General information for g5904.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Ras-related protein Rab-14.
Parent gene
- The parent gene g5904 is located on chr_2: 12703249..12704835 (- 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 | g5904 | g5904.t3 | isoform | g5904.t3 | 12700336 | 12702084 |
| chr_2 | g5904 | g5904.t3 | exon | g5904.t3.exon1 | 12700336 | 12702006 |
| chr_2 | g5904 | g5904.t3 | cds | g5904.t3.CDS1 | 12701554 | 12701940 |
| chr_2 | g5904 | g5904.t3 | exon | g5904.t3.exon2 | 12702070 | 12702084 |
| chr_2 | g5904 | g5904.t3 | TSS | g5904.t3 | 12703071 | 12703071 |
| chr_2 | g5904 | g5904.t3 | TTS | g5904.t3 | NA | NA |
Sequences
>g5904.t3 Gene=g5904 Length=1686
CTTCAAATTTGGGACACTGCTGGACAGGAAAGATTTCGTGCGGTAACAAGAAGTTATTAT
AGAGGTGCAGCTGGATGTTTAATGGTCTATGACATTACACGACGGTCGACATACAACCAT
TTGAGTTCATGGCTTACAGACACTAAAAATTTAACTAATCCGTCTACTGTGATTTTCCTT
ATTGGAAACAAATCAGATCTCGAATCTACGAGAGAAGTTACATATGAAGAGGCGAAAAAG
TTTGCAGATGAAAATGGTTTGATGTTTGCCGAAACAAGTGCGATGTCTGGACAAAATGTT
GAAGAAGCATTTTTAGAGACAGCGAGAAAGATTTATCAGAGCGTGCAAGATGGTAGATTA
GATTTGAATAGCGCAGAGAGTGGTGTCCAACAGAAAACCCAACAACGACCGGGTAGAACT
TCTTTAACAGATGATACTCAAACTAACAAAGATAATTGTTCATGCTAATTCTAAAATTTA
ATGAAAACATCTGGTGCAAATATTTCTTTCTTCTTCGTAAATTTCTAACTAAAATACCTA
AACACAATTTAATATAGGATGAGTCTTTTTTTGTGGTAATAACCAAACATTGTCGAAAAT
GAGATCTAAACATCTTTCTTTTTATCCTCTCTAATCTCATCATAAAAATATTCTTATTCA
TTTTATGTTACATTTAATGCGAAAGAATATATTACATTACCAAACCAAACAAATAGAATC
GCCCATAATCTATATATTTTACTTAGCTGATAAAAAAGTGAGAACAGAGCCCATGTATAA
TAATGATATTCTTTTGTTATGCAAGCGTGATGATTCAGTATTTCAATTATTTTCTTGCAT
ATTATTACATCCAATAATATGATTTTCTTTAATAACACAAAAGTATGATGCATGCATATT
GATCGCACGATGACTAATGATGGGCAGCAGTGAGTTTTTGTTGGAAAACAAAAATAAAAT
AATATAATTATAAAGTGAATGTATAAAGTTGATGTGTATTAAGTTCTTTACCAATAATGA
TGTAGATGTTAGCATAGCAGAATTTATATCTTCCTTTGTTTATCTTTTTATTAATCTATT
GCAGCATATTTGCATAAATGCATTTTTTGAACTATTTTTTTTATCGACATGACAATGAAC
AAATTAATAGTTTTATATTACACCTATCTAAATATTTTGTTGAGTTATGAGAAATCTTAT
TTTCTATGTAGATATTATTATTACCGAATTATTCTTCTAACATACACATTAATGAAATGA
AAAAATTCCAAATAAAAAATTCAAATATAAAAGAAAAATTTATCCTTAAAGAAATTTAAA
TTGAAAATCACACATGTAGAGAGATATAGTCGAATATATAATAAAAATTTGAATGAATGA
AAAAGAACTCTGGATTTATTGCTTTATACTATTCTTTTATTATTAGATAATAATTATTTA
TGCTTGATATAATTCATTTAAAAATTTAAAATTCATATAATAAAAAGAAGTGCATTAACC
AATTTAATGGTTTAAAAGAGATACTCATAATTTATTTTTGACAGAATGTAAAGTTTTGAC
TTTTCTTTTTGATTAAAATAATATCACAAACATTTAAAATAAAAAATACGGAAATCATCA
TAAAAATGCAATTGATTTGGATTACTTCATAAGTTCATCATATCTGTATCTTTAAATATC
AAATTT
>g5904.t3 Gene=g5904 Length=128
MVYDITRRSTYNHLSSWLTDTKNLTNPSTVIFLIGNKSDLESTREVTYEEAKKFADENGL
MFAETSAMSGQNVEEAFLETARKIYQSVQDGRLDLNSAESGVQQKTQQRPGRTSLTDDTQ
TNKDNCSC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g5904.t3 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 128 | 3.7E-28 |
| 10 | g5904.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 95 | 128 | - |
| 2 | g5904.t3 | PANTHER | PTHR47979:SF73 | RAS-RELATED PROTEIN RAB-4A | 1 | 128 | 4.7E-43 |
| 3 | g5904.t3 | PANTHER | PTHR47979 | DRAB11-RELATED | 1 | 128 | 4.7E-43 |
| 4 | g5904.t3 | PRINTS | PR00449 | Transforming protein P21 ras signature | 27 | 40 | 1.5E-10 |
| 5 | g5904.t3 | PRINTS | PR00449 | Transforming protein P21 ras signature | 62 | 84 | 1.5E-10 |
| 1 | g5904.t3 | Pfam | PF00071 | Ras family | 1 | 85 | 1.9E-23 |
| 11 | g5904.t3 | ProSiteProfiles | PS51419 | small GTPase Rab1 family profile. | 1 | 126 | 18.208 |
| 8 | g5904.t3 | SMART | SM00173 | ras_sub_4 | 1 | 87 | 1.3E-4 |
| 9 | g5904.t3 | SMART | SM00175 | rab_sub_5 | 1 | 87 | 7.8E-12 |
| 6 | g5904.t3 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 2 | 97 | 1.47E-22 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5904/g5904.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5904.t3.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.
