General information for g5596.t11
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Ras-related protein Rab-5C.
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.t11 | isoform | g5596.t11 | 10449252 | 10452843 |
| chr_2 | g5596 | g5596.t11 | exon | g5596.t11.exon1 | 10449252 | 10449411 |
| chr_2 | g5596 | g5596.t11 | TSS | g5596.t11 | 10449274 | 10449274 |
| chr_2 | g5596 | g5596.t11 | exon | g5596.t11.exon2 | 10450750 | 10450991 |
| chr_2 | g5596 | g5596.t11 | exon | g5596.t11.exon3 | 10451390 | 10451515 |
| chr_2 | g5596 | g5596.t11 | cds | g5596.t11.CDS1 | 10451414 | 10451515 |
| chr_2 | g5596 | g5596.t11 | exon | g5596.t11.exon4 | 10451581 | 10451749 |
| chr_2 | g5596 | g5596.t11 | cds | g5596.t11.CDS2 | 10451581 | 10451749 |
| chr_2 | g5596 | g5596.t11 | exon | g5596.t11.exon5 | 10451808 | 10451929 |
| chr_2 | g5596 | g5596.t11 | cds | g5596.t11.CDS3 | 10451808 | 10451908 |
| chr_2 | g5596 | g5596.t11 | exon | g5596.t11.exon6 | 10451989 | 10452565 |
| chr_2 | g5596 | g5596.t11 | TTS | g5596.t11 | 10452049 | 10452049 |
| chr_2 | g5596 | g5596.t11 | exon | g5596.t11.exon7 | 10452630 | 10452843 |
Sequences
>g5596.t11 Gene=g5596 Length=1610
CTTCTTGCTCACTCTCTAAATTTGAGTGATTGAATTTTTATAATAAAAGAAGATCCAAGT
TGAAAATTTGTCGACAATTTTAGTAAAAAATATTGAATTTTAAGCCAAGTAAAGTTGATT
ATTGTGTGTATTAAGACATCTTTAAAGTGAATAAAATAAAATAAATTATGGCAAATAATC
AACGTGGAGGAGGAATTCAACGTCCAAATGGTTCAACACAGAGCAAAATTTGCCAATTTA
AGCTGGTACTTTTGGGCGAATCGGCTGTTGGAAAATCATCACTCGTGCTAAGATTTGTCA
AGGGTCAATTTCATGAATATCAAGAGAGTACCATTGGAGCCGCTTTTCTTACTCAGACCG
TGCACATCGACGAGACTGCAGTCAAATTTGAAATTTGGATAAGAACGTTATCATAGTTTA
GCTCCAATGTATTATCGAGGTGCTCAGGCGGCTATTGTCGTGTATGACATTCAAAATCAG
GACAGTTTTTCTCGTGCTCAGACGTGGGTCAAAGAACTTCAACGACAGGCATCGCCAAAT
ATCGTTATAGCCTTGGCTGGCAATAAAGCGGATCTTGCAGCAAGTCGAGCTGTTGACTAT
GAAGAAGCAAAACAATATGCTGACGAAAACGGATTACTATTCATGGAAACTTCGGCAAAG
ACAGCAGTCAATGTGAATGAGATATTTTTAGCAATAGCAAAAAAACTTCCCAAGAACGAA
GGTACTGGGCAGCAAACAAATATACGTCCGCAAGCGGGTGAAACGAATAGAACTTCAGGG
AATTGCTGTAATAAGTGATCACATGTTCTGGCATCGAAGATCAGTGGAAGTCAGAAAAAA
AATTCTATTATTGTCTTTTTTATTACTTTATAGAACAAAAAGAAATTTAAAAAAAAAAAA
CTGAATGAAAAGTTTGTTTCCGAGAATGAATTTTTTGTTTAAAATATTTAGAAGAAAAAA
ATTTTTCTTGGATTTGCATGGATATGAGGATGATAAAAAAATAAAATTATATTATTATCA
CCCTGCTTTTATATTGATTTAAAAATATAAAAATGTGGTAAGAAAAACTTTATTATTGCA
TATAAAATATATTATTATTATTGTATTAAGTGGAGATAAAAACAACAAGAAAAAACGTGA
AGAAGAAAAATCAATTGTACTGTTCTATTCTGTCTTATTAATAACATCTTCTTATCTATA
TGTATAAACATACACAATCACTGATCACATTCTTTATCATTATTTTTCCGTTTTTTAAAA
AATTGGCTTATTGCTGCATAAATTACATAAAAACATGTGCTTTCAGTTTAACATCAGCTA
CTTTTTTCATGACGTAATTCTCAATACACATATTTTTCATATTCACTCACACAAATCATA
TAGAAAGAAAAGAAGATCCAAAACACTTCTTTATCTCAAAAAATTTCAAAAATTTCTAAT
GACATAAAATGTGAATTGAAAGAAACTTATATTTTTATTTTGTAAATTTAATTTTGTGGA
AATAAAATTTTCGGGAGCGATTGAAATTTCACAAAAAGAAAATTAAATGTATTTATCATA
ACATGAATCGTTATACTACAATAAAGATTTGAGTAAAACTGAAAAATTCT
>g5596.t11 Gene=g5596 Length=123
MYYRGAQAAIVVYDIQNQDSFSRAQTWVKELQRQASPNIVIALAGNKADLAASRAVDYEE
AKQYADENGLLFMETSAKTAVNVNEIFLAIAKKLPKNEGTGQQTNIRPQAGETNRTSGNC
CNK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g5596.t11 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 121 | 9.4E-36 |
| 7 | g5596.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 97 | 123 | - |
| 2 | g5596.t11 | PANTHER | PTHR24073:SF366 | RAS-RELATED PROTEIN RAB-5C | 1 | 105 | 3.4E-51 |
| 3 | g5596.t11 | PANTHER | PTHR24073 | DRAB5-RELATED | 1 | 105 | 3.4E-51 |
| 1 | g5596.t11 | Pfam | PF00071 | Ras family | 1 | 94 | 1.4E-30 |
| 9 | g5596.t11 | ProSiteProfiles | PS51419 | small GTPase Rab1 family profile. | 1 | 123 | 21.275 |
| 6 | g5596.t11 | SMART | SM00175 | rab_sub_5 | 1 | 97 | 2.0E-20 |
| 5 | g5596.t11 | SMART | SM00173 | ras_sub_4 | 2 | 97 | 2.4E-5 |
| 4 | g5596.t11 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 1 | 102 | 4.56E-29 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5596/g5596.t11; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5596.t11.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