General information for g11236.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ras-related protein Rab-35.
Parent gene
- The parent gene g11236 is located on chr_1: 14846104..14847212 (+ 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 | g11236 | g11236.t1 | TSS | g11236.t1 | 14842856 | 14842856 |
| chr_1 | g11236 | g11236.t1 | isoform | g11236.t1 | 14843314 | 14846360 |
| chr_1 | g11236 | g11236.t1 | exon | g11236.t1.exon1 | 14843314 | 14843365 |
| chr_1 | g11236 | g11236.t1 | cds | g11236.t1.CDS1 | 14843314 | 14843365 |
| chr_1 | g11236 | g11236.t1 | exon | g11236.t1.exon2 | 14845575 | 14845711 |
| chr_1 | g11236 | g11236.t1 | cds | g11236.t1.CDS2 | 14845575 | 14845711 |
| chr_1 | g11236 | g11236.t1 | exon | g11236.t1.exon3 | 14845770 | 14845807 |
| chr_1 | g11236 | g11236.t1 | cds | g11236.t1.CDS3 | 14845770 | 14845807 |
| chr_1 | g11236 | g11236.t1 | exon | g11236.t1.exon4 | 14845914 | 14846038 |
| chr_1 | g11236 | g11236.t1 | cds | g11236.t1.CDS4 | 14845914 | 14846038 |
| chr_1 | g11236 | g11236.t1 | exon | g11236.t1.exon5 | 14846104 | 14846360 |
| chr_1 | g11236 | g11236.t1 | cds | g11236.t1.CDS5 | 14846104 | 14846360 |
| chr_1 | g11236 | g11236.t1 | TTS | g11236.t1 | 14847140 | 14847140 |
Sequences
>g11236.t1 Gene=g11236 Length=609
ATGGCAAGAGACTATGATCATTTATTTAAGTTACTGATAATAGGCGATAGCGGTGTCGGA
AAGTCATCATTACTCATACGGTTTAGCGACAATACTTTTAGCGGTAGCTACATTACAACA
ATCGGTGTTGATTTCAAAATACGAACAGTTGTCATCGGTGGTGAACGAGTAAAACTTCAG
ATTTGGGACACTGCTGGACAAGAGCGATTCAGAACAATAACAAACACATATTACAGAGGA
ACACACGGTGTGATTGTTGTGTACGATGTTACAAATGGCGAATCGTTTGCTAATGTAAAG
AGGTGGCTTCAAGAAATTGACTCTAATTGTGAAGTTGTAAATAAAGTGCTTGTTGGAAAC
AAAAATGATGATCCGCAGAGGAAGGTTGTTCTAACCGAAGACGCACAACGATTTGCCGAG
CAAATGGGAATACCATTATATGAGACATCCGCCAAAGATAATTTGAATGTAGAAGAAATG
TTCTTAGCAATAACGGAAAAAGTTCTGCGTCATAAAAAACAGACTCAGCGTCAACAGAAT
GATCAGAACGATGATCGAATTAAAATAAATAATACAAGTGGCATTAAGAAGAAGAAAAAA
TGTTGCTAG
>g11236.t1 Gene=g11236 Length=202
MARDYDHLFKLLIIGDSGVGKSSLLIRFSDNTFSGSYITTIGVDFKIRTVVIGGERVKLQ
IWDTAGQERFRTITNTYYRGTHGVIVVYDVTNGESFANVKRWLQEIDSNCEVVNKVLVGN
KNDDPQRKVVLTEDAQRFAEQMGIPLYETSAKDNLNVEEMFLAITEKVLRHKKQTQRQQN
DQNDDRIKINNTSGIKKKKKCC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g11236.t1 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 202 | 2.0E-72 |
| 16 | g11236.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 172 | 202 | - |
| 2 | g11236.t1 | PANTHER | PTHR47977 | LD21953P-RELATED | 1 | 202 | 6.3E-101 |
| 3 | g11236.t1 | PANTHER | PTHR47977:SF29 | RAS-RELATED PROTEIN RAB-35 | 1 | 202 | 6.3E-101 |
| 4 | g11236.t1 | PRINTS | PR00449 | Transforming protein P21 ras signature | 9 | 30 | 5.2E-40 |
| 7 | g11236.t1 | PRINTS | PR00449 | Transforming protein P21 ras signature | 32 | 48 | 5.2E-40 |
| 5 | g11236.t1 | PRINTS | PR00449 | Transforming protein P21 ras signature | 50 | 72 | 5.2E-40 |
| 6 | g11236.t1 | PRINTS | PR00449 | Transforming protein P21 ras signature | 111 | 124 | 5.2E-40 |
| 8 | g11236.t1 | PRINTS | PR00449 | Transforming protein P21 ras signature | 146 | 168 | 5.2E-40 |
| 1 | g11236.t1 | Pfam | PF00071 | Ras family | 10 | 169 | 8.5E-60 |
| 18 | g11236.t1 | ProSiteProfiles | PS51419 | small GTPase Rab1 family profile. | 4 | 202 | 37.492 |
| 12 | g11236.t1 | SMART | SM00177 | arf_sub_2 | 1 | 183 | 0.0093 |
| 11 | g11236.t1 | SMART | SM00173 | ras_sub_4 | 6 | 171 | 1.4E-29 |
| 13 | g11236.t1 | SMART | SM00175 | rab_sub_5 | 9 | 171 | 1.5E-90 |
| 15 | g11236.t1 | SMART | SM00174 | rho_sub_3 | 11 | 171 | 2.0E-17 |
| 14 | g11236.t1 | SMART | SM00176 | ran_sub_2 | 14 | 202 | 1.6E-7 |
| 9 | g11236.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 4 | 197 | 6.6E-64 |
| 17 | g11236.t1 | TIGRFAM | TIGR00231 | small_GTP: small GTP-binding protein domain | 9 | 161 | 1.6E-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 K07876 (Ras-related protein Rab-35)
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.
