General information for g284.t5
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Ras-related protein Rab-11A.
Parent gene
- The parent gene g284 is located on chr_3: 2414357..2416849 (- 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_3 | g284 | g284.t5 | TTS | g284.t5 | 2413823 | 2413823 |
| chr_3 | g284 | g284.t5 | isoform | g284.t5 | 2414027 | 2415429 |
| chr_3 | g284 | g284.t5 | exon | g284.t5.exon1 | 2414027 | 2414490 |
| chr_3 | g284 | g284.t5 | cds | g284.t5.CDS1 | 2414357 | 2414490 |
| chr_3 | g284 | g284.t5 | exon | g284.t5.exon2 | 2414572 | 2414884 |
| chr_3 | g284 | g284.t5 | cds | g284.t5.CDS2 | 2414572 | 2414725 |
| chr_3 | g284 | g284.t5 | exon | g284.t5.exon3 | 2414953 | 2415110 |
| chr_3 | g284 | g284.t5 | exon | g284.t5.exon4 | 2415427 | 2415429 |
| chr_3 | g284 | g284.t5 | TSS | g284.t5 | 2415508 | 2415508 |
Sequences
>g284.t5 Gene=g284 Length=938
CCTTGGTTTTAATTGGAGATTCAGGCGTTGGAAAGTCGAATCTTCTTTCGCGATTCACAC
GTAATGAATTCAATTTAGAATCGAAATCTACAATTGGAGTCGAATTTGCAACTCGTAGTA
TTGTTGTGGATAATAAAACTATCAAAGCTCAAATTTGGGATACTGCTGGTCAAGAAAGAT
ATCGAGCGATTACATCTGCTTATTACCGTGGTGCTGTTGGTGCTCTTTTGGTTTATGATA
TTGCTAAACATCTCACATATGAGAATGTAGAGAGATGGCTTCGTGAATTGCGTGATCATG
CAGATCAAAATATCGTGATAATGTTGGTTGGTAACAAGAGCGATTTGAGGCATTTGCGTG
CTGTGCCAACGGATGAGGCAAAGACTTTTGCTGAACGTAATGGTCTCAGTTTCATCGAAA
CATCAGCACTTGATTCAACAAATGTGGAAACGGCATTTCAAAATATACTCACAGAAATTT
ACCGAATCGTCTCGCAAAAACAAATTCGCGATCCACCAGAAGGAGATGTGATTCGTCCAT
CGAATGTAGAGCCGATTGATGTTAAACCGACAGTAACATCAGAAGTTAGAAAGCAATGTT
GTCAGTGAGCCAGTGATTCGCTTGTGTTTTTATTTCCATCATGTAATGCAATTATATATG
CATTCAAATTATGAAAGCCCGAGAAAGAAAAACAATTTTCCATTTTATAATTTTCCTGCA
AACGCTTCCCTACTTTCCTTACATAAATCATTTACTTCATCATGCGATGAAATTTTTTTA
TAATGAATATTTTTCCAATATTCCCTTCTCATATTGAAGAATATAAATTTTTTTCATTGA
AGAGAATTTGATTGTTACAATTATTACCTATTCCTCGCATATTTAATTGTGTCATAATAA
TCAATTTTGAATTCCTTAATTTTTTAATTTGTATTATT
>g284.t5 Gene=g284 Length=95
MLVGNKSDLRHLRAVPTDEAKTFAERNGLSFIETSALDSTNVETAFQNILTEIYRIVSQK
QIRDPPEGDVIRPSNVEPIDVKPTVTSEVRKQCCQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g284.t5 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 70 | 0.000000 |
| 2 | g284.t5 | PANTHER | PTHR47979:SF49 | RAS-RELATED PROTEIN RAB-11A | 1 | 95 | 0.000000 |
| 3 | g284.t5 | PANTHER | PTHR47979 | DRAB11-RELATED | 1 | 95 | 0.000000 |
| 1 | g284.t5 | Pfam | PF00071 | Ras family | 1 | 54 | 0.000000 |
| 7 | g284.t5 | ProSiteProfiles | PS51419 | small GTPase Rab1 family profile. | 1 | 94 | 12.148000 |
| 5 | g284.t5 | SMART | SM00175 | rab_sub_5 | 1 | 56 | 0.000036 |
| 4 | g284.t5 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 1 | 67 | 0.000000 |
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.
