Gene loci information

Transcript annotation

  • This transcript has been annotated as GTP-binding protein SAR1b.

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.t62 TSS g1978.t62 14174170 14174170
chr_3 g1978 g1978.t62 isoform g1978.t62 14174770 14175675
chr_3 g1978 g1978.t62 exon g1978.t62.exon1 14174770 14175494
chr_3 g1978 g1978.t62 cds g1978.t62.CDS1 14175060 14175494
chr_3 g1978 g1978.t62 exon g1978.t62.exon2 14175559 14175675
chr_3 g1978 g1978.t62 cds g1978.t62.CDS2 14175559 14175675
chr_3 g1978 g1978.t62 TTS g1978.t62 14176066 14176066

Sequences

>g1978.t62 Gene=g1978 Length=842
AGATTACAGCAAATTATTCACAATGTTCATTTGGGACTGGTTCACTGGTGTTTTAGGATA
TTTGGGTGAGTTTCTTTATTTCATTTCACTTTCTTTTGTTCATGTTCTTTTTTTAAACGC
TCATCATCTGATCATGCTATACGTACGTAAAAAATCATTCATCTGATTGTATGCATTGTT
TTTTACTTTATTATTAATAATATCATTGAACAAAGAGAGAATTCAATAAATTTTCCCTCA
TCACTTCTTATCATTTTTGTTTACAAAATTAATAATTCTCTTATTATTTTATGTCTATTT
TAGGATTATGGAAGAAGTCGGGCAAATTATTATTTCTCGGATTAGATAATGCTGGTAAAA
CAACTTTATTACATATGCTTAAGGACGACAGATTAGCACAACATGTTCCAACACTTCATC
CAACGTCAGAAGAATTGTCTATAGGCAATATGCGCTTCACAACTTTCGATTTAGGTGGTC
ACACACAGGCACGTCGTGTGTGGAAGGACTATTTTCCAGCTGTTGATGCAATTGTCTTCT
TAATTGATGCATGGGATCGTAGTCGTTTTCAAGAGAGCAAAAATGAATTGGATTCATTGT
TAACTGATGAAGCATTATCGAATTGTCCCGTTCTCATATTGGGAAATAAAATTGACAAAC
CGGGAGCTGCCAGTGAAGACGAATTGAGAAATTTTTATGGACTTTATCAACTTACAACAG
GAAAGGGAAAAATTTCAAGATCAGATTTAGCAGGCCGTCCATTAGAACTTTTTATGTGCT
CGGTGCTGAAGAGACAAGGATATGGTGAAGGTTTTCGCTGGTTAGCTCAATATATCGATT
AA

>g1978.t62 Gene=g1978 Length=183
MSILGLWKKSGKLLFLGLDNAGKTTLLHMLKDDRLAQHVPTLHPTSEELSIGNMRFTTFD
LGGHTQARRVWKDYFPAVDAIVFLIDAWDRSRFQESKNELDSLLTDEALSNCPVLILGNK
IDKPGAASEDELRNFYGLYQLTTGKGKISRSDLAGRPLELFMCSVLKRQGYGEGFRWLAQ
YID

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g1978.t62 CDD cd00879 Sar1 4 182 0.000
10 g1978.t62 Gene3D G3DSA:3.40.50.300 - 11 182 0.000
2 g1978.t62 PANTHER PTHR45684 RE74312P 3 183 0.000
3 g1978.t62 PANTHER PTHR45684:SF20 GTP-BINDING PROTEIN SAR1B 3 183 0.000
8 g1978.t62 PRINTS PR00328 GTP-binding SAR1 protein signature 12 35 0.000
6 g1978.t62 PRINTS PR00328 GTP-binding SAR1 protein signature 40 64 0.000
5 g1978.t62 PRINTS PR00328 GTP-binding SAR1 protein signature 67 92 0.000
7 g1978.t62 PRINTS PR00328 GTP-binding SAR1 protein signature 112 133 0.000
4 g1978.t62 PRINTS PR00328 GTP-binding SAR1 protein signature 156 180 0.000
1 g1978.t62 Pfam PF00025 ADP-ribosylation factor family 3 182 0.000
15 g1978.t62 ProSiteProfiles PS51422 small GTPase SAR1 family profile. 4 182 31.336
13 g1978.t62 SMART SM00178 sar_sub_1 1 182 0.000
12 g1978.t62 SMART SM00177 arf_sub_2 4 170 0.000
9 g1978.t62 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 7 182 0.000
14 g1978.t62 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 9 132 0.000

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