General information for g4072.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ras GTPase-activating protein raskol.
Parent gene
- The parent gene g4072 is located on chr_3: 30383881..30395601 (+ 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 | g4072 | g4072.t2 | isoform | g4072.t2 | 30383881 | 30395601 |
| chr_3 | g4072 | g4072.t2 | exon | g4072.t2.exon1 | 30383881 | 30384754 |
| chr_3 | g4072 | g4072.t2 | cds | g4072.t2.CDS1 | 30383881 | 30384754 |
| chr_3 | g4072 | g4072.t2 | exon | g4072.t2.exon2 | 30390307 | 30390418 |
| chr_3 | g4072 | g4072.t2 | cds | g4072.t2.CDS2 | 30390307 | 30390418 |
| chr_3 | g4072 | g4072.t2 | exon | g4072.t2.exon3 | 30391275 | 30391435 |
| chr_3 | g4072 | g4072.t2 | cds | g4072.t2.CDS3 | 30391275 | 30391435 |
| chr_3 | g4072 | g4072.t2 | exon | g4072.t2.exon4 | 30391507 | 30392864 |
| chr_3 | g4072 | g4072.t2 | cds | g4072.t2.CDS4 | 30391507 | 30392864 |
| chr_3 | g4072 | g4072.t2 | exon | g4072.t2.exon5 | 30392929 | 30393288 |
| chr_3 | g4072 | g4072.t2 | cds | g4072.t2.CDS5 | 30392929 | 30393288 |
| chr_3 | g4072 | g4072.t2 | exon | g4072.t2.exon6 | 30393444 | 30394682 |
| chr_3 | g4072 | g4072.t2 | cds | g4072.t2.CDS6 | 30393444 | 30394682 |
| chr_3 | g4072 | g4072.t2 | exon | g4072.t2.exon7 | 30394746 | 30394902 |
| chr_3 | g4072 | g4072.t2 | cds | g4072.t2.CDS7 | 30394746 | 30394902 |
| chr_3 | g4072 | g4072.t2 | exon | g4072.t2.exon8 | 30395115 | 30395316 |
| chr_3 | g4072 | g4072.t2 | cds | g4072.t2.CDS8 | 30395115 | 30395316 |
| chr_3 | g4072 | g4072.t2 | exon | g4072.t2.exon9 | 30395376 | 30395601 |
| chr_3 | g4072 | g4072.t2 | cds | g4072.t2.CDS9 | 30395376 | 30395601 |
| chr_3 | g4072 | g4072.t2 | TTS | g4072.t2 | 30396307 | 30396307 |
| chr_3 | g4072 | g4072.t2 | TSS | g4072.t2 | NA | NA |
Sequences
>g4072.t2 Gene=g4072 Length=4689
ATGGCGTTGATATTGCAAACAGCTGATCAAACATCATTCTCTGGCGATGAGTCATCACGT
CGTCGATCAACATTTTATGTGCCGTTATCGACTGAAGATTTGACACAGACAGAAGAAATT
GAAGAGATGAAAAAATCAAATGAAAATTTAAATATGAGTCGTTATTCATATGACTGGAGT
ATAAATGATTCCATTGATAGCTCAGATATTTTGCGAGAAAAATCGCAATATGCGTCAGAT
GATAGTACACGACTTAAACGTTATGGAATCGTATTAAATGGAAGTGTAAACATTGACGAC
