General information for g5904.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t4 | isoform | g5904.t4 | 12700336 | 12703136 |
| chr_2 | g5904 | g5904.t4 | exon | g5904.t4.exon1 | 12700336 | 12702006 |
| chr_2 | g5904 | g5904.t4 | cds | g5904.t4.CDS1 | 12701554 | 12702006 |
| chr_2 | g5904 | g5904.t4 | exon | g5904.t4.exon2 | 12702162 | 12702306 |
| chr_2 | g5904 | g5904.t4 | cds | g5904.t4.CDS2 | 12702162 | 12702287 |
| chr_2 | g5904 | g5904.t4 | exon | g5904.t4.exon3 | 12702363 | 12702408 |
| chr_2 | g5904 | g5904.t4 | exon | g5904.t4.exon4 | 12702952 | 12703136 |
| chr_2 | g5904 | g5904.t4 | TSS | g5904.t4 | NA | NA |
| chr_2 | g5904 | g5904.t4 | TTS | g5904.t4 | NA | NA |
Sequences
>g5904.t4 Gene=g5904 Length=2047
AATAACGGCTTTTAGTTTATTAATTTTTACAATTCTATAAAGTAATTTTTCCCCTTATTG
CTTTTGATTGAAGAAAAATAGAAAGGAAGATAGAAAGAAAAAATAATTTTCTGCAATTTA
ACAATATTCTCGCTGGAATCGAGTTATAAAACATTCTTTTATTGATATTAAAGACGTCAA
AAAATTTTCCATGATGACGTCTGCACCCTATTCATACTCTTATATATTCAAATATATTAT
AATTGGCGACATGGGTGTCGGAAAGAGTTGCCTCTTACATCAATTCACAGAGAAAAAATT
TATGGCATCATGTCCACATACGATCGGAGTCGAATTCGGAACAAGAATTATTGAAGTTGA
TAAGCAAAAGATAAAGACTGCTGGACAGGAAAGATTTCGTGCGGTAACAAGAAGTTATTA
TAGAGGTGCAGCTGGATGTTTAATGGTCTATGACATTACACGACGGTCGACATACAACCA
TTTGAGTTCATGGCTTACAGACACTAAAAATTTAACTAATCCGTCTACTGTGATTTTCCT
TATTGGAAACAAATCAGATCTCGAATCTACGAGAGAAGTTACATATGAAGAGGCGAAAAA
GTTTGCAGATGAAAATGGTTTGATGTTTGCCGAAACAAGTGCGATGTCTGGACAAAATGT
TGAAGAAGCATTTTTAGAGACAGCGAGAAAGATTTATCAGAGCGTGCAAGATGGTAGATT
AGATTTGAATAGCGCAGAGAGTGGTGTCCAACAGAAAACCCAACAACGACCGGGTAGAAC
TTCTTTAACAGATGATACTCAAACTAACAAAGATAATTGTTCATGCTAATTCTAAAATTT
AATGAAAACATCTGGTGCAAATATTTCTTTCTTCTTCGTAAATTTCTAACTAAAATACCT
AAACACAATTTAATATAGGATGAGTCTTTTTTTGTGGTAATAACCAAACATTGTCGAAAA
TGAGATCTAAACATCTTTCTTTTTATCCTCTCTAATCTCATCATAAAAATATTCTTATTC
ATTTTATGTTACATTTAATGCGAAAGAATATATTACATTACCAAACCAAACAAATAGAAT
CGCCCATAATCTATATATTTTACTTAGCTGATAAAAAAGTGAGAACAGAGCCCATGTATA
ATAATGATATTCTTTTGTTATGCAAGCGTGATGATTCAGTATTTCAATTATTTTCTTGCA
TATTATTACATCCAATAATATGATTTTCTTTAATAACACAAAAGTATGATGCATGCATAT
TGATCGCACGATGACTAATGATGGGCAGCAGTGAGTTTTTGTTGGAAAACAAAAATAAAA
TAATATAATTATAAAGTGAATGTATAAAGTTGATGTGTATTAAGTTCTTTACCAATAATG
ATGTAGATGTTAGCATAGCAGAATTTATATCTTCCTTTGTTTATCTTTTTATTAATCTAT
TGCAGCATATTTGCATAAATGCATTTTTTGAACTATTTTTTTTATCGACATGACAATGAA
