General information for g2471.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ras GTPase-activating protein 1.
Parent gene
- The parent gene g2471 is located on chr_3: 18128041..18128851 (- 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 | g2471 | g2471.t1 | TTS | g2471.t1 | 18123995 | 18123995 |
| chr_3 | g2471 | g2471.t1 | isoform | g2471.t1 | 18124712 | 18128851 |
| chr_3 | g2471 | g2471.t1 | exon | g2471.t1.exon1 | 18124712 | 18124875 |
| chr_3 | g2471 | g2471.t1 | cds | g2471.t1.CDS1 | 18124712 | 18124875 |
| chr_3 | g2471 | g2471.t1 | exon | g2471.t1.exon2 | 18124935 | 18125100 |
| chr_3 | g2471 | g2471.t1 | cds | g2471.t1.CDS2 | 18124935 | 18125100 |
| chr_3 | g2471 | g2471.t1 | exon | g2471.t1.exon3 | 18125397 | 18125417 |
| chr_3 | g2471 | g2471.t1 | cds | g2471.t1.CDS3 | 18125397 | 18125417 |
| chr_3 | g2471 | g2471.t1 | exon | g2471.t1.exon4 | 18125676 | 18127842 |
| chr_3 | g2471 | g2471.t1 | cds | g2471.t1.CDS4 | 18125676 | 18127842 |
| chr_3 | g2471 | g2471.t1 | exon | g2471.t1.exon5 | 18128039 | 18128111 |
| chr_3 | g2471 | g2471.t1 | cds | g2471.t1.CDS5 | 18128039 | 18128111 |
| chr_3 | g2471 | g2471.t1 | exon | g2471.t1.exon6 | 18128317 | 18128390 |
| chr_3 | g2471 | g2471.t1 | cds | g2471.t1.CDS6 | 18128317 | 18128390 |
| chr_3 | g2471 | g2471.t1 | exon | g2471.t1.exon7 | 18128472 | 18128524 |
| chr_3 | g2471 | g2471.t1 | cds | g2471.t1.CDS7 | 18128472 | 18128524 |
| chr_3 | g2471 | g2471.t1 | exon | g2471.t1.exon8 | 18128849 | 18128851 |
| chr_3 | g2471 | g2471.t1 | cds | g2471.t1.CDS8 | 18128849 | 18128851 |
| chr_3 | g2471 | g2471.t1 | TSS | g2471.t1 | NA | NA |
Sequences
>g2471.t1 Gene=g2471 Length=2721
ATGGCAGTTCCAACGACCATAGAGCTTTACCAGCTATTCCCGAGAACCTATGGAAAGTAT
CATGGACGACTCGATAGATTTAGTGCAGAACAAAGGCTTAAAGCAGCATATAAACTCGGA
AGCTACTTAGTGAGAGAAAGTGACAGAAAGCCTGGATCATATGTATTATCTTATTTAGGA
AAAACTGGAATAAATCATTTCCGCATTGCTGCTGTGTGTGGCGATTTTTATATTGGCGGT
CGCCAATTCTTCTCATTAAGTGACTTGGTTGCATATTACTCATGTAATGATTTGTTGAAA
CGTGAACGACTCATCCATGCTATTGCACCGCCTGAACCTGTTTCAGACACACGACGTGTT
GTCGCTATTCTGCCATATACAAAAATGCCAGATACTGATGAGTTGAGTTTTCAAAAGGGT
GATATCTTTTTTGTTCACAATAATATGGGCGATGGATGGATATGGACAACGAAACATAGA
ACTGGCGAGCAGGGAATGATCTTTAGCGAACTTGTTGAAGATCTTGATCCAACAATTGAT
CCCAATACTGTTTTCTCATGGTTTCATCCTAATTGCACTAAAAATGAAGCTGTCGATATG
