General information for g2988.t16
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ras-related protein rab7.
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.t16 | TSS | g2988.t16 | 21748744 | 21748744 |
| chr_3 | g2988 | g2988.t16 | isoform | g2988.t16 | 21749092 | 21750217 |
| chr_3 | g2988 | g2988.t16 | exon | g2988.t16.exon1 | 21749092 | 21749161 |
| chr_3 | g2988 | g2988.t16 | exon | g2988.t16.exon2 | 21749261 | 21749506 |
| chr_3 | g2988 | g2988.t16 | cds | g2988.t16.CDS1 | 21749323 | 21749506 |
| chr_3 | g2988 | g2988.t16 | exon | g2988.t16.exon3 | 21749719 | 21749924 |
| chr_3 | g2988 | g2988.t16 | cds | g2988.t16.CDS2 | 21749719 | 21749924 |
| chr_3 | g2988 | g2988.t16 | exon | g2988.t16.exon4 | 21749987 | 21750217 |
| chr_3 | g2988 | g2988.t16 | cds | g2988.t16.CDS3 | 21749987 | 21750217 |
| chr_3 | g2988 | g2988.t16 | TTS | g2988.t16 | 21750766 | 21750766 |
Sequences
>g2988.t16 Gene=g2988 Length=753
TCTGGAAAATGAATTGATAAGAATTCAAAATATATTCATGATTTTCATTACGACCACTTT
GAATACAAATTTTTACTATACATTTTCTTGTTATTTCATACACAATTCATAAGAATTAAT
TTGTAAAGTAAAATGGCAACAAGAAAGAAGGTTTTGTTGAAAGTGATCATATTGGGAGAT
TCAAGTGTGGGAAAGACATCTCTAATGAATCAATATGTGAATAAACGTTTTTCAAACCAG
TATAAAGCTACTATCGGGGCTGATTTCTTAACAAAGGAAGTAGTTGTTGATGATCGAGTC
GTCACAATGCAAGTAACTGGTCAAGAAAGATTTCAATCACTCGGAGTTGCATTTTATCGT
GGAGCGGATTGTTGTGTATTGGTATTTGATACAACAGCACCAAACACATTTAAAAATCTT
GATTCTTGGCGTGATGAGTTTTTAATACAAGCAAGTCCAAGAAATCCTGAACATTTTCCA
TTTGTAGTTTTGGGCAATAAAGTAGATTTGGAAAATCGAGCTGTTTCAACAAAACGTGCA
CAGCAATGGTGCCAATCGAAAAATGATATTCCATATTTTGAGACATCTGCTAAAGAGGGT
ATAAATGTTGACATTGCTTTCCAAACGATCGCTAAAAACGCACTCGCGCAAGAAAGTGAT
GAGGGTATTGATTCTGCATTCAGTCCATCTCTAACATTGGGCTCATCGTCAGACTCTAAT
AATAGACCCAACAGTAGTGACTGTTCATGCTAA
>g2988.t16 Gene=g2988 Length=206
MATRKKVLLKVIILGDSSVGKTSLMNQYVNKRFSNQYKATIGADFLTKEVVVDDRVVTMQ
VTGQERFQSLGVAFYRGADCCVLVFDTTAPNTFKNLDSWRDEFLIQASPRNPEHFPFVVL
GNKVDLENRAVSTKRAQQWCQSKNDIPYFETSAKEGINVDIAFQTIAKNALAQESDEGID
SAFSPSLTLGSSSDSNNRPNSSDCSC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g2988.t16 | CDD | cd01862 | Rab7 | 9 | 175 | 1.75766E-126 |
| 9 | g2988.t16 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 183 | 3.0E-61 |
| 2 | g2988.t16 | PANTHER | PTHR47981 | RAB FAMILY | 1 | 206 | 2.7E-105 |
| 3 | g2988.t16 | PANTHER | PTHR47981:SF3 | RAB7B, MEMBER RAS ONCOGENE FAMILY-RELATED | 1 | 206 | 2.7E-105 |
| 4 | g2988.t16 | PRINTS | PR00449 | Transforming protein P21 ras signature | 9 | 30 | 8.0E-28 |
| 6 | g2988.t16 | PRINTS | PR00449 | Transforming protein P21 ras signature | 32 | 48 | 8.0E-28 |
| 5 | g2988.t16 | PRINTS | PR00449 | Transforming protein P21 ras signature | 113 | 126 | 8.0E-28 |
| 7 | g2988.t16 | PRINTS | PR00449 | Transforming protein P21 ras signature | 148 | 170 | 8.0E-28 |
| 1 | g2988.t16 | Pfam | PF00071 | Ras family | 10 | 170 | 1.5E-48 |
| 11 | g2988.t16 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 20 | - |
| 12 | g2988.t16 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 6 | - |
| 13 | g2988.t16 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 7 | 15 | - |
| 14 | g2988.t16 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 20 | - |
| 10 | g2988.t16 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 21 | 206 | - |
| 21 | g2988.t16 | ProSiteProfiles | PS51419 | small GTPase Rab1 family profile. | 4 | 206 | 29.6 |
| 16 | g2988.t16 | SMART | SM00173 | ras_sub_4 | 6 | 173 | 6.5E-21 |
| 17 | g2988.t16 | SMART | SM00175 | rab_sub_5 | 9 | 173 | 1.9E-81 |
| 19 | g2988.t16 | SMART | SM00174 | rho_sub_3 | 11 | 173 | 1.5E-9 |
| 18 | g2988.t16 | SMART | SM00176 | ran_sub_2 | 14 | 206 | 3.4E-5 |
| 8 | g2988.t16 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 5 | 173 | 2.04E-47 |
| 20 | g2988.t16 | TIGRFAM | TIGR00231 | small_GTP: small GTP-binding protein domain | 10 | 167 | 3.2E-20 |
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 K07897 (Ras-related protein Rab-7A)
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.