CAAATTAATAGTTTTATATTACACCTATCTAAATATTTTGTTGAGTTATGAGAAATCTTA
TTTTCTATGTAGATATTATTATTACCGAATTATTCTTCTAACATACACATTAATGAAATG
AAAAAATTCCAAATAAAAAATTCAAATATAAAAGAAAAATTTATCCTTAAAGAAATTTAA
ATTGAAAATCACACATGTAGAGAGATATAGTCGAATATATAATAAAAATTTGAATGAATG
AAAAAGAACTCTGGATTTATTGCTTTATACTATTCTTTTATTATTAGATAATAATTATTT
ATGCTTGATATAATTCATTTAAAAATTTAAAATTCATATAATAAAAAGAAGTGCATTAAC
CAATTTAATGGTTTAAAAGAGATACTCATAATTTATTTTTGACAGAATGTAAAGTTTTGA
CTTTTCTTTTTGATTAAAATAATATCACAAACATTTAAAATAAAAAATACGGAAATCATC
ATAAAAATGCAATTGATTTGGATTACTTCATAAGTTCATCATATCTGTATCTTTAAATAT
CAAATTT
>g5904.t4 Gene=g5904 Length=192
MGVGKSCLLHQFTEKKFMASCPHTIGVEFGTRIIEVDKQKIKTAGQERFRAVTRSYYRGA
AGCLMVYDITRRSTYNHLSSWLTDTKNLTNPSTVIFLIGNKSDLESTREVTYEEAKKFAD
ENGLMFAETSAMSGQNVEEAFLETARKIYQSVQDGRLDLNSAESGVQQKTQQRPGRTSLT
DDTQTNKDNCSC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g5904.t4 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 192 | 1.3E-53 |
| 13 | g5904.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 162 | 192 | - |
| 2 | g5904.t4 | PANTHER | PTHR47979:SF73 | RAS-RELATED PROTEIN RAB-4A | 1 | 192 | 2.3E-79 |
| 3 | g5904.t4 | PANTHER | PTHR47979 | DRAB11-RELATED | 1 | 192 | 2.3E-79 |
| 4 | g5904.t4 | PRINTS | PR00449 | Transforming protein P21 ras signature | 29 | 51 | 6.5E-13 |
| 6 | g5904.t4 | PRINTS | PR00449 | Transforming protein P21 ras signature | 91 | 104 | 6.5E-13 |
| 5 | g5904.t4 | PRINTS | PR00449 | Transforming protein P21 ras signature | 126 | 148 | 6.5E-13 |
| 1 | g5904.t4 | Pfam | PF00071 | Ras family | 2 | 149 | 2.1E-47 |
| 15 | g5904.t4 | ProSiteProfiles | PS51419 | small GTPase Rab1 family profile. | 1 | 190 | 30.135 |
| 10 | g5904.t4 | SMART | SM00175 | rab_sub_5 | 1 | 151 | 6.5E-77 |
| 9 | g5904.t4 | SMART | SM00173 | ras_sub_4 | 2 | 151 | 2.7E-15 |
| 11 | g5904.t4 | SMART | SM00176 | ran_sub_2 | 2 | 187 | 0.0024 |
| 12 | g5904.t4 | SMART | SM00174 | rho_sub_3 | 2 | 151 | 1.3E-5 |
| 7 | g5904.t4 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 2 | 160 | 1.72E-44 |
| 14 | g5904.t4 | TIGRFAM | TIGR00231 | small_GTP: small GTP-binding protein domain | 2 | 141 | 2.3E-21 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5904/g5904.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5904.t4.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.
