Gene loci information

Transcript annotation

  • This transcript has been annotated as GTPase-activating protein.

Parent gene

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_1 g9874 g9874.t1 TSS g9874.t1 5841970 5841970
chr_1 g9874 g9874.t1 isoform g9874.t1 5842235 5852847
chr_1 g9874 g9874.t1 exon g9874.t1.exon1 5842235 5842280
chr_1 g9874 g9874.t1 cds g9874.t1.CDS1 5842235 5842280
chr_1 g9874 g9874.t1 exon g9874.t1.exon2 5845107 5846746
chr_1 g9874 g9874.t1 cds g9874.t1.CDS2 5845107 5846746
chr_1 g9874 g9874.t1 exon g9874.t1.exon3 5846814 5846909
chr_1 g9874 g9874.t1 cds g9874.t1.CDS3 5846814 5846909
chr_1 g9874 g9874.t1 exon g9874.t1.exon4 5848798 5849039
chr_1 g9874 g9874.t1 cds g9874.t1.CDS4 5848798 5849039
chr_1 g9874 g9874.t1 exon g9874.t1.exon5 5849598 5849796
chr_1 g9874 g9874.t1 cds g9874.t1.CDS5 5849598 5849796
chr_1 g9874 g9874.t1 exon g9874.t1.exon6 5852107 5852258
chr_1 g9874 g9874.t1 cds g9874.t1.CDS6 5852107 5852258
chr_1 g9874 g9874.t1 exon g9874.t1.exon7 5852316 5852440
chr_1 g9874 g9874.t1 cds g9874.t1.CDS7 5852316 5852440
chr_1 g9874 g9874.t1 exon g9874.t1.exon8 5852501 5852847
chr_1 g9874 g9874.t1 cds g9874.t1.CDS8 5852501 5852847
chr_1 g9874 g9874.t1 TTS g9874.t1 5852950 5852950

