General information for g14235.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ras-related protein Rab-10.
Parent gene
- The parent gene g14235 is located on chr_1: 35699630..35701706 (+ 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 | g14235 | g14235.t1 | TSS | g14235.t1 | 35698312 | 35698312 |
| chr_1 | g14235 | g14235.t1 | isoform | g14235.t1 | 35698390 | 35699830 |
| chr_1 | g14235 | g14235.t1 | exon | g14235.t1.exon1 | 35698390 | 35698437 |
| chr_1 | g14235 | g14235.t1 | cds | g14235.t1.CDS1 | 35698390 | 35698437 |
| chr_1 | g14235 | g14235.t1 | exon | g14235.t1.exon2 | 35698566 | 35698644 |
| chr_1 | g14235 | g14235.t1 | cds | g14235.t1.CDS2 | 35698566 | 35698644 |
| chr_1 | g14235 | g14235.t1 | exon | g14235.t1.exon3 | 35699139 | 35699187 |
| chr_1 | g14235 | g14235.t1 | cds | g14235.t1.CDS3 | 35699139 | 35699187 |
| chr_1 | g14235 | g14235.t1 | exon | g14235.t1.exon4 | 35699261 | 35699276 |
| chr_1 | g14235 | g14235.t1 | cds | g14235.t1.CDS4 | 35699261 | 35699276 |
| chr_1 | g14235 | g14235.t1 | exon | g14235.t1.exon5 | 35699340 | 35699564 |
| chr_1 | g14235 | g14235.t1 | cds | g14235.t1.CDS5 | 35699340 | 35699564 |
| chr_1 | g14235 | g14235.t1 | exon | g14235.t1.exon6 | 35699630 | 35699830 |
| chr_1 | g14235 | g14235.t1 | cds | g14235.t1.CDS6 | 35699630 | 35699830 |
| chr_1 | g14235 | g14235.t1 | TTS | g14235.t1 | 35699972 | 35699972 |
Sequences
>g14235.t1 Gene=g14235 Length=618
ATGTCTAAGAAGACTTACGATTTGCTGTTTAAATTATTATTGATTGGTGACTCGGGTGTC
GGAAAAACTTGCATTCTGTTTAGATTCAGTGATGATGCATTTACATCAACGTTTATATCT
ACCATAGGAATTGATTTCAAAATCAAAACAGTCGAGTTAAGAGGAAAGAAAATCAAATTG
CAAATATGGGATACCGCTGGTCAAGAAAGATTTCACACAATCACAACCTCTTATTATCGT
GGAGCTATGGGTATTATGTTGGTGTATGACATAACAAATGAAAAGAGTTTTGAGAATATA
ATAAAGTGGCTTCGGAATATTGATGAACATGCTAATGAAGATGTTGAACGAATGATTCTT
GGCAATAAATGTGATATGACTGATAAACGAGTTGTCAGTAAAGAACGTGGTGAAAATATT
GCTCGCGAATATGGAATTCGCTTCATGGAAACATCAGCCAAAGCAAACATTAATATTGAA
AAAGCATTTAGCGAACTTGCAGAAGCAATTCTAGATCAAACAGCTGGAAAAGAAAATAAT
GATAATCAAGAGCGCGTTGTTGTAGATCGAAAAAATCAAGAAAAATCACCGGCTTACAGT
AGATGTTGTACATCTTAA
>g14235.t1 Gene=g14235 Length=205
MSKKTYDLLFKLLLIGDSGVGKTCILFRFSDDAFTSTFISTIGIDFKIKTVELRGKKIKL
QIWDTAGQERFHTITTSYYRGAMGIMLVYDITNEKSFENIIKWLRNIDEHANEDVERMIL
GNKCDMTDKRVVSKERGENIAREYGIRFMETSAKANINIEKAFSELAEAILDQTAGKENN
DNQERVVVDRKNQEKSPAYSRCCTS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g14235.t1 | CDD | cd01867 | Rab8_Rab10_Rab13_like | 7 | 173 | 1.3631E-117 |
| 10 | g14235.t1 | Gene3D | G3DSA:3.40.50.300 | - | 3 | 203 | 6.4E-71 |
| 2 | g14235.t1 | PANTHER | PTHR47980 | LD44762P | 1 | 193 | 2.9E-97 |
| 3 | g14235.t1 | PANTHER | PTHR47980:SF36 | RAS-RELATED PROTEIN RAB-10 | 1 | 193 | 2.9E-97 |
| 4 | g14235.t1 | PRINTS | PR00449 | Transforming protein P21 ras signature | 10 | 31 | 3.2E-43 |
| 5 | g14235.t1 | PRINTS | PR00449 | Transforming protein P21 ras signature | 33 | 49 | 3.2E-43 |
| 7 | g14235.t1 | PRINTS | PR00449 | Transforming protein P21 ras signature | 51 | 73 | 3.2E-43 |
| 6 | g14235.t1 | PRINTS | PR00449 | Transforming protein P21 ras signature | 113 | 126 | 3.2E-43 |
| 8 | g14235.t1 | PRINTS | PR00449 | Transforming protein P21 ras signature | 148 | 170 | 3.2E-43 |
| 1 | g14235.t1 | Pfam | PF00071 | Ras family | 11 | 171 | 4.5E-66 |
| 12 | g14235.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 21 | - |
| 13 | g14235.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 7 | - |
| 14 | g14235.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 8 | 16 | - |
| 15 | g14235.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 17 | 21 | - |
| 11 | g14235.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 22 | 205 | - |
| 23 | g14235.t1 | ProSiteProfiles | PS51419 | small GTPase Rab1 family profile. | 5 | 203 | 37.027 |
| 18 | g14235.t1 | SMART | SM00177 | arf_sub_2 | 1 | 174 | 0.0036 |
| 17 | g14235.t1 | SMART | SM00173 | ras_sub_4 | 7 | 173 | 6.5E-30 |
| 19 | g14235.t1 | SMART | SM00175 | rab_sub_5 | 10 | 173 | 1.4E-105 |
| 21 | g14235.t1 | SMART | SM00174 | rho_sub_3 | 12 | 173 | 1.4E-12 |
| 20 | g14235.t1 | SMART | SM00176 | ran_sub_2 | 15 | 199 | 3.7E-6 |
| 9 | g14235.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 5 | 183 | 2.01E-62 |
| 22 | g14235.t1 | TIGRFAM | TIGR00231 | small_GTP: small GTP-binding protein domain | 10 | 165 | 3.9E-31 |
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:0005525 | GTP binding | MF |
| GO:0003924 | GTPase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K07903 (Ras-related protein Rab-10)
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.
