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.t5 isoform g2471.t5 18126742 18128851
chr_3 g2471 g2471.t5 exon g2471.t5.exon1 18126742 18127842
chr_3 g2471 g2471.t5 cds g2471.t5.CDS1 18126744 18127661
chr_3 g2471 g2471.t5 exon g2471.t5.exon2 18128039 18128111
chr_3 g2471 g2471.t5 exon g2471.t5.exon3 18128317 18128390
chr_3 g2471 g2471.t5 exon g2471.t5.exon4 18128849 18128851
chr_3 g2471 g2471.t5 TSS g2471.t5 NA NA
chr_3 g2471 g2471.t5 TTS g2471.t5 NA NA

Sequences

>g2471.t5 Gene=g2471 Length=1251
ATGGTATCATGGACGACTCGATAGATTTAGTGCAGAACAAAGGCTTAAAGCAGCATATAA
ACTCGGAAGCTACTTAGTGAGAGAAAGTGACAGAAAGCCTGGATCATATGTATTATCTTA
TTTAGGAAAAACTGGAATAAATCATTTCCGCATTGCTGCTGTGTGTGGCGATTTTTATAT
TGGCGGTCGCCAATTCTTCTCATTAAGTGACTTGGTTGCATATTACTCATGTAATGATTT
GTTGAAACGTGAACGACTCATCCATGCTATTGCACCGCCTGAACCTGTTTCAGACACACG
ACGTGTTGTCGCTATTCTGCCATATACAAAAATGCCAGATACTGATGAGTTGAGTTTTCA
AAAGGGTGATATCTTTTTTGTTCACAATAATATGGGCGATGGATGGATATGGACAACGAA
ACATAGAACTGGCGAGCAGGGAATGATCTTTAGCGAACTTGTTGAAGATCTTGATCCAAC
AATTGATCCCAATACTGTTTTCTCATGGTTTCATCCTAATTGCACTAAAAATGAAGCTGT
CGATATGCTAGTAAAAAATGGCCCTGGTTCATTTTTAGTTCGACCTAGTGACAACAGTCC
TGGTGATTATTCTCTCTTTTTTCACATCAATAATCAAATTCAGAGATTTCGAATTGAGAA
AAAGGGCGTTCGTTATTTAATGGGTGGAAGAACTTTTGAATGCTTAGATGCAGTTATCAA
TCGTTACCGTAAAGAACAAATAGTTGAAGGACATACTTTACAAAATCCAGTCTCAAATGG
ATCATGTCAGGCTGAATTTCAACAGCAAACAGCAGTATCAGCTGCTGCTGAAAAAATTTA
TGCAACATTACGAGAATGTCGTGATCAAAATATGATTAAAAAGATTAAAGGAATTAAACA
GCAAGGATATCTAATGAAAAGGTCTGATAAAACTGGTAAATGGAAGCAACTTTATTTTGC
ACTCATCAATGATGGCGCTGAAACACATTTGTTCTTTTATGATAGTCCCAAAAAGACAAA
ACCAAAAGGATTAATTGATTTATCATGCGCTTATCTCTATCAAGTCCACGAATCGCTTTG
GGAGAAAACAAATTGCTTTCAAATTGTTGAACGAGCACTGCCTTGTTTGGCGACCATTTC
GCATTTATGTGACAAAAATACTGAATCATATCAGGAATGGATCACTGTTCTTAAACAGCA
TTGTCGTGCTCAATTTAGTCGAGCTCAGTCAAAATTGCCTCGATTACGCGA

>g2471.t5 Gene=g2471 Length=306
MPDTDELSFQKGDIFFVHNNMGDGWIWTTKHRTGEQGMIFSELVEDLDPTIDPNTVFSWF
HPNCTKNEAVDMLVKNGPGSFLVRPSDNSPGDYSLFFHINNQIQRFRIEKKGVRYLMGGR
TFECLDAVINRYRKEQIVEGHTLQNPVSNGSCQAEFQQQTAVSAAAEKIYATLRECRDQN
MIKKIKGIKQQGYLMKRSDKTGKWKQLYFALINDGAETHLFFYDSPKKTKPKGLIDLSCA
YLYQVHESLWEKTNCFQIVERALPCLATISHLCDKNTESYQEWITVLKQHCRAQFSRAQS
KLPRLR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g2471.t5 Gene3D G3DSA:2.30.30.40 SH3 Domains 1 48 0.0000000
16 g2471.t5 Gene3D G3DSA:3.30.505.10 SHC Adaptor Protein 49 170 0.0000000
15 g2471.t5 Gene3D G3DSA:2.30.29.30 - 179 298 0.0000000
4 g2471.t5 PANTHER PTHR10194 RAS GTPASE-ACTIVATING PROTEINS 1 301 0.0000000
5 g2471.t5 PANTHER PTHR10194:SF19 RAS GTPASE-ACTIVATING PROTEIN 1 1 301 0.0000000
6 g2471.t5 PRINTS PR00401 SH2 domain signature 59 73 0.0000390
8 g2471.t5 PRINTS PR00401 SH2 domain signature 78 88 0.0000390
9 g2471.t5 PRINTS PR00401 SH2 domain signature 90 101 0.0000390
7 g2471.t5 PRINTS PR00401 SH2 domain signature 121 135 0.0000390
1 g2471.t5 Pfam PF00018 SH3 domain 3 39 0.0000007
2 g2471.t5 Pfam PF00017 SH2 domain 59 132 0.0000000
3 g2471.t5 Pfam PF00169 PH domain 189 292 0.0000000
17 g2471.t5 ProSiteProfiles PS50002 Src homology 3 (SH3) domain profile. 1 49 14.3990000
18 g2471.t5 ProSiteProfiles PS50001 Src homology 2 (SH2) domain profile. 59 147 16.8850000
19 g2471.t5 ProSiteProfiles PS50003 PH domain profile. 187 292 12.4160000
13 g2471.t5 SMART SM00252 SH2_5 57 138 0.0000000
12 g2471.t5 SMART SM00233 PH_update 188 294 0.0000000
11 g2471.t5 SUPERFAMILY SSF55550 SH2 domain 20 142 0.0000000
10 g2471.t5 SUPERFAMILY SSF50729 PH domain-like 189 292 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.

Raw TPM values