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.t5 isoform g3525.t5 26194728 26196873
chr_3 g3525 g3525.t5 exon g3525.t5.exon1 26194728 26194911
chr_3 g3525 g3525.t5 TSS g3525.t5 26194763 26194763
chr_3 g3525 g3525.t5 exon g3525.t5.exon2 26195295 26195543
chr_3 g3525 g3525.t5 cds g3525.t5.CDS1 26195501 26195543
chr_3 g3525 g3525.t5 exon g3525.t5.exon3 26195624 26195715
chr_3 g3525 g3525.t5 cds g3525.t5.CDS2 26195624 26195715
chr_3 g3525 g3525.t5 exon g3525.t5.exon4 26195788 26196043
chr_3 g3525 g3525.t5 cds g3525.t5.CDS3 26195788 26196043
chr_3 g3525 g3525.t5 exon g3525.t5.exon5 26196117 26196873
chr_3 g3525 g3525.t5 cds g3525.t5.CDS4 26196117 26196259
chr_3 g3525 g3525.t5 TTS g3525.t5 26196875 26196875

Sequences

>g3525.t5 Gene=g3525 Length=1538
GACATTATGAAAAAACTTTTCATTTTAACACTCTTATTTCTGCAAGGGCTTAAGTTTAGA
AAAGATTTTTCGATTTTACATTTTACTCAATAATTTCTCTTATTTTCTAAAAAATGGCAT
TAATTTTATATTTCTGTGATGAATAATAAGTAAATCAATCTATTAGACCTAAGAGTAAAT
CGATCAAGAGCGACTTATTTTCAACAATATAGTCTTAAAAAGAGTAAAAATTATATATAC
ACAAAATATTTAAAGAAGGAGAATAAAAAAGAGAGATACATAAAAAGGGTTTGAAAAAAG
GACTATCTATAAATTTAATTTTGCTCAAACACTAATTGCAATTTATTAACACGTCCGGAT
AAACTCCATATTTTACATTGATATTAAAGAATGCGTGAATTCAAAGTTGTTGTTCTTGGC
TCAGGTGGCGTAGGAAAATCGGCCTTAACAGTGCAGTTTGTTTCAGGATGTTTCATTGAA
AAATATGACCCAACAGTGGAAGATTTTTATAGGAAAGAAATTGAAGTCGATAATTCACCA
TGCGTCTTGGAAATTCTTGATACGGCGGGAACTGAACAGTTTGCCTCGATGCGCGATCTC
TATATTAAAAATGGTCACGGATTTATCGTTATGTATTCACTCACAAATCACCAGACGTTT
CAAGATATTACAACTATGCGAAATGTCATTAGCCGAGTAAAGGGAGGTCAACCGACTCCA
ATTTTATTAGTTGCTAATAAACTTGATTTAGAATACCAAAGAGAAGTTTCCACTGAAGAA
GAGATGTGGGGTTGTCCATTTATTGAAGCTTCTGCCAAAAGTCGTATCAATGTGAATGAA
GTTTTTGCGACAGTTGTTCGCGAAATGAACATGTCCAACGAAAAGCGAAAGAAAAAAAGT
TATTGTTGTTGCACGATATTATAGGACGCACGTGTTTATATAATCCAATGAAATTAGTAA
TTAAGGCCGATTTAAAAATTGATGATATGGATTAGGATGATCGTGTTTTAGGATCATCGT
AAAATGGACTATTCTTTACTGATATCTGTCTCTAGCCCAAATATGCTATAACGACTTTTA
GTCACGTGTTTCCCTTCAATTGAGCGAAAACGTCTCATTAACACTTTTTCCACCACTTTT
CGCTTTTTCTTTTACTATATCTCTGTCCAAAAACAATTAATGTCGATTTTTGACCCTTAA
TTAATCTTTGTAAATTTTAATTTGACGGAATTGCAGCATTGCAATTTACATAAATGTGGA
CCCATAAAAAGTCATTTTTAATCATATCTAAAAACCATCATCTTTTAGACTGTAATTTTA
AGACTATCATCATTGTAGAACAGGACAATTGCAAAATTTATCTTCTTCTCTCAACAATAC
CTATCTATTTTTTTAAACAATAATGAAAAAGCTCACAAGGCATACATTTCTTTTTATTTT
CCAATCGCTTCTACATATACTTAGAGAAAATGTAATAAATAAATTTTTCTACAGAAAATT
AAAACGATAAGGATGAAAAATTTAGCTTTATACTTTTA

>g3525.t5 Gene=g3525 Length=177
MREFKVVVLGSGGVGKSALTVQFVSGCFIEKYDPTVEDFYRKEIEVDNSPCVLEILDTAG
TEQFASMRDLYIKNGHGFIVMYSLTNHQTFQDITTMRNVISRVKGGQPTPILLVANKLDL
EYQREVSTEEEMWGCPFIEASAKSRINVNEVFATVVREMNMSNEKRKKKSYCCCTIL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g3525.t5 Gene3D G3DSA:3.40.50.300 - 1 165 0.00
2 g3525.t5 PANTHER PTHR24070 RAS, DI-RAS, AND RHEB FAMILY MEMBERS OF SMALL GTPASE SUPERFAMILY 1 174 0.00
3 g3525.t5 PANTHER PTHR24070:SF419 RAP2A, MEMBER OF RAS ONCOGENE FAMILY A 1 174 0.00
8 g3525.t5 PRINTS PR00449 Transforming protein P21 ras signature 4 25 0.00
4 g3525.t5 PRINTS PR00449 Transforming protein P21 ras signature 27 43 0.00
6 g3525.t5 PRINTS PR00449 Transforming protein P21 ras signature 44 66 0.00
7 g3525.t5 PRINTS PR00449 Transforming protein P21 ras signature 107 120 0.00
5 g3525.t5 PRINTS PR00449 Transforming protein P21 ras signature 137 159 0.00
1 g3525.t5 Pfam PF00071 Ras family 5 159 0.00
14 g3525.t5 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile. 1 27 6.00
15 g3525.t5 ProSiteProfiles PS51421 small GTPase Ras family profile. 1 177 33.79
11 g3525.t5 SMART SM00173 ras_sub_4 1 162 0.00
12 g3525.t5 SMART SM00175 rab_sub_5 4 162 0.00
13 g3525.t5 SMART SM00174 rho_sub_3 6 162 0.00
9 g3525.t5 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 2 162 0.00
16 g3525.t5 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 1 155 0.00

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