AGCAATTTGGAAGTTCATGCTAATCATAAGCGCACGAAAACGAAGACAATCATGTCCTCT
ACACCCATTAAAGAGATTGTCAAGTGCAAAGAAATTATAAATGAACCACAGGCAACTGTC
ACTATCACATTGACAAGTCCGGTCAAAGAAAAATCTAAAACATTGCCAGTCAATACTGCA
CCAATTTTCCCGTCTAAAAATTCTTTTCTTCTAAAATCAACACCAAAGATCTCGTCATCA
GTTAATTATACTTCCCTTTCTGACTCATATGATCATCACCATAAAGTTGTAGCATCGCCA
AAGAAATCACTAAGCTTCATCCGGCGCACGCATTCGACAAAATTGTCACGTAATAATTCG
CTGCTCAAGTCACTGACGTCAAAATGTGTTGAGCATTCAAATGAGAATTTACCAGTGAAT
GTTTATGATTTGACAGTCGAAAGACTTGAATTGTATTTGAAGGCAGAAAATTGCGATGAA
TTGATGAAGGAACTTTTCTTACGTGAACCATTAGATATTTCTTTAACAGAAAATAATCAT
AATAAAGAAAATGAGGACGATGATGCACAATCGGACACATCGTATGAGAAAGCATGCAGA
CGAGGCTCAGCACCAAGTACACCGATGCTTACACAAAAACCTGAATCATCGTCAACCTCA
CGATTCACAATATTTTTCTCGAAACGTCTGAGCTCGTTTAGATCAAATCCATTGAAGCGC
ACAAAATCGGTGACAAAGCTGGAAAGAACGAAACGAGGAAGTGGAAATGGTAGTGGCGGC
GGTGGAATACGAGGGTCACGATCGCATGAGAGTCTTTTATCGAATCATGCAGTCATGTCA
ACGATCGATTTATCAGTAATAGGCGCTGTAGGAGTCGCACCAGTTCACTCATCCGTGCTT
GGTCGACGTCATTGTTTTCAAGTGCGTGGTGGTCCTAGAGGGGAAAGATATTACAGCTGC
GGTTCACGACAAGAACGTGACTTGTGGATTTATAGTTTGAGGAAGTCAATTCAACCAAAT
GCAGAAGGAACAAGACGAACTGACAATTCATTAAAAATGTGGATTTATGAGGCAAAAGCA
TTGCCACCAAAGAAGAAATATTTTTGTGAAATTTGTCTCGATAAAACACTTTATGGTCGA
ACATCAGTGAAATTAAAGACCGATTTACTATTTTGGGGTGAACATTTTGATTTTCCTGAT
ATACCTGAAATCAATGTCATTTATGTCAATGTTTTTCGTGAATGTGAAAAGAAAAAGAAA
CGAGACAAACATCAACTTATTGGTACAGTTAAAATTCCAATACATGAAGTCACAAGTCGA
ACATTTTCTGAAGATTGGTATCCAATAATTTCGGATAAGCATGATAGTCTCAGTAAGAGC
TCTTCGAAAGAGCCAATACCAACTTTACGCATAAAATGCCGCTTTCAAAGCATTGATATT
TTACCAATTGATGTTTATTCAACATTTCAAGCTTACCTTAAAGAACATTATAAGAAAATT
TGTGAATGTCTTGAACCAGTTATTGGTGTTAAAGCTAAAGAAGATATTGGACAAGCAATG
GTTTTATTAATGCATCATCAAGGAATGGCTGCAGAATTTTTAACAGAAATTATAACACTC
GATTTACTTAGAGTTGGCGATCAACGTCTGACGTTCCGTGGAAATTCACTTGCAACTAAA
AGTATGGAAGCATTTTTGAAACTTACTGGTGAGCAATATTTACAAGACACATTGTCAGCA
CCTATCAATGAAATTATCTCATCAGAACGTGATTGTGAAGTTGATCCATTAAAAGCAACA
GGTTCATTATCAAGACAACAACAAGCATTAAGAAGTGCAGTTAAATTAGCATGGAATGCA
ATTAATGAAAGTTATCGACATTTTCCATCACAATTACGTGAATGCTTTGCAATTTTTCGT
GAAAGACTTGTCAATATTTCACGTGAAGATATGGCTGACAATTTAATATCGGCCAGTATC
TTTTTGAGATTCTTATGTCCAGCAATTTTATCACCAAGTTTATTCAATATCACAAATGAA
CTGCCATCACAAAGAGCGACAAGGAATTTGACACTTGTAGCCAAAACATTGCAAACACTC