CTAGTAAAAAATGGCCCTGGTTCATTTTTAGTTCGACCTAGTGACAACAGTCCTGGTGAT
TATTCTCTCTTTTTTCACATCAATAATCAAATTCAGAGATTTCGAATTGAGAAAAAGGGC
GTTCGTTATTTAATGGGTGGAAGAACTTTTGAATGCTTAGATGCAGTTATCAATCGTTAC
CGTAAAGAACAAATAGTTGAAGGACATACTTTACAAAATCCAGTCTCAAATGGATCATGT
CAGGCTGAATTTCAACAGCAAACAGCAGTATCAGCTGCTGCTGAAAAAATTTATGCAACA
TTACGAGAATGTCGTGATCAAAATATGATTAAAAAGATTAAAGGAATTAAACAGCAAGGA
TATCTAATGAAAAGGTCTGATAAAACTGGTAAATGGAAGCAACTTTATTTTGCACTCATC
AATGATGGCGCTGAAACACATTTGTTCTTTTATGATAGTCCCAAAAAGACAAAACCAAAA
GGATTAATTGATTTATCATGCGCTTATCTCTATCAAGTCCACGAATCGCTTTGGGAGAAA
ACAAATTGCTTTCAAATTGTTGAACGAGCACTGCCTTGTTTGGCGACCATTTCGCATTTA
TGTGACAAAAATACTGAATCATATCAGGAATGGATCACTGTTCTTAAACAGCATTGTCGT
GCTCAATTTAGTCGAGCTCAGTCAAAATTGCCTCGATTACGCGAATTGCGCTGCTTAAAT
TTGCAAGTGCTTGAAGCTCATCGTATTCCATTTAAGCTAGTTCCGCATTGCTTCATTACC
ATTGCTCTTAATCAAATAAAAATTGCAAAAACAAAAGTCAAATCGACACCAGATCCAATA
TTTGAGGAGGAATTTGTCATTGATGATTTACCAATAGATATTGCTACACTCAACATGACA
CTCGTGTCGCGAGCCAAGAGAAATAAAGACTCGGACGTTGCAGAATTAACAATTGATCTG
TCAAGTCTTAAGAATGGTGCCGAAACTGAAAATTGGTATGACTTGACGGGAATAACTCCA
ATTGGTGAATGGGGATCATTACGTTTAAGAATAAGATATATGGATGATCTAGTCATGCCT
GCTGAAGAATACTCACCGCTACAGGAACTTTTACTCGAAAATGAATTTCATTCAGTGCGT
GCACTCGCTGATTTATGTCACTCAAATCGTATTCCATTGGCATCATCTTTGCTAAAGATT
TTTCGACATGAGAGAAAAGAATGCGAACTAATGAAATCATTGTGCCAAGCAGAAATCGCT
CGTGAAAGTGACACCAGCACATTATTTAGAGCCACTTCATTAGCAACAACATTAATGGAC
ATTTATATGAGATCTGAATGCGGACTATTTCTAGAGTCAGCATTATTGGATACGATACAA
AAATTACTAGACAGCAAACAGAGTGCAGAATTAAATCCAACAAAAATGGAAGTTAATGAT
GATGCATGCACAAACGCAGAATTTCTACTGCTTATACTTGATCAAATTACACAATCCATT
TTTACTTCGATTGAGGCATGTCCGAGAGGTGTTCGATACATTTGTAATTGTCTGCAAAAG
GCCGTTGTTGCAAAATGGCCTGGTGAGCGTCTCGTTCGAACACGAGTGGTCTCTGGATTC
ATTTTTCTTCGCTTATTATGTCCTGCATTGCTTAATCCGAGACAGTTTGGACTTGTTCAG
GAACAGCCATCTCAAATGGCAACTCGATCTCTCATTATGGTTGCAAAATGCCTTCAAAAT
CTCGCAAATCTCATCGAATTCGGTGGAAAAGGCGAATTGCCAACATTTCATGAAAGCTAC
ATGGAAGTGGTAAATCCGTTTATATTGAAGAATAAAGAACGAATGATAGTTTTTCTTGAT
CAACTATCGAGTATTTCTGATCCATTTGTACCATCACAAGTTGGAATGGATATATCAGGA
AATATTAATATTAATGCCAATAATAGTTCTGATACAGGAAGAGAACTTGCAACATTACAC
CATATATGTGTCTCACACCTGGCAGAACTTCAAAACATGTCAAAAGTCAATGCTTCGATT
AAAAAATTGGTAACAGTTACAGAGATGTTATCGAAGCATAAACTAAAGTATTTAGAAATG
ATTAATGACAACGCACGTTAG
>g2471.t1 Gene=g2471 Length=906
MAVPTTIELYQLFPRTYGKYHGRLDRFSAEQRLKAAYKLGSYLVRESDRKPGSYVLSYLG
KTGINHFRIAAVCGDFYIGGRQFFSLSDLVAYYSCNDLLKRERLIHAIAPPEPVSDTRRV
