Gene loci information

Transcript annotation

  • This transcript has been annotated as Ras GTPase-activating protein 1.

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_3 g2471 g2471.t4 isoform g2471.t4 18126742 18128851
chr_3 g2471 g2471.t4 exon g2471.t4.exon1 18126742 18127842
chr_3 g2471 g2471.t4 cds g2471.t4.CDS1 18126744 18127842
chr_3 g2471 g2471.t4 exon g2471.t4.exon2 18128039 18128111
chr_3 g2471 g2471.t4 cds g2471.t4.CDS2 18128039 18128111
chr_3 g2471 g2471.t4 exon g2471.t4.exon3 18128317 18128390
chr_3 g2471 g2471.t4 cds g2471.t4.CDS3 18128317 18128390
chr_3 g2471 g2471.t4 exon g2471.t4.exon4 18128472 18128524
chr_3 g2471 g2471.t4 cds g2471.t4.CDS4 18128472 18128524
chr_3 g2471 g2471.t4 exon g2471.t4.exon5 18128849 18128851
chr_3 g2471 g2471.t4 cds g2471.t4.CDS5 18128849 18128851
chr_3 g2471 g2471.t4 TSS g2471.t4 NA NA
chr_3 g2471 g2471.t4 TTS g2471.t4 NA NA

Sequences

>g2471.t4 Gene=g2471 Length=1304
ATGGCAGTTCCAACGACCATAGAGCTTTACCAGCTATTCCCGAGAACCTATGGAAAGTAT
CATGGACGACTCGATAGATTTAGTGCAGAACAAAGGCTTAAAGCAGCATATAAACTCGGA
AGCTACTTAGTGAGAGAAAGTGACAGAAAGCCTGGATCATATGTATTATCTTATTTAGGA
AAAACTGGAATAAATCATTTCCGCATTGCTGCTGTGTGTGGCGATTTTTATATTGGCGGT
CGCCAATTCTTCTCATTAAGTGACTTGGTTGCATATTACTCATGTAATGATTTGTTGAAA
CGTGAACGACTCATCCATGCTATTGCACCGCCTGAACCTGTTTCAGACACACGACGTGTT
GTCGCTATTCTGCCATATACAAAAATGCCAGATACTGATGAGTTGAGTTTTCAAAAGGGT
GATATCTTTTTTGTTCACAATAATATGGGCGATGGATGGATATGGACAACGAAACATAGA
ACTGGCGAGCAGGGAATGATCTTTAGCGAACTTGTTGAAGATCTTGATCCAACAATTGAT
CCCAATACTGTTTTCTCATGGTTTCATCCTAATTGCACTAAAAATGAAGCTGTCGATATG
CTAGTAAAAAATGGCCCTGGTTCATTTTTAGTTCGACCTAGTGACAACAGTCCTGGTGAT
TATTCTCTCTTTTTTCACATCAATAATCAAATTCAGAGATTTCGAATTGAGAAAAAGGGC
GTTCGTTATTTAATGGGTGGAAGAACTTTTGAATGCTTAGATGCAGTTATCAATCGTTAC
CGTAAAGAACAAATAGTTGAAGGACATACTTTACAAAATCCAGTCTCAAATGGATCATGT
CAGGCTGAATTTCAACAGCAAACAGCAGTATCAGCTGCTGCTGAAAAAATTTATGCAACA
TTACGAGAATGTCGTGATCAAAATATGATTAAAAAGATTAAAGGAATTAAACAGCAAGGA
TATCTAATGAAAAGGTCTGATAAAACTGGTAAATGGAAGCAACTTTATTTTGCACTCATC
AATGATGGCGCTGAAACACATTTGTTCTTTTATGATAGTCCCAAAAAGACAAAACCAAAA
GGATTAATTGATTTATCATGCGCTTATCTCTATCAAGTCCACGAATCGCTTTGGGAGAAA
ACAAATTGCTTTCAAATTGTTGAACGAGCACTGCCTTGTTTGGCGACCATTTCGCATTTA
TGTGACAAAAATACTGAATCATATCAGGAATGGATCACTGTTCTTAAACAGCATTGTCGT
GCTCAATTTAGTCGAGCTCAGTCAAAATTGCCTCGATTACGCGA

