General information for g3526.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ras-related protein Rap-2a.
Parent gene
- The parent gene g3526 is located on chr_3: 26201094..26202337 (+ 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_3 | g3526 | g3526.t3 | isoform | g3526.t3 | 26197211 | 26202337 |
| chr_3 | g3526 | g3526.t3 | exon | g3526.t3.exon1 | 26197211 | 26197588 |
| chr_3 | g3526 | g3526.t3 | exon | g3526.t3.exon2 | 26200231 | 26200527 |
| chr_3 | g3526 | g3526.t3 | cds | g3526.t3.CDS1 | 26200485 | 26200527 |
| chr_3 | g3526 | g3526.t3 | exon | g3526.t3.exon3 | 26200607 | 26200698 |
| chr_3 | g3526 | g3526.t3 | cds | g3526.t3.CDS2 | 26200607 | 26200698 |
| chr_3 | g3526 | g3526.t3 | exon | g3526.t3.exon4 | 26200771 | 26201026 |
| chr_3 | g3526 | g3526.t3 | cds | g3526.t3.CDS3 | 26200771 | 26201026 |
| chr_3 | g3526 | g3526.t3 | exon | g3526.t3.exon5 | 26201085 | 26202337 |
| chr_3 | g3526 | g3526.t3 | cds | g3526.t3.CDS4 | 26201085 | 26201236 |
| chr_3 | g3526 | g3526.t3 | TTS | g3526.t3 | 26202331 | 26202331 |
| chr_3 | g3526 | g3526.t3 | TSS | g3526.t3 | NA | NA |
Sequences
>g3526.t3 Gene=g3526 Length=2276
AGTAAATTTTTCTTGATTATGAATGTTATGCCGTTTGGTCATGACTATAAACATTCGTAA
CGTTTTATTTTTTTCAAATTTGTAATTTCATTTTTATAGGAAATTTTTTATATAATACAG
TTGCTATCGCATAGAGTATACATCTCTCATAGTGTGAACAACAAGTATCAGTAGTCTTAC
AAAAAAAGTTTTTTATTCATCTTTATTCACTTATCAAAAAAAAAATTATTTATCTTCGCA
CTGTAGCTAAACGCTGAATTGCATATTGTGAGTTTAATCATTATATGGTAGTGAACAGCA
AAAGGACTGTGATAAAAATAATTAAAAGAGCCAAAAAACAACAAGAAAAAAAATATGAAA
TTATAAAAAGAGAATTGATACTCAACAATTGATATCAACCAATTACATACCAAGCAACTG
ACAGTGATTTTTTTTATTTAATTAGATGAAAAAAATCTTTTGTGAAACAATTGAACGAGT
GAAAAATTGACAACCTTTTTCAATCAAATCACTATTTTTTGTGTGTTTGTGAGAGAAAAG
AAGCAGTAATAATTTTTTGTACATTGCAAAAGATTGTTTTGCATAACACAACTTAGTGAA
ATAATCCTAAACCCGCCCGTACCCAAAGAACGATGCGTGAATTCAAAGTTGTTGTTCTTG
GCTCAGGTGGCGTAGGAAAATCGGCCTTAACAGTGCAGTTTGTTTCAGGATGTTTCATTG
AAAAATATGACCCAACAGTGGAAGATTTTTATAGGAAAGAAATTGAAGTCGATAATTCAC
CATGCGTCTTGGAAATTCTTGATACGGCGGGAACTGAACAGTTTGCCTCGATGCGCGATC
TCTATATTAAAAATGGTCACGGATTTATCGTTATGTATTCACTCACAAATCACCAGACGT
TTCAAGATATTACAACTATGCGAAATGTCATTAGCCGAGTAAAGGGAGGTCAACCGACTC
CAATTTTATTAGTTGCTAATAAACTTGATTTAGAATACCAAAGAGAAGTTTCCACTGAAG
AAGGACATGCACTTGCAGAGATGTGGGGTTGTCCATTTATTGAAGCTTCTGCCAAAAGTC
GTATCAATGTGAATGAAGTGTTTGCGATAATAGTTCGTGAGATGAATATGATGAGCGAAA
AGCGACAGAAAAAATCATTTTGCTGTTGCTTATAGGGAAACGTTTCTCAATAAGCATTCA
TTTATAAAAAAATATATCACTCAGTTTTTTCTCTCACTCTCTTTTTCTCTATTCTATGAG
AATTCATAGAAAAGTTAAAGAGTTTTTCCGGATTTCAACTAGTTATCTGTATCATACACC
ATACACACAAACATACACATAAATTTAAAAATGAAAACAATTCGCCATCAATTTTATTAC
TTATTTTTAAGTATAAATAAAATTTATACAATTATGTATTTTTAACTTACTTCTACTTAT
ATTTTAGAATGAAAATATCTCTTTTCGTTTCTTCATTATTAATGATAATGGCCATAAATT
TTATTTCTAATTATTTAAGATCATGTGACTTTAAATTTTGTGTTTTTAGCTTTTCTATCG
