General information for g5904.t1
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.t1 | TTS | g5904.t1 | 12700643 | 12700643 |
| chr_2 | g5904 | g5904.t1 | isoform | g5904.t1 | 12701554 | 12704334 |
| chr_2 | g5904 | g5904.t1 | exon | g5904.t1.exon1 | 12701554 | 12702006 |
| chr_2 | g5904 | g5904.t1 | cds | g5904.t1.CDS1 | 12701554 | 12702006 |
| chr_2 | g5904 | g5904.t1 | exon | g5904.t1.exon2 | 12702070 | 12702084 |
| chr_2 | g5904 | g5904.t1 | cds | g5904.t1.CDS2 | 12702070 | 12702084 |
| chr_2 | g5904 | g5904.t1 | exon | g5904.t1.exon3 | 12702162 | 12702306 |
| chr_2 | g5904 | g5904.t1 | cds | g5904.t1.CDS3 | 12702162 | 12702306 |
| chr_2 | g5904 | g5904.t1 | exon | g5904.t1.exon4 | 12702363 | 12702408 |
| chr_2 | g5904 | g5904.t1 | cds | g5904.t1.CDS4 | 12702363 | 12702408 |
| chr_2 | g5904 | g5904.t1 | exon | g5904.t1.exon5 | 12702952 | 12702963 |
| chr_2 | g5904 | g5904.t1 | cds | g5904.t1.CDS5 | 12702952 | 12702963 |
| chr_2 | g5904 | g5904.t1 | TSS | g5904.t1 | 12703071 | 12703071 |
| chr_2 | g5904 | g5904.t1 | exon | g5904.t1.exon6 | 12703283 | 12704029 |
| chr_2 | g5904 | g5904.t1 | cds | g5904.t1.CDS6 | 12703283 | 12704029 |
| chr_2 | g5904 | g5904.t1 | exon | g5904.t1.exon7 | 12704097 | 12704334 |
| chr_2 | g5904 | g5904.t1 | cds | g5904.t1.CDS7 | 12704097 | 12704334 |
Sequences
>g5904.t1 Gene=g5904 Length=1656
ATGTTGTCACGCTTAGCTTGCACAAGAGCTGTCATTAACCCAGTGTTGCTTAAAAGCGCA
ATTCAAAATGTCCCGAAACAGCGACAAGTCTTCAGACAATTTGCCGAAGATGTCAAGTTC
AGAACTAGATCAGAACGAATTAATGAGCGAATGTCTTTAAAAGAACGAGCAATGGCACCA
GCTGGTCCAAATGCTTATGCTATAGGAAAAGGAGCACTCGCAGGAGGTAGTTTATTAGGT
CTCGGTGCATTATGTTATTATGGATTAGGCTTAGGATCAGGAACAAATGCTTTACAAAAC
TCAATGTTATGGCCACAATATGTTAGAGATCGCATTCATGACACATACTTATACTTTGGT
GGCTCCATTCTGATTTCAGCAGCATCAGCAGCTGCCGTATTTCGCACACCGGCCTTGCTT
CGACTTGTTTCTGGAGGTGGTTGGTTATCAATAATCGGTACTTTTGCTGTAATGATTGGT
TCAGGTATGGTGGCACAATCGATTCCCTATTCACCTGGCTTCGGAGCAAAACAATTAGCT
TGGATGGCGCATTCAGCAATCCTCGGAGGAGTTGTCGCTCCTCTTTGCTTTGTGGGCGGT
CCTATAATGATCAGAGCAGCATGGTACACTGCAGGCATTGTTGCTGGTTTGTCAACTGTT
GCAGTTTGTGCACCAAGCGAAAAGTTCCTTAATATGGCCGGACCATTATCTATCGGTCTT
GGTGTAGTGTTTGCTTCATCTATTGGCTCAATGTTCCTTTCCCCAGCAACAGCTCTCGGT
GCATCACTCTACTCAATGAGTTTGTACGGTGGTCTATTGTTATTCTCTGGATTTTTACTC
TACGATACACAAAAGATTATTAGACGTGCAGAAACACATCCACCATTCGGATTTGCACCA
TATGATCCAATCAACAATAGCATTTCAATTTACTTGGACACATTAAACATTTTCATTCGT
ATTGTCACACTTTTGGCTGGTGGTGACGTCAAAAAATTTTCCATGATGACGTCTGCACCC
TATTCATACTCTTATATATTCAAATATATTATAATTGGCGACATGGGTGTCGGAAAGAGT
TGCCTCTTACATCAATTCACAGAGAAAAAATTTATGGCATCATGTCCACATACGATCGGA
GTCGAATTCGGAACAAGAATTATTGAAGTTGATAAGCAAAAGATAAAGCTTCAAATTTGG
GACACTGCTGGACAGGAAAGATTTCGTGCGGTAACAAGAAGTTATTATAGAGGTGCAGCT
GGATGTTTAATGGTCTATGACATTACACGACGGTCGACATACAACCATTTGAGTTCATGG
CTTACAGACACTAAAAATTTAACTAATCCGTCTACTGTGATTTTCCTTATTGGAAACAAA
TCAGATCTCGAATCTACGAGAGAAGTTACATATGAAGAGGCGAAAAAGTTTGCAGATGAA
AATGGTTTGATGTTTGCCGAAACAAGTGCGATGTCTGGACAAAATGTTGAAGAAGCATTT
TTAGAGACAGCGAGAAAGATTTATCAGAGCGTGCAAGATGGTAGATTAGATTTGAATAGC
GCAGAGAGTGGTGTCCAACAGAAAACCCAACAACGACCGGGTAGAACTTCTTTAACAGAT
GATACTCAAACTAACAAAGATAATTGTTCATGCTAA
>g5904.t1 Gene=g5904 Length=551
MLSRLACTRAVINPVLLKSAIQNVPKQRQVFRQFAEDVKFRTRSERINERMSLKERAMAP
AGPNAYAIGKGALAGGSLLGLGALCYYGLGLGSGTNALQNSMLWPQYVRDRIHDTYLYFG
GSILISAASAAAVFRTPALLRLVSGGGWLSIIGTFAVMIGSGMVAQSIPYSPGFGAKQLA
WMAHSAILGGVVAPLCFVGGPIMIRAAWYTAGIVAGLSTVAVCAPSEKFLNMAGPLSIGL
GVVFASSIGSMFLSPATALGASLYSMSLYGGLLLFSGFLLYDTQKIIRRAETHPPFGFAP
YDPINNSISIYLDTLNIFIRIVTLLAGGDVKKFSMMTSAPYSYSYIFKYIIIGDMGVGKS
CLLHQFTEKKFMASCPHTIGVEFGTRIIEVDKQKIKLQIWDTAGQERFRAVTRSYYRGAA
GCLMVYDITRRSTYNHLSSWLTDTKNLTNPSTVIFLIGNKSDLESTREVTYEEAKKFADE
NGLMFAETSAMSGQNVEEAFLETARKIYQSVQDGRLDLNSAESGVQQKTQQRPGRTSLTD
DTQTNKDNCSC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 26 | g5904.t1 | CDD | cd10431 | GHITM | 85 | 328 | 1.00437E-123 |
| 25 | g5904.t1 | CDD | cd04122 | Rab14 | 345 | 510 | 9.34919E-119 |
| 11 | g5904.t1 | Gene3D | G3DSA:3.40.50.300 | - | 341 | 551 | 3.3E-65 |