VAILPYTKMPDTDELSFQKGDIFFVHNNMGDGWIWTTKHRTGEQGMIFSELVEDLDPTID
PNTVFSWFHPNCTKNEAVDMLVKNGPGSFLVRPSDNSPGDYSLFFHINNQIQRFRIEKKG
VRYLMGGRTFECLDAVINRYRKEQIVEGHTLQNPVSNGSCQAEFQQQTAVSAAAEKIYAT
LRECRDQNMIKKIKGIKQQGYLMKRSDKTGKWKQLYFALINDGAETHLFFYDSPKKTKPK
GLIDLSCAYLYQVHESLWEKTNCFQIVERALPCLATISHLCDKNTESYQEWITVLKQHCR
AQFSRAQSKLPRLRELRCLNLQVLEAHRIPFKLVPHCFITIALNQIKIAKTKVKSTPDPI
FEEEFVIDDLPIDIATLNMTLVSRAKRNKDSDVAELTIDLSSLKNGAETENWYDLTGITP
IGEWGSLRLRIRYMDDLVMPAEEYSPLQELLLENEFHSVRALADLCHSNRIPLASSLLKI
FRHERKECELMKSLCQAEIARESDTSTLFRATSLATTLMDIYMRSECGLFLESALLDTIQ
KLLDSKQSAELNPTKMEVNDDACTNAEFLLLILDQITQSIFTSIEACPRGVRYICNCLQK
AVVAKWPGERLVRTRVVSGFIFLRLLCPALLNPRQFGLVQEQPSQMATRSLIMVAKCLQN
LANLIEFGGKGELPTFHESYMEVVNPFILKNKERMIVFLDQLSSISDPFVPSQVGMDISG
NININANNSSDTGRELATLHHICVSHLAELQNMSKVNASIKKLVTVTEMLSKHKLKYLEM
INDNAR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 27 | g2471.t1 | CDD | cd11788 | SH3_RasGAP | 118 | 175 | 1.18141E-30 |
| 26 | g2471.t1 | CDD | cd10354 | SH2_Cterm_RasGAP | 187 | 260 | 1.49233E-38 |
| 24 | g2471.t1 | Gene3D | G3DSA:3.30.505.10 | SHC Adaptor Protein | 17 | 117 | 7.2E-21 |
| 21 | g2471.t1 | Gene3D | G3DSA:2.30.30.40 | SH3 Domains | 118 | 176 | 6.5E-30 |
| 23 | g2471.t1 | Gene3D | G3DSA:3.30.505.10 | SHC Adaptor Protein | 177 | 298 | 1.6E-22 |
| 22 | g2471.t1 | Gene3D | G3DSA:2.30.29.30 | - | 307 | 426 | 1.5E-16 |
| 25 | g2471.t1 | Gene3D | G3DSA:2.60.40.150 | - | 435 | 558 | 8.7E-10 |
| 19 | g2471.t1 | Gene3D | G3DSA:1.10.506.10 | - | 562 | 875 | 2.1E-117 |
| 20 | g2471.t1 | Gene3D | G3DSA:1.10.506.10 | - | 647 | 829 | 2.1E-117 |
| 7 | g2471.t1 | PANTHER | PTHR10194 | RAS GTPASE-ACTIVATING PROTEINS | 52 | 902 | 4.1E-267 |
| 8 | g2471.t1 | PANTHER | PTHR10194:SF19 | RAS GTPASE-ACTIVATING PROTEIN 1 | 52 | 902 | 4.1E-267 |
| 10 | g2471.t1 | PRINTS | PR00401 | SH2 domain signature | 19 | 33 | 3.8E-6 |
| 9 | g2471.t1 | PRINTS | PR00401 | SH2 domain signature | 39 | 49 | 3.8E-6 |
| 12 | g2471.t1 | PRINTS | PR00401 | SH2 domain signature | 51 | 62 | 3.8E-6 |
| 11 | g2471.t1 | PRINTS | PR00401 | SH2 domain signature | 82 | 96 | 3.8E-6 |
| 4 | g2471.t1 | Pfam | PF00017 | SH2 domain | 20 | 93 | 6.7E-15 |
| 1 | g2471.t1 | Pfam | PF00018 | SH3 domain | 121 | 167 | 1.3E-8 |
| 3 | g2471.t1 | Pfam | PF00017 | SH2 domain | 187 | 260 | 3.1E-15 |