Sequences

>g9874.t1 Gene=g9874 Length=2847
ATGGAACAACTAGTGCGAACGGAAGAGTTTTTAAGAATCAAAATTGGTGAAGCAAAAAAT
CTTGCCGGTCGTTCAGCAACTTCATCATCATCAAATACTCGAGATATTTATTGCACAGTA
GCACTCGATCAGGAAGAAATATGTCGAACACAATCACAACGCACTCAATCGCCATTTTTT
GGTGAAGAATTTTCCTTTGAAATTCCAAGAAAATTTCGATATTTATCAGTATATGTGCTA
GAACGTGATCGACATTTAAAACAGGATAAAGCGATAGGAAAAATAGCAATAAGACGTGGT
GATCTGCATTTATATAATCATAAAGATCATTGGTTTCCATTAAGACAAGTTGATGATGAT
AGTGAAGTGCAAGGCATGGCACATATAGAAGTTAAAATTATTGATGATGATGATCATGCA
AAAGAAAATTTTAAATCAACTAGTAATAATTATACAACTACAACAATTCTCTCGCCCGCC
TCAAATAACACATCAAATCATAAATCACCAAAACTCCTTCATTCCACACATAGTACACAA
CAAATTGTTCAACGATCCAGCAGCCAGCAGGACGTGAGTCTTAAACATCAAGGCAATTTC
CTTCGAGTTCCTTACACAAACTCCTTTCATCAGCATCAACGTATACAAGTACGACTGAAA
GGCTGTTCAGATCTCACAAGAAAAAATAATCAGTGTGATCCATATGCCATTGTAACAGCA
CTTTATACAAATAAAAGAAAAATCACGAGACGTACGAAAGTTAGAAAGAAAACAATTCAT
CCAACATTTGACGATGTCTTCGAATTCAGTCTTTATGATTTTACACATGGCAGCGGCTCA
CATGGGCCAAGTGATAGTAAAATTTATACAGTGACACCATTTGGTGGTAATGATTTGTGT
GAAATTGTCGTGCAAGTTTGGCATTCAGCTGGAATGGCTGATGATAATTTCTTAGGTGAA
GTAAGACTGCCAGCAAGAGGAAAACAAGAGCTTCAATATCTACAACAATCTGCCTGGTAT
TTTCTACTGCCACGATCAAGCCAATCAAGACCAGCAAAATCTTGTGCCACACCACCTGGT
ACAAGATTAAGCTGTGAAAATTCATTAGGTTCATTACGACTTAAATTACATTATCAGGCA
GATCATGTATTTCCACTCGCCAATTATGATCAATTGCTGAATTTATTAATACAAAGCGTC
GATCAAAGACCAATTACTTCCTCGGCTGTGTATCTATTAGGCGAGATGGTTGCAAATAAA
CAAGAAATTGCACAGCCCTTAGTGAGACTATTTACACATAATAAACGTATAGTTGACATC
ATTCAAAGATTAGCTGAATATGAAATTTGTAAATTGACTGATCCGACAACAATTTTTCGC
GGCAATACACTCGTTTCAAAGATGATGGACGAGGCGATGAAATTGAGTGGTCTTCATTAT
CTTCATGCGACGCTAAGACCAATTGTAGAGCTCATATTGCAAGAAAAAAAGTGCTGTGAA
ATTGATCCGATGCGCATTAACCGCGAAAAGACTTCAATCGAGCAAAATTTAAACAATCTT
CATGAATATGTGGAAAAAGTTTTTGATGCCATTGTCAAAAGTTCAAATAAATGTCCGCGT
GTACTTTGTGAAATTTTTCATAATATGCGCGAGAGTGCGACTAAATATTTTCCACAAAAT
AAAGAGGTGCGATATAGTGTAGTATCTGGCTTCATCTTTTTACGTTTCTTTGCACCCGCC
ATTCTTGGACCAAAATTATTCGATCTGACGGCAGAGCCATTGGATTCACAAACAAACCGA
ACGCTCACATTAATCTCAAAGACGATACAATCGTTAGGCAATTTGGTGAGCTCACGATCA
GCACAGCAACACGCAAAAGAAGAATTTATGGTGGAATTGAATAAAAAATTTTGTACTGAA
AAGCATGTCGCTGCAGTAAAGCAATTTCTTGATGCCATTTCTGCGGTCGACTCACGCGAG
GCTGCTGAAATATGTGTACATGAACCGATATTGCTGAAGGACGGGATGATGACGAAGCAT
GCCCAAAATCGAAAACGCTTTGGACGGCGGAATTTCAAGCAGCGCTATTTCCGATTAACA
ACACATTCGCTGAGCTATGCAAAGGCAAAGGGCAAACGACCAATCTGTGATATACAATTA
ACGGAACTTATTGCTGTCGAGAGGCTCGAGGAGAAAAGTTTTAAGCTGCAAAATATCTTT
CGCATCACACGAAAGGATCGACCATTATACATTCAAACAGCAAATTGTGTGGAGGAGAAA
AAGTGGGTAGATTTACTAAGTAAAATATGTGAGAATAATAAGCGACGACTTGATACTTTC
CATCCATGTGCGTTCATTCATGGAGAATGGACTTGTTGTAATGAGAGAGATCAAAATGCG
CGAGGTTGCAAAGCAGTTGATGAAACACCATTAGAAGTTGATCTAGTGACGCAGCTTGAT
CCAGCGCGTGATCTACAACGACTTCACTCACTAATTATTGCAAACATGAGTGTGATGACA
AAATTCTTCGACACGAGTATGCCAAAAACCGACGAGATTGATCTGACAAGACAAACAATC
CGACGACTTAGTGATGAAGCAATGAATCTCGAGCAAATCCATCGCAATCATAGAAATAAA
GAGGCAAAAGATGCAAAGCTAGGCAGTAAACAAGAACCAATTGGTGATGATAATTATCTA
CGTGGCATTGGCTCATCAAGTCTCAATTCGGGAGCTTCAACAACTCCTCGATCCGTAACA
ACCACAACTCAACACTTTGATCTTCCACCTACTCACTTTCAACGCGGACACTTTTTACGT
AATTCCGATGGATTTTCACATTTCTAA

