Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t7 TSS g3525.t7 26194763 26194763
chr_3 g3525 g3525.t7 isoform g3525.t7 26195501 26196259
chr_3 g3525 g3525.t7 exon g3525.t7.exon1 26195501 26195543
chr_3 g3525 g3525.t7 cds g3525.t7.CDS1 26195501 26195543
chr_3 g3525 g3525.t7 exon g3525.t7.exon2 26195624 26195715
chr_3 g3525 g3525.t7 cds g3525.t7.CDS2 26195624 26195715
chr_3 g3525 g3525.t7 exon g3525.t7.exon3 26195788 26196259
chr_3 g3525 g3525.t7 cds g3525.t7.CDS3 26195788 26196054
chr_3 g3525 g3525.t7 TTS g3525.t7 26196875 26196875

Sequences

>g3525.t7 Gene=g3525 Length=607
ATGCGTGAATTCAAAGTTGTTGTTCTTGGCTCAGGTGGCGTAGGAAAATCGGCCTTAACA
GTGCAGTTTGTTTCAGGATGTTTCATTGAAAAATATGACCCAACAGTGGAAGATTTTTAT
AGGAAAGAAATTGAAGTCGATAATTCACCATGCGTCTTGGAAATTCTTGATACGGCGGGA
ACTGAACAGTTTGCCTCGATGCGCGATCTCTATATTAAAAATGGTCACGGATTTATCGTT
ATGTATTCACTCACAAATCACCAGACGTTTCAAGATATTACAACTATGCGAAATGTCATT
AGCCGAGTAAAGGGAGGTCAACCGACTCCAATTTTATTAGTTGCTAATAAACTTGATTTA
GAATACCAAAGAGAAGTTTCCACTGAAGAAGGTACTGATTAATTTTATGCAATAGTATAA
TAATGTTAATATTTAAAAATATTTTCTAGGACATGCACTTGCAGAGATGTGGGGTTGTCC
ATTTATTGAAGCTTCTGCCAAAAGTCGTATCAATGTGAATGAAGTTTTTGCGACAGTTGT
TCGCGAAATGAACATGTCCAACGAAAAGCGAAAGAAAAAAAGTTATTGTTGTTGCACGAT
ATTATAG

>g3525.t7 Gene=g3525 Length=133
MREFKVVVLGSGGVGKSALTVQFVSGCFIEKYDPTVEDFYRKEIEVDNSPCVLEILDTAG
TEQFASMRDLYIKNGHGFIVMYSLTNHQTFQDITTMRNVISRVKGGQPTPILLVANKLDL
EYQREVSTEEGTD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g3525.t7 Gene3D G3DSA:3.40.50.300 - 1 133 0.0000000
2 g3525.t7 PANTHER PTHR24070 RAS, DI-RAS, AND RHEB FAMILY MEMBERS OF SMALL GTPASE SUPERFAMILY 1 132 0.0000000
3 g3525.t7 PANTHER PTHR24070:SF419 RAP2A, MEMBER OF RAS ONCOGENE FAMILY A 1 132 0.0000000
7 g3525.t7 PRINTS PR00449 Transforming protein P21 ras signature 4 25 0.0000000
4 g3525.t7 PRINTS PR00449 Transforming protein P21 ras signature 27 43 0.0000000
5 g3525.t7 PRINTS PR00449 Transforming protein P21 ras signature 44 66 0.0000000
6 g3525.t7 PRINTS PR00449 Transforming protein P21 ras signature 107 120 0.0000000
1 g3525.t7 Pfam PF00071 Ras family 5 132 0.0000000
13 g3525.t7 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile. 1 27 6.0000000
14 g3525.t7 ProSiteProfiles PS51421 small GTPase Ras family profile. 1 133 29.5780000
10 g3525.t7 SMART SM00173 ras_sub_4 1 133 0.0000000
11 g3525.t7 SMART SM00175 rab_sub_5 4 133 0.0000000
12 g3525.t7 SMART SM00174 rho_sub_3 6 133 0.0000064
8 g3525.t7 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 2 131 0.0000000
15 g3525.t7 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 1 130 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:0016020 membrane CC
GO:0007165 signal transduction BP
GO:0005525 GTP binding MF
GO:0003924 GTPase 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