General information for g9936.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ras-related protein Rac1.
Parent gene
- The parent gene g9936 is located on chr_1: 6093213..6094323 (+ strand)
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.t12 | TSS | g9936.t12 | 6091368 | 6091368 |
| chr_1 | g9936 | g9936.t12 | isoform | g9936.t12 | 6092298 | 6094323 |
| chr_1 | g9936 | g9936.t12 | exon | g9936.t12.exon1 | 6092298 | 6092819 |
| chr_1 | g9936 | g9936.t12 | cds | g9936.t12.CDS1 | 6092645 | 6092819 |
| chr_1 | g9936 | g9936.t12 | exon | g9936.t12.exon2 | 6092880 | 6093115 |
| chr_1 | g9936 | g9936.t12 | cds | g9936.t12.CDS2 | 6092880 | 6093115 |
| chr_1 | g9936 | g9936.t12 | exon | g9936.t12.exon3 | 6093199 | 6094323 |
| chr_1 | g9936 | g9936.t12 | cds | g9936.t12.CDS3 | 6093199 | 6093354 |
| chr_1 | g9936 | g9936.t12 | TTS | g9936.t12 | 6094759 | 6094759 |
Sequences
>g9936.t12 Gene=g9936 Length=1883
ATGCAGGCCATCAAATGTGTTGTTGTTGGTGACGGGTGAGTTACAGAATTTTTTTTATTA
AACATTCTTGCTGTTGCATAATTTTTTCACATTACATGTTTATTACAAAAGGGTCAAATT
TCATTGATGTGTGCACATAAATTTGGCTTGTGCATGCATCAAATCGGATATGCATTAAGA
GTTTAAATATGTGTATAAAACAAAATATCATACAATGACCGACCCTATATACAATAATAT
TAATGTATAAAGAATCAGTTTATTTAATTCAATTTATTATAACACATTAATGATTGAGCT
TCCATTGTGATTCATTCATCATAATTTACATTTTTTGCTTATGTATCATGAATTTTTTTG
TAATTTACAGTGCTGTCGGTAAGACGTGTCTTCTTATCAGTTACACCACAAATGCATTTC
CAGGAGAATATATTCCGACAGTCTTCGATAATTATTCTGCCAATGTTATGGTTGATGGCA
AACCAATCAATTTAGGCCTTTGGGATACAGCTGGTCAAGAAGATTACGACAGATTGCGTC
CATTGTCTTATCCACAAACTGATGTCTTCTTAATATGCTTTTCACTCGTAAACCCAGCAT
CTTTTGAAAATGTAAGAGCAAAGTGGTATCCTGAAGTTCGTCATCATTGTCCATCAACGC
CGATAATTTTGGTTGGAACAAAATTAGATTTACGAGACGACAAAAACACAATTGATAAAT
TGCGCGATAAAAAATTACAGCCAATTACATATCCACAGGGTCTTGCAATGGCAAAAGAAA
TTGGCTCAGTAAAGTATTTAGAATGTTCAGCGTTGACACAGAAAGGTTTAAAAACTGTAT
TTGACGAAGCAATTCGAGCAGTTTTGTGTCCTATAGTGCAGCCAAAGAAGAAAAATAAAT
GTACATTACTTTAAGCTGCTTTCAATTCTACATACACACCACCAATTTATACACACACAT
ACATTTCTTCTGCCTCTTGTTTTACCAAAATCTTGTTAAGAAAGAATAAAAAAACTTCAG
CAACAATTTAATTTCTACATGGACACACATGCATGATCGTACAAAAATAAGTGAAAAAAA
TTATGTGAAAGATTACATATGTAATGAAACTGAAAAATCAACTTGTTAGTGTCGCCAATT
TACATAAACTGAAAGTGAATTTGTACCGTCATTTTTTTGCATACTGTAAGATTCCTTCTT
AATATAATAACGAAACAAAAAGAAACAGAAAATCTTTTACTCGATGACGCGTCTAAAAAT
CAAAAAGAAGAAAAGTAGTGTATTGATAAAGCAAAAATGCAACAAAGGACGCATCAATTA
TTTAAAGTAAAAAGGTATATAAAAAATAATAAATTCTAATAACCAGATGTAAAACTTTTT
CTACTAAAACAGAACACAAAGAAAAAAATGATGTGAAAAACCAGAATATGAAAGTTTAGA
AAATAATTAATTGGTGAGAATCATAAAAATAGTAAAATATGATAATTGATTCTTTAATTT
TCATCAGCTTATTTTCAATTTCAACATACACTTTGTATGTGTGTATCTAAAAAAACTACC
TACCTACTACCTTTCTACTAGAGAATCCACAAGAAATGTGAACGAAATTGTTTATATATG
TTTTAACATTTAAAAAACTTTTATTATTGTATAACCTTGTTTAGCTATCTCGTTTAGCAT
ATTTTTATTTTTTCGCTTAAAGATTTTTTAATTTTATTTGAAACAAAAATTTTATTGCAA
AATCATTCTTAATGATAAAGTCATAATACTTTTCTCTTCCGTTCAAATCATGATGAATTT
TCATTTTAGTATCATAATTTTGATTTTAATTTACTGATTCACATAAAGTTTTCTCCATTT
TTAAGTTCACTAATTCTTATTTC
>g9936.t12 Gene=g9936 Length=188
MNFFVIYSAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDY
DRLRPLSYPQTDVFLICFSLVNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKN
TIDKLRDKKLQPITYPQGLAMAKEIGSVKYLECSALTQKGLKTVFDEAIRAVLCPIVQPK
KKNKCTLL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g9936.t12 | CDD | cd01871 | Rac1_like | 9 | 172 | 0.000 |
| 9 | g9936.t12 | Gene3D | G3DSA:3.40.50.300 | - | 4 | 177 | 0.000 |
| 2 | g9936.t12 | PANTHER | PTHR24072 | RHO FAMILY GTPASE | 7 | 188 | 0.000 |
| 3 | g9936.t12 | PANTHER | PTHR24072:SF105 | RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 | 7 | 188 | 0.000 |
| 7 | g9936.t12 | PRINTS | PR00449 | Transforming protein P21 ras signature | 23 | 39 | 0.000 |
| 6 | g9936.t12 | PRINTS | PR00449 | Transforming protein P21 ras signature | 40 | 62 | 0.000 |
| 4 | g9936.t12 | PRINTS | PR00449 | Transforming protein P21 ras signature | 102 | 115 | 0.000 |
| 5 | g9936.t12 | PRINTS | PR00449 | Transforming protein P21 ras signature | 150 | 172 | 0.000 |
| 1 | g9936.t12 | Pfam | PF00071 | Ras family | 8 | 173 | 0.000 |
| 15 | g9936.t12 | ProSiteProfiles | PS51420 | small GTPase Rho family profile. | 1 | 172 | 28.237 |
| 11 | g9936.t12 | SMART | SM00173 | ras_sub_4 | 1 | 175 | 0.000 |
| 12 | g9936.t12 | SMART | SM00175 | rab_sub_5 | 8 | 175 | 0.000 |
| 13 | g9936.t12 | SMART | SM00174 | rho_sub_3 | 8 | 175 | 0.000 |
| 8 | g9936.t12 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 8 | 172 | 0.000 |
| 14 | g9936.t12 | TIGRFAM | TIGR00231 | small_GTP: small GTP-binding protein domain | 9 | 143 | 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: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.