>g9874.t1 Gene=g9874 Length=948
MEQLVRTEEFLRIKIGEAKNLAGRSATSSSSNTRDIYCTVALDQEEICRTQSQRTQSPFF
GEEFSFEIPRKFRYLSVYVLERDRHLKQDKAIGKIAIRRGDLHLYNHKDHWFPLRQVDDD
SEVQGMAHIEVKIIDDDDHAKENFKSTSNNYTTTTILSPASNNTSNHKSPKLLHSTHSTQ
QIVQRSSSQQDVSLKHQGNFLRVPYTNSFHQHQRIQVRLKGCSDLTRKNNQCDPYAIVTA
LYTNKRKITRRTKVRKKTIHPTFDDVFEFSLYDFTHGSGSHGPSDSKIYTVTPFGGNDLC
EIVVQVWHSAGMADDNFLGEVRLPARGKQELQYLQQSAWYFLLPRSSQSRPAKSCATPPG
TRLSCENSLGSLRLKLHYQADHVFPLANYDQLLNLLIQSVDQRPITSSAVYLLGEMVANK
QEIAQPLVRLFTHNKRIVDIIQRLAEYEICKLTDPTTIFRGNTLVSKMMDEAMKLSGLHY
LHATLRPIVELILQEKKCCEIDPMRINREKTSIEQNLNNLHEYVEKVFDAIVKSSNKCPR
VLCEIFHNMRESATKYFPQNKEVRYSVVSGFIFLRFFAPAILGPKLFDLTAEPLDSQTNR
TLTLISKTIQSLGNLVSSRSAQQHAKEEFMVELNKKFCTEKHVAAVKQFLDAISAVDSRE
AAEICVHEPILLKDGMMTKHAQNRKRFGRRNFKQRYFRLTTHSLSYAKAKGKRPICDIQL
TELIAVERLEEKSFKLQNIFRITRKDRPLYIQTANCVEEKKWVDLLSKICENNKRRLDTF
HPCAFIHGEWTCCNERDQNARGCKAVDETPLEVDLVTQLDPARDLQRLHSLIIANMSVMT
KFFDTSMPKTDEIDLTRQTIRRLSDEAMNLEQIHRNHRNKEAKDAKLGSKQEPIGDDNYL
RGIGSSSLNSGASTTPRSVTTTTQHFDLPPTHFQRGHFLRNSDGFSHF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g9874.t1 CDD cd04010 C2B_RasA3 214 377 1.81357E-53
18 g9874.t1 CDD cd05128 RasGAP_GAP1_like 388 656 1.5768E-139
17 g9874.t1 CDD cd01244 PH_GAP1-like 673 777 1.75505E-45
16 g9874.t1 Coils Coil Coil 853 880 -
14 g9874.t1 Gene3D G3DSA:2.60.40.150 - 2 134 2.3E-17
15 g9874.t1 Gene3D G3DSA:2.60.40.150 - 179 355 2.6E-19
12 g9874.t1 Gene3D G3DSA:1.10.506.10 - 438 664 3.7E-67
13 g9874.t1 Gene3D G3DSA:2.30.29.30 - 666 812 1.1E-36
26 g9874.t1 MobiDBLite mobidb-lite consensus disorder prediction 878 897 -
6 g9874.t1 PANTHER PTHR10194:SF126 GTPASE-ACTIVATING PROTEIN 6 891 2.2E-222
7 g9874.t1 PANTHER PTHR10194 RAS GTPASE-ACTIVATING PROTEINS 6 891 2.2E-222
4 g9874.t1 Pfam PF00168 C2 domain 11 114 1.7E-14
3 g9874.t1 Pfam PF00168 C2 domain 214 338 7.8E-8
1 g9874.t1 Pfam PF00616 GTPase-activator protein for Ras-like GTPase 508 613 3.9E-25
2 g9874.t1 Pfam PF00169 PH domain 672 770 4.1E-8
5 g9874.t1 Pfam PF00779 BTK motif 779 807 1.6E-10
25 g9874.t1 ProSitePatterns PS00509 Ras GTPase-activating proteins domain signature. 570 584 -
28 g9874.t1 ProSiteProfiles PS50004 C2 domain profile. 11 96 10.93
27 g9874.t1 ProSiteProfiles PS50004 C2 domain profile. 214 322 10.501
30 g9874.t1 ProSiteProfiles PS50018 Ras GTPase-activating proteins profile. 419 614 53.835
31 g9874.t1 ProSiteProfiles PS50003 PH domain profile. 670 771 12.235
29 g9874.t1 ProSiteProfiles PS51113 Zinc finger Btk-type profile. 773 809 13.867
21 g9874.t1 SMART SM00239 C2_3c 10 111 3.2E-11
20 g9874.t1 SMART SM00239 C2_3c 214 340 1.1E-11
22 g9874.t1 SMART SM00323 RasGAP_2 364 708 3.3E-132
23 g9874.t1 SMART SM00233 PH_update 671 773 9.3E-12
24 g9874.t1 SMART SM00107 ph_extension_3 773 809 1.1E-8
10 g9874.t1 SUPERFAMILY SSF49562 C2 domain (Calcium/lipid-binding domain, CaLB) 11 143 2.34E-19
11 g9874.t1 SUPERFAMILY SSF49562 C2 domain (Calcium/lipid-binding domain, CaLB) 208 346 6.55E-17
8 g9874.t1 SUPERFAMILY SSF48350 GTPase activation domain, GAP 385 713 5.49E-82
9 g9874.t1 SUPERFAMILY SSF50729 PH domain-like 671 806 3.29E-36

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
GO:0035556 intracellular signal transduction BP

KEGG

Orthology

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.

Raw TPM values