Gene loci information

Transcript annotation

  • This transcript has been annotated as Ras-related protein Rap-2a.

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 g3525 g3525.t1 TSS g3525.t1 26194763 26194763
chr_3 g3525 g3525.t1 isoform g3525.t1 26195501 26196259
chr_3 g3525 g3525.t1 exon g3525.t1.exon1 26195501 26195543
chr_3 g3525 g3525.t1 cds g3525.t1.CDS1 26195501 26195543
chr_3 g3525 g3525.t1 exon g3525.t1.exon2 26195624 26195715
chr_3 g3525 g3525.t1 cds g3525.t1.CDS2 26195624 26195715
chr_3 g3525 g3525.t1 exon g3525.t1.exon3 26195788 26196043
chr_3 g3525 g3525.t1 cds g3525.t1.CDS3 26195788 26196043
chr_3 g3525 g3525.t1 exon g3525.t1.exon4 26196102 26196259
chr_3 g3525 g3525.t1 cds g3525.t1.CDS4 26196102 26196259
chr_3 g3525 g3525.t1 TTS g3525.t1 26196875 26196875

Sequences

>g3525.t1 Gene=g3525 Length=549
ATGCGTGAATTCAAAGTTGTTGTTCTTGGCTCAGGTGGCGTAGGAAAATCGGCCTTAACA
GTGCAGTTTGTTTCAGGATGTTTCATTGAAAAATATGACCCAACAGTGGAAGATTTTTAT
AGGAAAGAAATTGAAGTCGATAATTCACCATGCGTCTTGGAAATTCTTGATACGGCGGGA
ACTGAACAGTTTGCCTCGATGCGCGATCTCTATATTAAAAATGGTCACGGATTTATCGTT
ATGTATTCACTCACAAATCACCAGACGTTTCAAGATATTACAACTATGCGAAATGTCATT
AGCCGAGTAAAGGGAGGTCAACCGACTCCAATTTTATTAGTTGCTAATAAACTTGATTTA
GAATACCAAAGAGAAGTTTCCACTGAAGAAGGACATGCACTTGCAGAGATGTGGGGTTGT
CCATTTATTGAAGCTTCTGCCAAAAGTCGTATCAATGTGAATGAAGTTTTTGCGACAGTT
GTTCGCGAAATGAACATGTCCAACGAAAAGCGAAAGAAAAAAAGTTATTGTTGTTGCACG
ATATTATAG

>g3525.t1 Gene=g3525 Length=182
MREFKVVVLGSGGVGKSALTVQFVSGCFIEKYDPTVEDFYRKEIEVDNSPCVLEILDTAG
TEQFASMRDLYIKNGHGFIVMYSLTNHQTFQDITTMRNVISRVKGGQPTPILLVANKLDL
EYQREVSTEEGHALAEMWGCPFIEASAKSRINVNEVFATVVREMNMSNEKRKKKSYCCCT
IL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g3525.t1 Gene3D G3DSA:3.40.50.300 - 1 170 0.000
2 g3525.t1 PANTHER PTHR24070 RAS, DI-RAS, AND RHEB FAMILY MEMBERS OF SMALL GTPASE SUPERFAMILY 1 179 0.000
3 g3525.t1 PANTHER PTHR24070:SF419 RAP2A, MEMBER OF RAS ONCOGENE FAMILY A 1 179 0.000
8 g3525.t1 PRINTS PR00449 Transforming protein P21 ras signature 4 25 0.000
4 g3525.t1 PRINTS PR00449 Transforming protein P21 ras signature 27 43 0.000
6 g3525.t1 PRINTS PR00449 Transforming protein P21 ras signature 44 66 0.000
7 g3525.t1 PRINTS PR00449 Transforming protein P21 ras signature 107 120 0.000
5 g3525.t1 PRINTS PR00449 Transforming protein P21 ras signature 142 164 0.000
1 g3525.t1 Pfam PF00071 Ras family 5 164 0.000
14 g3525.t1 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile. 1 27 6.000
15 g3525.t1 ProSiteProfiles PS51421 small GTPase Ras family profile. 1 182 37.935
11 g3525.t1 SMART SM00173 ras_sub_4 1 167 0.000
12 g3525.t1 SMART SM00175 rab_sub_5 4 167 0.000
13 g3525.t1 SMART SM00174 rho_sub_3 6 167 0.000
9 g3525.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 2 167 0.000
16 g3525.t1 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 1 160 0.000

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:0016020 membrane CC
GO:0007165 signal transduction BP
GO:0005525 GTP binding MF
GO:0003924 GTPase activity MF

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