General information for g11879.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ras-like GTP-binding protein RhoL.
Parent gene
- The parent gene g11879 is located on chr_1: 18945276..18946630 (- 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 | g11879 | g11879.t1 | TTS | g11879.t1 | 18944415 | 18944415 |
| chr_1 | g11879 | g11879.t1 | isoform | g11879.t1 | 18945276 | 18946225 |
| chr_1 | g11879 | g11879.t1 | exon | g11879.t1.exon1 | 18945276 | 18945481 |
| chr_1 | g11879 | g11879.t1 | cds | g11879.t1.CDS1 | 18945276 | 18945481 |
| chr_1 | g11879 | g11879.t1 | exon | g11879.t1.exon2 | 18945547 | 18945664 |
| chr_1 | g11879 | g11879.t1 | cds | g11879.t1.CDS2 | 18945547 | 18945664 |
| chr_1 | g11879 | g11879.t1 | exon | g11879.t1.exon3 | 18945723 | 18945757 |
| chr_1 | g11879 | g11879.t1 | cds | g11879.t1.CDS3 | 18945723 | 18945757 |
| chr_1 | g11879 | g11879.t1 | exon | g11879.t1.exon4 | 18945826 | 18945837 |
| chr_1 | g11879 | g11879.t1 | cds | g11879.t1.CDS4 | 18945826 | 18945837 |
| chr_1 | g11879 | g11879.t1 | exon | g11879.t1.exon5 | 18945919 | 18945926 |
| chr_1 | g11879 | g11879.t1 | cds | g11879.t1.CDS5 | 18945919 | 18945926 |
| chr_1 | g11879 | g11879.t1 | exon | g11879.t1.exon6 | 18946000 | 18946059 |
| chr_1 | g11879 | g11879.t1 | cds | g11879.t1.CDS6 | 18946000 | 18946059 |
| chr_1 | g11879 | g11879.t1 | exon | g11879.t1.exon7 | 18946119 | 18946225 |
| chr_1 | g11879 | g11879.t1 | cds | g11879.t1.CDS7 | 18946119 | 18946225 |
| chr_1 | g11879 | g11879.t1 | TSS | g11879.t1 | 18946677 | 18946677 |
Sequences
>g11879.t1 Gene=g11879 Length=546
ATGAGACCGTTAAAGATTACAACAGTTGGTGATGGAGCTGTCGGAAAAACGTGCATGTTG
ATTTCATACACACAAAATGAATTTCCCGTAGAATATGTACCGACAGTATTTGATAATCAT
GCATGTACAATTACTGTGGATAATAAAGAGTACTCACTAACATTATGGGACACAGCTGGA
CAAGAAGACTATGAGAGGCTGCGCCCATTAAGTTACCCGAATACTGATTGTTTTCTTTTG
TGCTATTCTATGGACTCCAGAACCTCTTTTGAGAATGTTTCTTCAAAATGGAATCCTGAA
ATAAGACACTTTTCGCCACATGTTCCAATCGTCCTAGTCGGCACAAAATCAGATTTGAGA
ATTCAGGGATCAGAAAAATATGTAACTACACAAGAGGCAAAAAAATTATGCAAAAAGATT
GGAGCATACACTTTAGTCGAGTGCTCTGCAAAGAAGAAAACAAATTTAGTGACGGTATTT
GAAGAGGCCGTCAGAGCGGTGGAAAAGAAAAAACCGAGAACTAGAGAACCTTGTAAAATT
CTCTAA
>g11879.t1 Gene=g11879 Length=181
MRPLKITTVGDGAVGKTCMLISYTQNEFPVEYVPTVFDNHACTITVDNKEYSLTLWDTAG
QEDYERLRPLSYPNTDCFLLCYSMDSRTSFENVSSKWNPEIRHFSPHVPIVLVGTKSDLR
IQGSEKYVTTQEAKKLCKKIGAYTLVECSAKKKTNLVTVFEEAVRAVEKKKPRTREPCKI
L
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g11879.t1 | CDD | cd00157 | Rho | 4 | 166 | 0.000 |
| 10 | g11879.t1 | Gene3D | G3DSA:3.40.50.300 | - | 3 | 181 | 0.000 |
| 2 | g11879.t1 | PANTHER | PTHR24072 | RHO FAMILY GTPASE | 2 | 178 | 0.000 |
| 3 | g11879.t1 | PANTHER | PTHR24072:SF305 | RAS-LIKE GTP-BINDING PROTEIN RHOL | 2 | 178 | 0.000 |
| 8 | g11879.t1 | PRINTS | PR00449 | Transforming protein P21 ras signature | 4 | 25 | 0.000 |
| 4 | g11879.t1 | PRINTS | PR00449 | Transforming protein P21 ras signature | 27 | 43 | 0.000 |
| 7 | g11879.t1 | PRINTS | PR00449 | Transforming protein P21 ras signature | 44 | 66 | 0.000 |
| 6 | g11879.t1 | PRINTS | PR00449 | Transforming protein P21 ras signature | 106 | 119 | 0.000 |
| 5 | g11879.t1 | PRINTS | PR00449 | Transforming protein P21 ras signature | 145 | 167 | 0.000 |
| 1 | g11879.t1 | Pfam | PF00071 | Ras family | 5 | 168 | 0.000 |
| 16 | g11879.t1 | ProSiteProfiles | PS51420 | small GTPase Rho family profile. | 1 | 167 | 24.478 |
| 12 | g11879.t1 | SMART | SM00173 | ras_sub_4 | 1 | 170 | 0.000 |
| 13 | g11879.t1 | SMART | SM00175 | rab_sub_5 | 4 | 170 | 0.000 |
| 14 | g11879.t1 | SMART | SM00174 | rho_sub_3 | 6 | 170 | 0.000 |
| 9 | g11879.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 3 | 167 | 0.000 |
| 15 | g11879.t1 | TIGRFAM | TIGR00231 | small_GTP: small GTP-binding protein domain | 1 | 162 | 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 transcript has been annotated with K04392 (Ras-related C3 botulinum toxin substrate 1)
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.
