General information for g2988.t17
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Ras-related protein Rab-7A.
Parent gene
- The parent gene g2988 is located on chr_3: 21749986..21750769 (+ 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 | g2988 | g2988.t17 | TSS | g2988.t17 | 21748744 | 21748744 |
| chr_3 | g2988 | g2988.t17 | isoform | g2988.t17 | 21749323 | 21749908 |
| chr_3 | g2988 | g2988.t17 | exon | g2988.t17.exon1 | 21749323 | 21749502 |
| chr_3 | g2988 | g2988.t17 | cds | g2988.t17.CDS1 | 21749323 | 21749502 |
| chr_3 | g2988 | g2988.t17 | exon | g2988.t17.exon2 | 21749719 | 21749908 |
| chr_3 | g2988 | g2988.t17 | cds | g2988.t17.CDS2 | 21749719 | 21749847 |
| chr_3 | g2988 | g2988.t17 | TTS | g2988.t17 | 21750766 | 21750766 |
Sequences
>g2988.t17 Gene=g2988 Length=370
ATGGCAACAAGAAAGAAGGTTTTGTTGAAAGTGATCATATTGGGAGATTCAAGTGTGGGA
AAGACATCTCTAATGAATCAATATGTGAATAAACGTTTTTCAAACCAGTATAAAGCTACT
ATCGGGGCTGATTTCTTAACAAAGGAAGTAGTTGTTGATGATCGAGTCGTCACAATGCAA
CTGGTCAAGAAAGATTTCAATCACTCGGAGTTGCATTTTATCGTGGAGCGGATTGTTGTG
TATTGGTATTTGATACAACAGCACCAAACACATTTAAAAATCTTGATTCTTGGCGTGATG
AGTTTTTAATACAAGCAAGTCCAAGAAATCCTGAACATTTTCCATTTGTAGTTTTGGGCA
ATAAAGTAGA
>g2988.t17 Gene=g2988 Length=102
MATRKKVLLKVIILGDSSVGKTSLMNQYVNKRFSNQYKATIGADFLTKEVVVDDRVVTMQ
LVKKDFNHSELHFIVERIVVYWYLIQQHQTHLKILILGVMSF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g2988.t17 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 70 | 2.5E-18 |
| 2 | g2988.t17 | PANTHER | PTHR47981 | RAB FAMILY | 1 | 62 | 9.2E-31 |
| 3 | g2988.t17 | PANTHER | PTHR47981:SF3 | RAB7B, MEMBER RAS ONCOGENE FAMILY-RELATED | 1 | 62 | 9.2E-31 |
| 4 | g2988.t17 | PRINTS | PR00449 | Transforming protein P21 ras signature | 9 | 30 | 1.2E-12 |
| 5 | g2988.t17 | PRINTS | PR00449 | Transforming protein P21 ras signature | 32 | 48 | 1.2E-12 |
| 1 | g2988.t17 | Pfam | PF00071 | Ras family | 10 | 62 | 2.9E-16 |
| 9 | g2988.t17 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 20 | - |
| 10 | g2988.t17 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 6 | - |
| 11 | g2988.t17 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 7 | 15 | - |
| 12 | g2988.t17 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 20 | - |
| 8 | g2988.t17 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 21 | 102 | - |
| 14 | g2988.t17 | ProSiteProfiles | PS51419 | small GTPase Rab1 family profile. | 4 | 102 | 11.128 |
| 13 | g2988.t17 | SMART | SM00175 | rab_sub_5 | 9 | 85 | 7.0E-6 |
| 6 | g2988.t17 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 5 | 62 | 3.34E-16 |
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. There were no conditions that were differentially expressed