Gene loci information

Transcript annotation

  • This transcript has been annotated as Ras-related protein Rac1.

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 g9936 g9936.t11 TSS g9936.t11 6091368 6091368
chr_1 g9936 g9936.t11 isoform g9936.t11 6091917 6093031
chr_1 g9936 g9936.t11 exon g9936.t11.exon1 6091917 6091973
chr_1 g9936 g9936.t11 exon g9936.t11.exon2 6092226 6092332
chr_1 g9936 g9936.t11 cds g9936.t11.CDS1 6092298 6092332
chr_1 g9936 g9936.t11 exon g9936.t11.exon3 6092668 6092819
chr_1 g9936 g9936.t11 cds g9936.t11.CDS2 6092668 6092819
chr_1 g9936 g9936.t11 exon g9936.t11.exon4 6092880 6093031
chr_1 g9936 g9936.t11 cds g9936.t11.CDS3 6092880 6093031
chr_1 g9936 g9936.t11 TTS g9936.t11 6093656 6093656

Sequences

>g9936.t11 Gene=g9936 Length=468
TCTCAGTAAATACCTTGAAAATGTTGACCTTCAGAATTAATACAGTCAGATTTTTTAGAT
AATTAATCTTTTTTTTCTAAGAAAAAAGTATATTGGATAATCACAACATATATAAAGCAT
AAAATAATTATGCAGGCCATCAAATGTGTTGTTGTTGGTGACGGTGCTGTCGGTAAGACG
TGTCTTCTTATCAGTTACACCACAAATGCATTTCCAGGAGAATATATTCCGACAGTCTTC
GATAATTATTCTGCCAATGTTATGGTTGATGGCAAACCAATCAATTTAGGCCTTTGGGAT
ACAGCTGGTCAAGAAGATTACGACAGATTGCGTCCATTGTCTTATCCACAAACTGATGTC
TTCTTAATATGCTTTTCACTCGTAAACCCAGCATCTTTTGAAAATGTAAGAGCAAAGTGG
TATCCTGAAGTTCGTCATCATTGTCCATCAACGCCGATAATTTTGGTT

>g9936.t11 Gene=g9936 Length=113
MQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAG
QEDYDRLRPLSYPQTDVFLICFSLVNPASFENVRAKWYPEVRHHCPSTPIILV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g9936.t11 Gene3D G3DSA:3.40.50.300 - 1 113 0.0000000
2 g9936.t11 PANTHER PTHR24072:SF291 - 1 113 0.0000000
3 g9936.t11 PANTHER PTHR24072 RHO FAMILY GTPASE 1 113 0.0000000
7 g9936.t11 PRINTS PR00449 Transforming protein P21 ras signature 4 25 0.0000000
5 g9936.t11 PRINTS PR00449 Transforming protein P21 ras signature 27 43 0.0000000
6 g9936.t11 PRINTS PR00449 Transforming protein P21 ras signature 44 66 0.0000000
4 g9936.t11 PRINTS PR00449 Transforming protein P21 ras signature 106 113 0.0000000
1 g9936.t11 Pfam PF00071 Ras family 5 113 0.0000000
13 g9936.t11 ProSiteProfiles PS51420 small GTPase Rho family profile. 1 113 21.2750000
10 g9936.t11 SMART SM00173 ras_sub_4 1 113 0.0000029
11 g9936.t11 SMART SM00175 rab_sub_5 4 113 0.0000019
12 g9936.t11 SMART SM00174 rho_sub_3 6 113 0.0000000
8 g9936.t11 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 4 113 0.0000000
14 g9936.t11 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 1 113 0.0000000

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:0007264 small GTPase mediated signal transduction BP
GO:0005525 GTP binding MF
GO:0003924 GTPase activity 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