General information for g11564.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Ras-related protein Rab-8A.
Parent gene
- The parent gene g11564 is located on chr_1: 17161541..17161973 (+ 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 | g11564 | g11564.t1 | TSS | g11564.t1 | 17161174 | 17161174 |
| chr_1 | g11564 | g11564.t1 | isoform | g11564.t1 | 17161177 | 17161620 |
| chr_1 | g11564 | g11564.t1 | exon | g11564.t1.exon1 | 17161177 | 17161464 |
| chr_1 | g11564 | g11564.t1 | cds | g11564.t1.CDS1 | 17161177 | 17161464 |
| chr_1 | g11564 | g11564.t1 | exon | g11564.t1.exon2 | 17161525 | 17161620 |
| chr_1 | g11564 | g11564.t1 | cds | g11564.t1.CDS2 | 17161525 | 17161620 |
| chr_1 | g11564 | g11564.t1 | TTS | g11564.t1 | 17161974 | 17161974 |
Sequences
>g11564.t1 Gene=g11564 Length=384
ATGGGTATCATGCTTGTATATGACATCACTCAAGAGAAGTCATTTGAAAATATTAAAAAT
TGGATAAGAAACATAGAAGAAAATGCTTCGACTGACGTTGAAAAGATGTTGTTAGGTAAT
AAGTGTGAGTTAAATGAGAAGAGACAAGTCACAAAGGAACGAGGAGAGCAGTTAGCTGTT
GAATACGGAATCAAATTTCTTGAAACATCAGCGAAGAATAGCATCAATGTAGAAGAAGCA
TTCTTTACATTAGCTCGAGATATAAAAATTAAAATGGAGAAGAGAATGGAAGCAAATAAT
CCACCGAAGGGCCATCAATTGAAAGCAAATGAACCGCCACGAAAACCTGGTCTCGGATGG
CTATCAAAGTGTAACTTCTTTTAG
>g11564.t1 Gene=g11564 Length=127
MGIMLVYDITQEKSFENIKNWIRNIEENASTDVEKMLLGNKCELNEKRQVTKERGEQLAV
EYGIKFLETSAKNSINVEEAFFTLARDIKIKMEKRMEANNPPKGHQLKANEPPRKPGLGW
LSKCNFF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g11564.t1 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 115 | 0.0000000 |
| 2 | g11564.t1 | PANTHER | PTHR47980 | LD44762P | 1 | 115 | 0.0000000 |
| 3 | g11564.t1 | PANTHER | PTHR47980:SF33 | RAS-RELATED PROTEIN RAB-8A | 1 | 115 | 0.0000000 |
| 5 | g11564.t1 | PRINTS | PR00449 | Transforming protein P21 ras signature | 31 | 44 | 0.0000000 |
| 4 | g11564.t1 | PRINTS | PR00449 | Transforming protein P21 ras signature | 66 | 88 | 0.0000000 |
| 1 | g11564.t1 | Pfam | PF00071 | Ras family | 2 | 89 | 0.0000000 |
| 10 | g11564.t1 | ProSiteProfiles | PS51419 | small GTPase Rab1 family profile. | 1 | 124 | 19.2470000 |
| 7 | g11564.t1 | SMART | SM00173 | ras_sub_4 | 1 | 91 | 0.0000004 |
| 8 | g11564.t1 | SMART | SM00175 | rab_sub_5 | 1 | 91 | 0.0000000 |
| 6 | g11564.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 2 | 118 | 0.0000000 |
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 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.
