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.t11 TSS g3525.t11 26194763 26194763
chr_3 g3525 g3525.t11 isoform g3525.t11 26195788 26196873
chr_3 g3525 g3525.t11 exon g3525.t11.exon1 26195788 26196043
chr_3 g3525 g3525.t11 cds g3525.t11.CDS1 26195851 26196043
chr_3 g3525 g3525.t11 exon g3525.t11.exon2 26196102 26196873
chr_3 g3525 g3525.t11 cds g3525.t11.CDS2 26196102 26196259
chr_3 g3525 g3525.t11 TTS g3525.t11 26196875 26196875

Sequences

>g3525.t11 Gene=g3525 Length=1028
GTCGATAATTCACCATGCGTCTTGGAAATTCTTGATACGGCGGGAACTGAACAGTTTGCC
TCGATGCGCGATCTCTATATTAAAAATGGTCACGGATTTATCGTTATGTATTCACTCACA
AATCACCAGACGTTTCAAGATATTACAACTATGCGAAATGTCATTAGCCGAGTAAAGGGA
GGTCAACCGACTCCAATTTTATTAGTTGCTAATAAACTTGATTTAGAATACCAAAGAGAA
GTTTCCACTGAAGAAGGACATGCACTTGCAGAGATGTGGGGTTGTCCATTTATTGAAGCT
TCTGCCAAAAGTCGTATCAATGTGAATGAAGTTTTTGCGACAGTTGTTCGCGAAATGAAC
ATGTCCAACGAAAAGCGAAAGAAAAAAAGTTATTGTTGTTGCACGATATTATAGGACGCA
CGTGTTTATATAATCCAATGAAATTAGTAATTAAGGCCGATTTAAAAATTGATGATATGG
ATTAGGATGATCGTGTTTTAGGATCATCGTAAAATGGACTATTCTTTACTGATATCTGTC
TCTAGCCCAAATATGCTATAACGACTTTTAGTCACGTGTTTCCCTTCAATTGAGCGAAAA
CGTCTCATTAACACTTTTTCCACCACTTTTCGCTTTTTCTTTTACTATATCTCTGTCCAA
AAACAATTAATGTCGATTTTTGACCCTTAATTAATCTTTGTAAATTTTAATTTGACGGAA
TTGCAGCATTGCAATTTACATAAATGTGGACCCATAAAAAGTCATTTTTAATCATATCTA
AAAACCATCATCTTTTAGACTGTAATTTTAAGACTATCATCATTGTAGAACAGGACAATT
GCAAAATTTATCTTCTTCTCTCAACAATACCTATCTATTTTTTTAAACAATAATGAAAAA
GCTCACAAGGCATACATTTCTTTTTATTTTCCAATCGCTTCTACATATACTTAGAGAAAA
TGTAATAAATAAATTTTTCTACAGAAAATTAAAACGATAAGGATGAAAAATTTAGCTTTA
TACTTTTA

>g3525.t11 Gene=g3525 Length=116
MRDLYIKNGHGFIVMYSLTNHQTFQDITTMRNVISRVKGGQPTPILLVANKLDLEYQREV
STEEGHALAEMWGCPFIEASAKSRINVNEVFATVVREMNMSNEKRKKKSYCCCTIL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g3525.t11 Gene3D G3DSA:3.40.50.300 - 1 107 0.0000
2 g3525.t11 PANTHER PTHR24070 RAS, DI-RAS, AND RHEB FAMILY MEMBERS OF SMALL GTPASE SUPERFAMILY 1 113 0.0000
3 g3525.t11 PANTHER PTHR24070:SF221 RAS-RELATED PROTEIN RAP-2A 1 113 0.0000
5 g3525.t11 PRINTS PR00449 Transforming protein P21 ras signature 41 54 0.0000
4 g3525.t11 PRINTS PR00449 Transforming protein P21 ras signature 76 98 0.0000
1 g3525.t11 Pfam PF00071 Ras family 1 98 0.0000
11 g3525.t11 ProSiteProfiles PS51421 small GTPase Ras family profile. 1 116 23.2490
8 g3525.t11 SMART SM00173 ras_sub_4 1 101 0.0000
9 g3525.t11 SMART SM00175 rab_sub_5 1 101 0.0000
10 g3525.t11 SMART SM00174 rho_sub_3 3 101 0.0043
6 g3525.t11 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 1 101 0.0000
12 g3525.t11 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 1 94 0.0000

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