>g2471.t4 Gene=g2471 Length=434
MAVPTTIELYQLFPRTYGKYHGRLDRFSAEQRLKAAYKLGSYLVRESDRKPGSYVLSYLG
KTGINHFRIAAVCGDFYIGGRQFFSLSDLVAYYSCNDLLKRERLIHAIAPPEPVSDTRRV
VAILPYTKMPDTDELSFQKGDIFFVHNNMGDGWIWTTKHRTGEQGMIFSELVEDLDPTID
PNTVFSWFHPNCTKNEAVDMLVKNGPGSFLVRPSDNSPGDYSLFFHINNQIQRFRIEKKG
VRYLMGGRTFECLDAVINRYRKEQIVEGHTLQNPVSNGSCQAEFQQQTAVSAAAEKIYAT
LRECRDQNMIKKIKGIKQQGYLMKRSDKTGKWKQLYFALINDGAETHLFFYDSPKKTKPK
GLIDLSCAYLYQVHESLWEKTNCFQIVERALPCLATISHLCDKNTESYQEWITVLKQHCR
AQFSRAQSKLPRLR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g2471.t4 CDD cd11788 SH3_RasGAP 118 175 0.0000000
18 g2471.t4 Gene3D G3DSA:3.30.505.10 SHC Adaptor Protein 17 118 0.0000000
15 g2471.t4 Gene3D G3DSA:2.30.30.40 SH3 Domains 119 176 0.0000000
17 g2471.t4 Gene3D G3DSA:3.30.505.10 SHC Adaptor Protein 177 298 0.0000000
16 g2471.t4 Gene3D G3DSA:2.30.29.30 - 307 426 0.0000000
5 g2471.t4 PANTHER PTHR10194 RAS GTPASE-ACTIVATING PROTEINS 52 429 0.0000000
6 g2471.t4 PANTHER PTHR10194:SF19 RAS GTPASE-ACTIVATING PROTEIN 1 52 429 0.0000000
8 g2471.t4 PRINTS PR00401 SH2 domain signature 19 33 0.0000003
7 g2471.t4 PRINTS PR00401 SH2 domain signature 39 49 0.0000003
10 g2471.t4 PRINTS PR00401 SH2 domain signature 51 62 0.0000003
9 g2471.t4 PRINTS PR00401 SH2 domain signature 82 96 0.0000003
3 g2471.t4 Pfam PF00017 SH2 domain 20 93 0.0000000
1 g2471.t4 Pfam PF00018 SH3 domain 121 167 0.0000000
2 g2471.t4 Pfam PF00017 SH2 domain 187 260 0.0000000
4 g2471.t4 Pfam PF00169 PH domain 317 420 0.0000000
26 g2471.t4 ProSiteProfiles PS50001 Src homology 2 (SH2) domain profile. 19 108 17.0630000
24 g2471.t4 ProSiteProfiles PS50002 Src homology 3 (SH3) domain profile. 115 177 17.4680000
25 g2471.t4 ProSiteProfiles PS50001 Src homology 2 (SH2) domain profile. 187 275 16.8850000
27 g2471.t4 ProSiteProfiles PS50003 PH domain profile. 315 420 12.4160000
23 g2471.t4 SMART SM00252 SH2_5 17 99 0.0000000
20 g2471.t4 SMART SM00326 SH3_2 118 176 0.0000000
22 g2471.t4 SMART SM00252 SH2_5 185 266 0.0000000
21 g2471.t4 SMART SM00233 PH_update 316 422 0.0000000
12 g2471.t4 SUPERFAMILY SSF55550 SH2 domain 15 100 0.0000000
14 g2471.t4 SUPERFAMILY SSF50044 SH3-domain 106 155 0.0000001
13 g2471.t4 SUPERFAMILY SSF55550 SH2 domain 148 270 0.0000000
11 g2471.t4 SUPERFAMILY SSF50729 PH domain-like 317 420 0.0000000

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:0005515 protein binding MF
GO:0043547 positive regulation of GTPase activity BP
GO:0005096 GTPase activator activity MF

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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. There were no conditions that were differentially expressed