAAGAAAATTATAGTAATTTAGTTGGTTTAAGAGGTA
GGCCATAGTGTGAATTAAAAAATTGTGCTATATTACATATAGTTATTGAGAAACAGTCAA
TTTGTTATTTTGGTGAAAATGTTCGAGAGTTGAAGATATGCTGGCCCTGAAAATTAGTCT
CTCATATGTAGTGTATAGCCACTATACTGCTTTATATTTTAAAAGTGTGATTGCTTACGA
ATGAAGAAAATTACTGACGATGATCAAAATATTAATTTTGATTGTATGCAATATCTCGAA
ACACAAAAACTCATCATTTCTTCTTGTGTAAACTGTACATATGAAAAGTAAAAGAAGCAA
TATTTAAAGTCATTATCTAAATATTGAGTATTGAGAAAAGACAGATAAACTAATAATCAG
CGAATTAAAATACTGTAAAAATATTTTTTAGTCTGCAATTAGTGACGTAGCATAATTTTT
TTTGAACTTTGTCTCTGATGATTTACTTGCATTGTATTGATATTCATCGTCCTCTTTTCT
ATTAGATTACAGCAAATTATTCACAATGTTCATTTGGGACTGGTTCACTGGTGTTTTAGG
ATATTTGGGATTATGGAAGAAGTCGGGCAAATTATTATTTCTCGGATTAGATAATGCTGG
TAAAACAACTTTATTACATATGCTTAAGGACGACAGATTAGCACAACATGTTCCAACACT
TCATCCAACGTCAGAAGAATTGTCTATAGGCAATATGCGCTTCACAACTTTCGATTTAGG
TGGTCACACACAGGCACGTCGTGTGTGGAAGGACTATTTTCCAGCTGTTGATGCAATTGT
CTTCTTAATTGATGCATGGGATCGTAGTCGTTTTCAAGAGAGCAAAAATGAATTGGATTC
ATTGTTAACTGATGAAGCATTATCGAATTGTCCCGTTCTCATATTGGGAAATAAAATTGA
CAAACCGGGAGCTGCCAGTGAAGACGAATTGAGAAATTTTTATGGACTTTATCAA

>g1978.t57 Gene=g1978 Length=150
MFIWDWFTGVLGYLGLWKKSGKLLFLGLDNAGKTTLLHMLKDDRLAQHVPTLHPTSEELS
IGNMRFTTFDLGGHTQARRVWKDYFPAVDAIVFLIDAWDRSRFQESKNELDSLLTDEALS
NCPVLILGNKIDKPGAASEDELRNFYGLYQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g1978.t57 CDD cd00879 Sar1 2 150 0.00
8 g1978.t57 Gene3D G3DSA:3.40.50.300 - 21 150 0.00
2 g1978.t57 PANTHER PTHR45684 RE74312P 1 149 0.00
6 g1978.t57 PRINTS PR00328 GTP-binding SAR1 protein signature 22 45 0.00
5 g1978.t57 PRINTS PR00328 GTP-binding SAR1 protein signature 50 74 0.00
4 g1978.t57 PRINTS PR00328 GTP-binding SAR1 protein signature 77 102 0.00
3 g1978.t57 PRINTS PR00328 GTP-binding SAR1 protein signature 122 143 0.00
1 g1978.t57 Pfam PF00025 ADP-ribosylation factor family 8 149 0.00
13 g1978.t57 ProSiteProfiles PS51422 small GTPase SAR1 family profile. 14 150 24.79
10 g1978.t57 SMART SM00177 arf_sub_2 3 150 0.00
11 g1978.t57 SMART SM00178 sar_sub_1 4 150 0.00
7 g1978.t57 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 17 144 0.00
12 g1978.t57 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 19 140 0.00

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:0005525 GTP 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