| 5 | g2471.t1 | Pfam | PF00169 | PH domain | 318 | 420 | 7.3E-9 |
| 6 | g2471.t1 | Pfam | PF00168 | C2 domain | 439 | 535 | 4.8E-8 |
| 2 | g2471.t1 | Pfam | PF00616 | GTPase-activator protein for Ras-like GTPase | 681 | 783 | 5.5E-20 |
| 28 | g2471.t1 | ProSitePatterns | PS00509 | Ras GTPase-activating proteins domain signature. | 739 | 753 | - |
| 37 | g2471.t1 | ProSiteProfiles | PS50001 | Src homology 2 (SH2) domain profile. | 19 | 108 | 17.063 |
| 35 | g2471.t1 | ProSiteProfiles | PS50002 | Src homology 3 (SH3) domain profile. | 115 | 177 | 17.468 |
| 36 | g2471.t1 | ProSiteProfiles | PS50001 | Src homology 2 (SH2) domain profile. | 187 | 275 | 16.885 |
| 39 | g2471.t1 | ProSiteProfiles | PS50003 | PH domain profile. | 315 | 420 | 12.416 |
| 38 | g2471.t1 | ProSiteProfiles | PS50018 | Ras GTPase-activating proteins profile. | 589 | 783 | 45.6 |
| 34 | g2471.t1 | SMART | SM00252 | SH2_5 | 17 | 99 | 3.0E-20 |
| 30 | g2471.t1 | SMART | SM00326 | SH3_2 | 118 | 176 | 4.6E-10 |
| 33 | g2471.t1 | SMART | SM00252 | SH2_5 | 185 | 266 | 1.2E-23 |
| 32 | g2471.t1 | SMART | SM00233 | PH_update | 316 | 422 | 5.5E-12 |
| 29 | g2471.t1 | SMART | SM00239 | C2_3c | 438 | 532 | 3.5E-5 |
| 31 | g2471.t1 | SMART | SM00323 | RasGAP_2 | 539 | 901 | 7.7E-118 |
| 15 | g2471.t1 | SUPERFAMILY | SSF55550 | SH2 domain | 15 | 100 | 2.96E-23 |
| 17 | g2471.t1 | SUPERFAMILY | SSF50044 | SH3-domain | 106 | 155 | 2.99E-7 |
| 16 | g2471.t1 | SUPERFAMILY | SSF55550 | SH2 domain | 148 | 270 | 1.13E-23 |
| 14 | g2471.t1 | SUPERFAMILY | SSF50729 | PH domain-like | 317 | 420 | 3.56E-18 |
| 18 | g2471.t1 | SUPERFAMILY | SSF49562 | C2 domain (Calcium/lipid-binding domain, CaLB) | 439 | 572 | 1.8E-13 |
| 13 | g2471.t1 | SUPERFAMILY | SSF48350 | GTPase activation domain, GAP | 559 | 898 | 1.61E-78 |
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:0046580 | negative regulation of Ras protein signal transduction | BP |
| GO:0043087 | regulation of GTPase activity | BP |
| GO:0007165 | signal transduction | BP |
| GO:0005515 | protein binding | MF |
| GO:0043547 | positive regulation of GTPase activity | BP |
| GO:0005096 | GTPase activator activity | MF |
KEGG
Orthology
- This transcript has been annotated with K04352 (Ras GTPase-activating protein 1)
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.