GCAAATTTCACTCGTTTTCAAGGCAAAGAGAATTTCATGGAATTTTTGAATGATTTTCTT
GAACAAGAAGCACCACGAATGAAGGACTTTTTAATGAAGATTTCGTCAAGAGTTGAACAA
CATCAAACTGATTCAATACTAGAATGGTCAGGTTATATTGATCAAGGCAAACAGTTGTCA
ATTTTACATTCATTACTTGTTGAAAATTTGCCAAAATTACCACCACAAAAGCAAGGAGAA
ATGACACAATTAATGTCAATTCTTGAAAAAATCAGTCAAATTAAGGAATCAACTGAAAAT
AATTATCAGCGACATTTATCAGAGCAAAGTTTCTCATCAATGGAAAGATTAAATGGACAC
AAGGCATCAATGAATTCATTGCATGGAATCTCAAATCCACAACAAGGTCCTGAAAGAGGA
ATTATTCGTGGAGTTTTGACACCGAATTCGTTGCAGAAAAATATTTTCTGCTATAACGAT
CCAACAGTATATTCACTATTAAATGGTGATCAAAAGATGAGCTTCAATCCATTGCAGCAT
TCACATTCAACATCGAGTATTCAATCTTCACAGCACAATAATTCAGTGATTAATGGAAAC
AGTATTCAACATCACAATATTACAAGCACAAAACGTAATGAAAATTATTATCAAATTACA
AGTAGTCTTGCACGTAATGAACCAAAGAGTCCAGCATCATCATCATCAATTCGTGCAAGT
ACACTGCCAAGAAATAATCAACAAATTCAAAATGATGAAACAAATATTATTCAAATTGGA
TTGGATCCAAGTAATCCTTTTTCACGTAAAAGTCCAACACCGAGAATGCATAGTGGTTTA
TTAACTACAGCAAATGGTAATAGCAATAAAATTTCACAGCCACCACCTACAGTTTATACA
ACAAATGGACGTCAATTGAATGGCTCACAATTGAGTTTATTGAGTGATCGATCACAACAT
CAGTACTACCATCATCAACCACAACATCATATGCATCGATCAAATGGTTTAAATCTTGGT
ATTCCACATACGGAAGCACCTTCGTCCTCATATGAATCACCAAATGGTAGCAATATGCCA
CGTGATTTAGAAGATTTTGATGATTTAATTAAATATAATGAAGAGCATGAACAGAGACAA
CAAAGACAACAAGAGCAAAATCATCATCATCATCATCATCCAAATTTAAAAGCCAAAGGC
AGTAATGTGTCAATTGGTCATTCATCTGGCTATCAATCGATACAAACACAATCACAAAGC
TCAAGTCCAATTGAAAATGTAATTAGTACTACAAATGCTGCTAATCAAGCTGCACAATCA
CTCATACAACAAAATATTGAATTCTTTAATTCTAAAATTCAAAGTTCGAGTTCATCAAGC
AATGCAAGCACAAGCAATCGACCAACAAAATTAAATGGAAAATATGGCTACATTAGTCCT
AAATATTCTGTTGTTCCACCATTAGCATTTAAAAATCCACTCTATCAAATGCAAAATGGT
AATAATAATAATGATGGAAAAAGTTCTTCATTAACACCATCAAGCAGTGAAGAACGAATT
ACAATTGATGATAGACAAAATGTGCTGAATAATAACAATCTCGTTTCGTCCTCAACAAAT
GCACCCGGTATTATTGACACATCATCACTGAATGGTAGACGAATGGGTAGCAATCGTATG
CCGCGAACAAATCCACTTGTTCAATATAAACGCGATGATGGAATCTACGACAATCATAAT
CATATGAATGGGAATAATAACAATAACAATAATCAGTTGGCATACTTTAATAATCGCTAT
GAAAGACGTCTGAGTGTTGAATCAGCAAGGACATTGTCTGATAGTTCTAGTGATACTGAA
GTTCATCATCATAAAGAGGGCAAAAGACGACGCAATGCGAATAAATCTCAAATCGAACAA
TGCGAGAAAGAAATTCATCGATTGCAATCTAGTGTCGATATTTTACGTCAGAAGTTGGAA
GAAAGTGAACTAAAAGAAACGAGCGATAGTATTGACGCAATTGCGCATCAGAGTGACAAT
AAAATTAGAAGTATCATATCAAGATTGCTAGCAATGGAAGAAGAATTAAGACGTGAACAA
