General information for g5596.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ras-related protein Rab-5B.
Parent gene
- The parent gene g5596 is located on chr_2: 10451987..10452843 (+ 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_2 | g5596 | g5596.t1 | TSS | g5596.t1 | 10449985 | 10449985 |
| chr_2 | g5596 | g5596.t1 | isoform | g5596.t1 | 10450757 | 10452059 |
| chr_2 | g5596 | g5596.t1 | exon | g5596.t1.exon1 | 10450757 | 10450948 |
| chr_2 | g5596 | g5596.t1 | cds | g5596.t1.CDS1 | 10450757 | 10450948 |
| chr_2 | g5596 | g5596.t1 | exon | g5596.t1.exon2 | 10451390 | 10451515 |
| chr_2 | g5596 | g5596.t1 | cds | g5596.t1.CDS2 | 10451390 | 10451515 |
| chr_2 | g5596 | g5596.t1 | exon | g5596.t1.exon3 | 10451581 | 10451749 |
| chr_2 | g5596 | g5596.t1 | cds | g5596.t1.CDS3 | 10451581 | 10451749 |
| chr_2 | g5596 | g5596.t1 | exon | g5596.t1.exon4 | 10451808 | 10451831 |
| chr_2 | g5596 | g5596.t1 | cds | g5596.t1.CDS4 | 10451808 | 10451831 |
| chr_2 | g5596 | g5596.t1 | exon | g5596.t1.exon5 | 10451906 | 10451929 |
| chr_2 | g5596 | g5596.t1 | cds | g5596.t1.CDS5 | 10451906 | 10451929 |
| chr_2 | g5596 | g5596.t1 | exon | g5596.t1.exon6 | 10451989 | 10452059 |
| chr_2 | g5596 | g5596.t1 | cds | g5596.t1.CDS6 | 10451989 | 10452059 |
| chr_2 | g5596 | g5596.t1 | TTS | g5596.t1 | 10452771 | 10452771 |
Sequences
>g5596.t1 Gene=g5596 Length=606
ATGGCAAATAATCAACGTGGAGGAGGAATTCAACGTCCAAATGGTTCAACACAGAGCAAA
ATTTGCCAATTTAAGCTGGTACTTTTGGGCGAATCGGCTGTTGGAAAATCATCACTCGTG
CTAAGATTTGTCAAGGGTCAATTTCATGAATATCAAGAGAGTACCATTGGAGCCGCTTTT
CTTACTCAGACCGAACGTTATCATAGTTTAGCTCCAATGTATTATCGAGGTGCTCAGGCG
GCTATTGTCGTGTATGACATTCAAAATCAGGACAGTTTTTCTCGTGCTCAGACGTGGGTC
AAAGAACTTCAACGACAGGCATCGCCAAATATCGTTATAGCCTTGGCTGGCAATAAAGCG
GATCTTGCAGCAAGTCGAGCTGTTGACTATGAAGAAGCAAAACAATATGCTGACGAAAAC
GGATTACTATTCATGGAAACTTCGGCAAAGACAGCAGTCAATGTGAATGAGATATTTTTA
GCAATAGCAAAAAAACTTCCCAAGAACGAAGTGATCACATGTTCTGGCATCGAAGATCAG
TGGAAGTCAGAAAAAAAATTCTATTATTGTCTTTTTTATTACTTTATAGAACAAAAAGAA
ATTTAA
>g5596.t1 Gene=g5596 Length=201
MANNQRGGGIQRPNGSTQSKICQFKLVLLGESAVGKSSLVLRFVKGQFHEYQESTIGAAF
LTQTERYHSLAPMYYRGAQAAIVVYDIQNQDSFSRAQTWVKELQRQASPNIVIALAGNKA
DLAASRAVDYEEAKQYADENGLLFMETSAKTAVNVNEIFLAIAKKLPKNEVITCSGIEDQ
WKSEKKFYYCLFYYFIEQKEI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g5596.t1 | CDD | cd01860 | Rab5_related | 23 | 167 | 3.18743E-102 |
| 12 | g5596.t1 | Coils | Coil | Coil | 196 | 201 | - |
| 11 | g5596.t1 | Gene3D | G3DSA:3.40.50.300 | - | 14 | 187 | 2.4E-50 |
| 4 | g5596.t1 | PANTHER | PTHR24073:SF366 | RAS-RELATED PROTEIN RAB-5C | 8 | 64 | 9.9E-87 |
| 6 | g5596.t1 | PANTHER | PTHR24073 | DRAB5-RELATED | 8 | 64 | 9.9E-87 |
| 3 | g5596.t1 | PANTHER | PTHR24073:SF366 | RAS-RELATED PROTEIN RAB-5C | 64 | 176 | 9.9E-87 |
| 5 | g5596.t1 | PANTHER | PTHR24073 | DRAB5-RELATED | 64 | 176 | 9.9E-87 |
| 8 | g5596.t1 | PRINTS | PR00449 | Transforming protein P21 ras signature | 24 | 45 | 7.8E-22 |
| 7 | g5596.t1 | PRINTS | PR00449 | Transforming protein P21 ras signature | 47 | 63 | 7.8E-22 |
| 9 | g5596.t1 | PRINTS | PR00449 | Transforming protein P21 ras signature | 144 | 166 | 7.8E-22 |
| 1 | g5596.t1 | Pfam | PF00071 | Ras family | 25 | 63 | 1.0E-10 |
| 2 | g5596.t1 | Pfam | PF00071 | Ras family | 65 | 166 | 1.0E-33 |
| 18 | g5596.t1 | ProSiteProfiles | PS51419 | small GTPase Rab1 family profile. | 17 | 201 | 26.564 |
| 14 | g5596.t1 | SMART | SM00173 | ras_sub_4 | 21 | 169 | 1.1E-17 |
| 15 | g5596.t1 | SMART | SM00175 | rab_sub_5 | 24 | 169 | 1.7E-68 |
| 16 | g5596.t1 | SMART | SM00174 | rho_sub_3 | 26 | 168 | 1.8E-7 |
| 10 | g5596.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 23 | 183 | 2.14E-43 |
| 17 | g5596.t1 | TIGRFAM | TIGR00231 | small_GTP: small GTP-binding protein domain | 24 | 159 | 8.3E-14 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5596/g5596.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5596.t1.fa.iupred3.txt does not exist
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