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.t60 TSS g1978.t60 14174170 14174170
chr_3 g1978 g1978.t60 isoform g1978.t60 14174406 14176064
chr_3 g1978 g1978.t60 exon g1978.t60.exon1 14174406 14174660
chr_3 g1978 g1978.t60 exon g1978.t60.exon2 14174772 14174834
chr_3 g1978 g1978.t60 cds g1978.t60.CDS1 14174792 14174834
chr_3 g1978 g1978.t60 exon g1978.t60.exon3 14175073 14175494
chr_3 g1978 g1978.t60 cds g1978.t60.CDS2 14175073 14175494
chr_3 g1978 g1978.t60 exon g1978.t60.exon4 14175559 14176064
chr_3 g1978 g1978.t60 cds g1978.t60.CDS3 14175559 14175675
chr_3 g1978 g1978.t60 TTS g1978.t60 14176066 14176066

Sequences

>g1978.t60 Gene=g1978 Length=1246
TCTCATATGTAGTGTATAGCCACTATACTGCTTTATATTTTAAAAGTGTGATTGCTTACG
AATGAAGAAAATTACTGACGATGATCAAAATATTAATTTTGATTGTATGCAATATCTCGA
AACACAAAAACTCATCATTTCTTCTTGTGTAAACTGTACATATGAAAAGTAAAAGAAGCA
ATATTTAAAGTCATTATCTAAATATTGAGTATTGAGAAAAGACAGATAAACTAATAATCA
GCGAATTAAAATACTATTACAGCAAATTATTCACAATGTTCATTTGGGACTGGTTCACTG
GTGTTTTAGGATATTTGGGATTATGGAAGAAGTCGGGCAAATTATTATTTCTCGGATTAG
ATAATGCTGGTAAAACAACTTTATTACATATGCTTAAGGACGACAGATTAGCACAACATG
TTCCAACACTTCATCCAACGTCAGAAGAATTGTCTATAGGCAATATGCGCTTCACAACTT
TCGATTTAGGTGGTCACACACAGGCACGTCGTGTGTGGAAGGACTATTTTCCAGCTGTTG
ATGCAATTGTCTTCTTAATTGATGCATGGGATCGTAGTCGTTTTCAAGAGAGCAAAAATG
AATTGGATTCATTGTTAACTGATGAAGCATTATCGAATTGTCCCGTTCTCATATTGGGAA
ATAAAATTGACAAACCGGGAGCTGCCAGTGAAGACGAATTGAGAAATTTTTATGGACTTT
ATCAACTTACAACAGGAAAGGGAAAAATTTCAAGATCAGATTTAGCAGGCCGTCCATTAG
AACTTTTTATGTGCTCGGTGCTGAAGAGACAAGGATATGGTGAAGGTTTTCGCTGGTTAG
CTCAATATATCGATTAAAAATTATGAAGTCGACCATAATATTTTTAAATCAACCAACAAC
AACAATAATTAAAAAGCGTAAAGTTTCAAAATTCCCAACGCAAAGGTTTCACAAAATGAA
ACAAATTTTTACAAATTAATTAATTTAATATGCAACATTTGTGAATGATATGATATCAAA
TTCTTCAAAAAAAGACATCGTGGGATACAATAAAATAAAAAAAATAGTGAAAGAATCCTT
TTTTAAACCATAATACCTAATTGTATAATGATTATCAACATATTTATATTTTTGGTTTCT
GAGCAACTTGATGTGTTATCATTACTTTTTTAAACTATTGGAATGAAATCTGCTTCAAAA
AAGGCCGTTTGAAATAATAAAAGGAAACAATCTTTTTCTCATAAAT

>g1978.t60 Gene=g1978 Length=193
MFIWDWFTGVLGYLGLWKKSGKLLFLGLDNAGKTTLLHMLKDDRLAQHVPTLHPTSEELS
IGNMRFTTFDLGGHTQARRVWKDYFPAVDAIVFLIDAWDRSRFQESKNELDSLLTDEALS
NCPVLILGNKIDKPGAASEDELRNFYGLYQLTTGKGKISRSDLAGRPLELFMCSVLKRQG
YGEGFRWLAQYID

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g1978.t60 CDD cd00879 Sar1 2 192 0.000
9 g1978.t60 Gene3D G3DSA:3.40.50.300 - 21 192 0.000
2 g1978.t60 PANTHER PTHR45684 RE74312P 1 192 0.000
7 g1978.t60 PRINTS PR00328 GTP-binding SAR1 protein signature 22 45 0.000
6 g1978.t60 PRINTS PR00328 GTP-binding SAR1 protein signature 50 74 0.000
4 g1978.t60 PRINTS PR00328 GTP-binding SAR1 protein signature 77 102 0.000
3 g1978.t60 PRINTS PR00328 GTP-binding SAR1 protein signature 122 143 0.000
5 g1978.t60 PRINTS PR00328 GTP-binding SAR1 protein signature 166 190 0.000
1 g1978.t60 Pfam PF00025 ADP-ribosylation factor family 8 192 0.000
14 g1978.t60 ProSiteProfiles PS51422 small GTPase SAR1 family profile. 14 192 31.336
11 g1978.t60 SMART SM00177 arf_sub_2 3 180 0.000
12 g1978.t60 SMART SM00178 sar_sub_1 4 192 0.000
8 g1978.t60 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 17 192 0.000
13 g1978.t60 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 19 142 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