TATAAAATGTCGCTAATAATAAATCACAAGCAGCGAGTGATTGAAGCACAGGGACAACAA
ATTGCAGAATTGGATGCTGCCAATAATCGCCTATTAACCGAATTGACATGTTTGAGAAAT
CGATTCGATATGAAAGGCAACAACCAAACACTGACTGTGACTGAAGATGACGATACGACC
AACTTTTAA
>g4072.t2 Gene=g4072 Length=1562
MALILQTADQTSFSGDESSRRRSTFYVPLSTEDLTQTEEIEEMKKSNENLNMSRYSYDWS
INDSIDSSDILREKSQYASDDSTRLKRYGIVLNGSVNIDDSNLEVHANHKRTKTKTIMSS
TPIKEIVKCKEIINEPQATVTITLTSPVKEKSKTLPVNTAPIFPSKNSFLLKSTPKISSS
VNYTSLSDSYDHHHKVVASPKKSLSFIRRTHSTKLSRNNSLLKSLTSKCVEHSNENLPVN
VYDLTVERLELYLKAENCDELMKELFLREPLDISLTENNHNKENEDDDAQSDTSYEKACR
RGSAPSTPMLTQKPESSSTSRFTIFFSKRLSSFRSNPLKRTKSVTKLERTKRGSGNGSGG
GGIRGSRSHESLLSNHAVMSTIDLSVIGAVGVAPVHSSVLGRRHCFQVRGGPRGERYYSC
GSRQERDLWIYSLRKSIQPNAEGTRRTDNSLKMWIYEAKALPPKKKYFCEICLDKTLYGR
TSVKLKTDLLFWGEHFDFPDIPEINVIYVNVFRECEKKKKRDKHQLIGTVKIPIHEVTSR
TFSEDWYPIISDKHDSLSKSSSKEPIPTLRIKCRFQSIDILPIDVYSTFQAYLKEHYKKI
CECLEPVIGVKAKEDIGQAMVLLMHHQGMAAEFLTEIITLDLLRVGDQRLTFRGNSLATK
SMEAFLKLTGEQYLQDTLSAPINEIISSERDCEVDPLKATGSLSRQQQALRSAVKLAWNA
INESYRHFPSQLRECFAIFRERLVNISREDMADNLISASIFLRFLCPAILSPSLFNITNE
LPSQRATRNLTLVAKTLQTLANFTRFQGKENFMEFLNDFLEQEAPRMKDFLMKISSRVEQ
HQTDSILEWSGYIDQGKQLSILHSLLVENLPKLPPQKQGEMTQLMSILEKISQIKESTEN
NYQRHLSEQSFSSMERLNGHKASMNSLHGISNPQQGPERGIIRGVLTPNSLQKNIFCYND
PTVYSLLNGDQKMSFNPLQHSHSTSSIQSSQHNNSVINGNSIQHHNITSTKRNENYYQIT
SSLARNEPKSPASSSSIRASTLPRNNQQIQNDETNIIQIGLDPSNPFSRKSPTPRMHSGL
LTTANGNSNKISQPPPTVYTTNGRQLNGSQLSLLSDRSQHQYYHHQPQHHMHRSNGLNLG
IPHTEAPSSSYESPNGSNMPRDLEDFDDLIKYNEEHEQRQQRQQEQNHHHHHHPNLKAKG
SNVSIGHSSGYQSIQTQSQSSSPIENVISTTNAANQAAQSLIQQNIEFFNSKIQSSSSSS
NASTSNRPTKLNGKYGYISPKYSVVPPLAFKNPLYQMQNGNNNNDGKSSSLTPSSSEERI
TIDDRQNVLNNNNLVSSSTNAPGIIDTSSLNGRRMGSNRMPRTNPLVQYKRDDGIYDNHN
HMNGNNNNNNNQLAYFNNRYERRLSVESARTLSDSSSDTEVHHHKEGKRRRNANKSQIEQ
CEKEIHRLQSSVDILRQKLEESELKETSDSIDAIAHQSDNKIRSIISRLLAMEEELRREQ
YKMSLIINHKQRVIEAQGQQIAELDAANNRLLTELTCLRNRFDMKGNNQTLTVTEDDDTT
NF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g4072.t2 | CDD | cd04013 | C2_SynGAP_like | 439 | 583 | 6.23345E-75 |
| 15 | g4072.t2 | CDD | cd05136 | RasGAP_DAB2IP | 574 | 897 | 3.61865E-171 |
| 12 | g4072.t2 | Coils | Coil | Coil | 888 | 908 | - |
| 14 | g4072.t2 | Coils | Coil | Coil | 1431 | 1465 | - |