| 38 | g5904.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 521 | 551 | - |
| 3 | g5904.t1 | PANTHER | PTHR47979:SF73 | RAS-RELATED PROTEIN RAB-4A | 340 | 551 | 6.0E-94 |
| 4 | g5904.t1 | PANTHER | PTHR47979 | DRAB11-RELATED | 340 | 551 | 6.0E-94 |
| 5 | g5904.t1 | PRINTS | PR00449 | Transforming protein P21 ras signature | 347 | 368 | 1.1E-37 |
| 9 | g5904.t1 | PRINTS | PR00449 | Transforming protein P21 ras signature | 370 | 386 | 1.1E-37 |
| 6 | g5904.t1 | PRINTS | PR00449 | Transforming protein P21 ras signature | 388 | 410 | 1.1E-37 |
| 8 | g5904.t1 | PRINTS | PR00449 | Transforming protein P21 ras signature | 450 | 463 | 1.1E-37 |
| 7 | g5904.t1 | PRINTS | PR00449 | Transforming protein P21 ras signature | 485 | 507 | 1.1E-37 |
| 2 | g5904.t1 | Pfam | PF01027 | Inhibitor of apoptosis-promoting Bax1 | 109 | 325 | 1.0E-41 |
| 1 | g5904.t1 | Pfam | PF00071 | Ras family | 348 | 508 | 9.0E-59 |
| 14 | g5904.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 115 | - |
| 24 | g5904.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 116 | 134 | - |
| 17 | g5904.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 135 | 145 | - |
| 22 | g5904.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 146 | 167 | - |
| 15 | g5904.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 168 | 178 | - |
| 23 | g5904.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 179 | 200 | - |
| 18 | g5904.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 201 | 205 | - |
| 19 | g5904.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 206 | 224 | - |
| 13 | g5904.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 225 | 235 | - |
| 21 | g5904.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 236 | 255 | - |
| 16 | g5904.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 256 | 260 | - |
| 20 | g5904.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 261 | 281 | - |
| 12 | g5904.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 282 | 551 | - |
| 40 | g5904.t1 | ProSiteProfiles | PS51419 | small GTPase Rab1 family profile. | 342 | 549 | 36.177 |
| 34 | g5904.t1 | SMART | SM00177 | arf_sub_2 | 335 | 512 | 0.0077 |
| 33 | g5904.t1 | SMART | SM00173 | ras_sub_4 | 344 | 510 | 1.2E-28 |
| 35 | g5904.t1 | SMART | SM00175 | rab_sub_5 | 347 | 510 | 4.3E-100 |
| 37 | g5904.t1 | SMART | SM00174 | rho_sub_3 | 349 | 510 | 2.8E-9 |
| 36 | g5904.t1 | SMART | SM00176 | ran_sub_2 | 352 | 546 | 6.8E-6 |
| 10 | g5904.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 343 | 518 | 1.18E-55 |
| 39 | g5904.t1 | TIGRFAM | TIGR00231 | small_GTP: small GTP-binding protein domain | 346 | 500 | 3.7E-30 |
| 32 | g5904.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 73 | 95 | - |
| 31 | g5904.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 115 | 134 | - |
| 30 | g5904.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 143 | 165 | - |
| 28 | g5904.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 180 | 202 | - |
| 29 | g5904.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 229 | 248 | - |
| 27 | g5904.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 258 | 280 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5904/g5904.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5904.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0090382 | phagosome maturation | BP |
| GO:0006895 | Golgi to endosome transport | BP |
| GO:0042742 | defense response to bacterium | BP |
| GO:0005802 | trans-Golgi network | CC |
| GO:0003924 | GTPase activity | MF |
| GO:0045335 | phagocytic vesicle | CC |
| GO:0005525 | GTP binding | MF |
| GO:0032456 | endocytic recycling | BP |
| GO:0055037 | recycling endosome | CC |
KEGG
Orthology
- This transcript has been annotated with K07881 (Ras-related protein Rab-14)
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.
