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.t6 TSS g9936.t6 6091368 6091368
chr_1 g9936 g9936.t6 isoform g9936.t6 6091418 6093354
chr_1 g9936 g9936.t6 exon g9936.t6.exon1 6091418 6091508
chr_1 g9936 g9936.t6 exon g9936.t6.exon2 6092226 6092332
chr_1 g9936 g9936.t6 cds g9936.t6.CDS1 6092298 6092332
chr_1 g9936 g9936.t6 exon g9936.t6.exon3 6092668 6092819
chr_1 g9936 g9936.t6 cds g9936.t6.CDS2 6092668 6092819
chr_1 g9936 g9936.t6 exon g9936.t6.exon4 6092880 6093115
chr_1 g9936 g9936.t6 cds g9936.t6.CDS3 6092880 6093115
chr_1 g9936 g9936.t6 exon g9936.t6.exon5 6093199 6093354
chr_1 g9936 g9936.t6 cds g9936.t6.CDS4 6093199 6093354
chr_1 g9936 g9936.t6 TTS g9936.t6 6093656 6093656

Sequences

>g9936.t6 Gene=g9936 Length=742
AAGTAAAATAAAGAATTTCTATTAAAATTGTGTTTAGAAAACATCAAATCGACTTTTGTT
TATAACAATTAATCTTTAAGTAGCCTTGTAAGATAATTAATCTTTTTTTTCTAAGAAAAA
AGTATATTGGATAATCACAACATATATAAAGCATAAAATAATTATGCAGGCCATCAAATG
TGTTGTTGTTGGTGACGGTGCTGTCGGTAAGACGTGTCTTCTTATCAGTTACACCACAAA
TGCATTTCCAGGAGAATATATTCCGACAGTCTTCGATAATTATTCTGCCAATGTTATGGT
TGATGGCAAACCAATCAATTTAGGCCTTTGGGATACAGCTGGTCAAGAAGATTACGACAG
ATTGCGTCCATTGTCTTATCCACAAACTGATGTCTTCTTAATATGCTTTTCACTCGTAAA
CCCAGCATCTTTTGAAAATGTAAGAGCAAAGTGGTATCCTGAAGTTCGTCATCATTGTCC
ATCAACGCCGATAATTTTGGTTGGAACAAAATTAGATTTACGAGACGACAAAAACACAAT
TGATAAATTGCGCGATAAAAAATTACAGCCAATTACATATCCACAGGGTCTTGCAATGGC
AAAAGAAATTGGCTCAGTAAAGTATTTAGAATGTTCAGCGTTGACACAGAAAGGTTTAAA
AACTGTATTTGACGAAGCAATTCGAGCAGTTTTGTGTCCTATAGTGCAGCCAAAGAAGAA
AAATAAATGTACATTACTTTAA

>g9936.t6 Gene=g9936 Length=192
MQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAG
QEDYDRLRPLSYPQTDVFLICFSLVNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLR
DDKNTIDKLRDKKLQPITYPQGLAMAKEIGSVKYLECSALTQKGLKTVFDEAIRAVLCPI
VQPKKKNKCTLL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g9936.t6 CDD cd01871 Rac1_like 3 176 0.0000
10 g9936.t6 Gene3D G3DSA:3.40.50.300 - 1 181 0.0000
2 g9936.t6 PANTHER PTHR24072 RHO FAMILY GTPASE 1 192 0.0000
3 g9936.t6 PANTHER PTHR24072:SF105 RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 1 192 0.0000
8 g9936.t6 PRINTS PR00449 Transforming protein P21 ras signature 4 25 0.0000
4 g9936.t6 PRINTS PR00449 Transforming protein P21 ras signature 27 43 0.0000
7 g9936.t6 PRINTS PR00449 Transforming protein P21 ras signature 44 66 0.0000
5 g9936.t6 PRINTS PR00449 Transforming protein P21 ras signature 106 119 0.0000
6 g9936.t6 PRINTS PR00449 Transforming protein P21 ras signature 154 176 0.0000
1 g9936.t6 Pfam PF00071 Ras family 5 177 0.0000
17 g9936.t6 ProSiteProfiles PS51420 small GTPase Rho family profile. 1 176 29.7600
12 g9936.t6 SMART SM00173 ras_sub_4 1 179 0.0000
13 g9936.t6 SMART SM00175 rab_sub_5 4 179 0.0000
15 g9936.t6 SMART SM00174 rho_sub_3 6 179 0.0000
14 g9936.t6 SMART SM00176 ran_sub_2 9 192 0.0069
9 g9936.t6 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 4 176 0.0000
16 g9936.t6 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 1 147 0.0000

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

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