CATTTAGCTATCACATGTAATTGCTAATCCTAATTGTTTCCATATTCTAGGAGAAAAACC
ATATATTGAATGAGCTAGAGTGAAGATCTCAGAAAATTCAAATATCTTACAATTACAATT
ACGATAGTCAAGAAACTTTCTCTAATAAAAAAAATTAAAAATTCACATTTAAGCTCAATA
AATATCGTGTCAAGCTTACATCATTTGAAATTAAATGTTCAAGTAGTTTTCCGAAAAAAA
TAATGATTCTCCAATTGATGGAAATCATAAAATTTAATTTTTTCTTTGCATTTTTTCATC
ATTTCGTGCCGAAATGTGAAGCGCAATTATAATTAAACTATAATCAAAAACGAGAAAGAA
ATAATTTGATTGCTTTCCATTTCACTCACATAAGACCCGAATAAATTTCACTTCTCATTT
TCTATTTCCCGAAAAAAAAGAAGAAAAATATTATGTGACGACTGCCTATAACCATGCTTT
GATGTGTAGCAAATAAGTAGTCAGTCGACGGTGAGAGAAGAAAAATTATTGAACAATAAC
CATTAATTAATAGATAATTTATTATTTGTAAGAAATGAAATATGCAGATTTAAGAGAGAG
AATGAATGATTGCTACAAGTTGTAAAATAATGAAAGTAAAACAAAATTCAGTCAATTTAT
ACCACAGAAGAAAGAAAGAATTGTGAAAAATAAAGTAGCAGTAATTTCATGAAAAA
>g3526.t3 Gene=g3526 Length=180
MREFKVVVLGSGGVGKSALTVQFVSGCFIEKYDPTVEDFYRKEIEVDNSPCVLEILDTAG
TEQFASMRDLYIKNGHGFIVMYSLTNHQTFQDITTMRNVISRVKGGQPTPILLVANKLDL
EYQREVSTEEGHALAEMWGCPFIEASAKSRINVNEVFAIIVREMNMMSEKRQKKSFCCCL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g3526.t3 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 170 | 0.000 |
| 2 | g3526.t3 | PANTHER | PTHR24070 | RAS, DI-RAS, AND RHEB FAMILY MEMBERS OF SMALL GTPASE SUPERFAMILY | 1 | 178 | 0.000 |
| 3 | g3526.t3 | PANTHER | PTHR24070:SF419 | RAP2A, MEMBER OF RAS ONCOGENE FAMILY A | 1 | 178 | 0.000 |
| 8 | g3526.t3 | PRINTS | PR00449 | Transforming protein P21 ras signature | 4 | 25 | 0.000 |
| 4 | g3526.t3 | PRINTS | PR00449 | Transforming protein P21 ras signature | 27 | 43 | 0.000 |
| 6 | g3526.t3 | PRINTS | PR00449 | Transforming protein P21 ras signature | 44 | 66 | 0.000 |
| 7 | g3526.t3 | PRINTS | PR00449 | Transforming protein P21 ras signature | 107 | 120 | 0.000 |
| 5 | g3526.t3 | PRINTS | PR00449 | Transforming protein P21 ras signature | 142 | 164 | 0.000 |
| 1 | g3526.t3 | Pfam | PF00071 | Ras family | 5 | 164 | 0.000 |
| 14 | g3526.t3 | ProSiteProfiles | PS51257 | Prokaryotic membrane lipoprotein lipid attachment site profile. | 1 | 27 | 6.000 |
| 15 | g3526.t3 | ProSiteProfiles | PS51421 | small GTPase Ras family profile. | 1 | 180 | 37.107 |
| 11 | g3526.t3 | SMART | SM00173 | ras_sub_4 | 1 | 167 | 0.000 |
| 12 | g3526.t3 | SMART | SM00175 | rab_sub_5 | 4 | 167 | 0.000 |
| 13 | g3526.t3 | SMART | SM00174 | rho_sub_3 | 6 | 165 | 0.000 |
| 9 | g3526.t3 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 2 | 166 | 0.000 |
| 16 | g3526.t3 | TIGRFAM | TIGR00231 | small_GTP: small GTP-binding protein domain | 1 | 160 | 0.000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016020 | membrane | CC |
| GO:0007165 | signal transduction | BP |
| GO:0005525 | GTP binding | MF |
| GO:0003924 | GTPase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K07839 (Ras-related protein Rap-2C)
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.