| 13 | g4072.t2 | Coils | Coil | Coil | 1514 | 1541 | - |
| 11 | g4072.t2 | Gene3D | G3DSA:2.60.40.150 | - | 430 | 573 | 1.6E-12 |
| 10 | g4072.t2 | Gene3D | G3DSA:1.10.506.20 | - | 581 | 892 | 1.8E-130 |
| 9 | g4072.t2 | Gene3D | G3DSA:1.10.506.10 | - | 631 | 850 | 1.8E-130 |
| 21 | g4072.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 277 | 316 | - |
| 22 | g4072.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 277 | 295 | - |
| 24 | g4072.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1023 | 1051 | - |
| 23 | g4072.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1176 | 1197 | - |
| 20 | g4072.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1407 | 1437 | - |
| 4 | g4072.t2 | PANTHER | PTHR10194 | RAS GTPASE-ACTIVATING PROTEINS | 325 | 1535 | 0.0 |
| 5 | g4072.t2 | PANTHER | PTHR10194:SF125 | RAS GTPASE-ACTIVATING PROTEIN-RELATED | 325 | 1535 | 0.0 |
| 2 | g4072.t2 | Pfam | PF00168 | C2 domain | 450 | 549 | 5.3E-10 |
| 1 | g4072.t2 | Pfam | PF00616 | GTPase-activator protein for Ras-like GTPase | 706 | 802 | 1.2E-15 |
| 3 | g4072.t2 | Pfam | PF12004 | Domain of unknown function (DUF3498) | 1478 | 1542 | 1.6E-16 |
| 19 | g4072.t2 | ProSitePatterns | PS00509 | Ras GTPase-activating proteins domain signature. | 758 | 772 | - |
| 25 | g4072.t2 | ProSiteProfiles | PS50018 | Ras GTPase-activating proteins profile. | 612 | 802 | 38.691 |
| 17 | g4072.t2 | SMART | SM00239 | C2_3c | 450 | 546 | 1.4E-7 |
| 18 | g4072.t2 | SMART | SM00323 | RasGAP_2 | 561 | 902 | 1.2E-84 |
| 7 | g4072.t2 | SUPERFAMILY | SSF50729 | PH domain-like | 378 | 470 | 2.03E-8 |
| 8 | g4072.t2 | SUPERFAMILY | SSF49562 | C2 domain (Calcium/lipid-binding domain, CaLB) | 451 | 577 | 1.87E-11 |
| 6 | g4072.t2 | SUPERFAMILY | SSF48350 | GTPase activation domain, GAP | 584 | 884 | 1.88E-73 |
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:0043087 | regulation of GTPase activity | BP |
| GO:0007165 | signal transduction | BP |
KEGG
Orthology
- This transcript has been annotated with K17633 (RAS protein activator-like 2)
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.
