Gene loci information

Transcript annotation

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

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_2 g6250 g6250.t1 isoform g6250.t1 15615070 15615952
chr_2 g6250 g6250.t1 exon g6250.t1.exon1 15615070 15615150
chr_2 g6250 g6250.t1 cds g6250.t1.CDS1 15615070 15615150
chr_2 g6250 g6250.t1 exon g6250.t1.exon2 15615230 15615304
chr_2 g6250 g6250.t1 cds g6250.t1.CDS2 15615230 15615304
chr_2 g6250 g6250.t1 exon g6250.t1.exon3 15615377 15615537
chr_2 g6250 g6250.t1 cds g6250.t1.CDS3 15615377 15615537
chr_2 g6250 g6250.t1 exon g6250.t1.exon4 15615596 15615773
chr_2 g6250 g6250.t1 cds g6250.t1.CDS4 15615596 15615773
chr_2 g6250 g6250.t1 exon g6250.t1.exon5 15615839 15615952
chr_2 g6250 g6250.t1 cds g6250.t1.CDS5 15615839 15615952
chr_2 g6250 g6250.t1 TTS g6250.t1 15616817 15616817
chr_2 g6250 g6250.t1 TSS g6250.t1 NA NA

Sequences

>g6250.t1 Gene=g6250 Length=609
ATGTCAAAAAAACCAAGTTCAAGCCCGCCTTCGCTTCATAAGGTCATTATGGTCGGCTCT
GGAGGTGTGGGCAAGAGTGCTCTCACGCTCCAATTTATGTACGATGAGTTTGTTGAAGAC
TATGAACCAACGAAAGCTGACAGTTATCGAAAGAAAGTGGTACTAGATGGTGAAGAGGTA
CAGATAGACATTCTTGATACAGCTGGCCAAGAAGACTATGCCGCAATTCGAGACAATTAC
TTTAGAAGTGGTGAAGGATTCCTTTGTGTGTTTTCTATAACAGATGATGAAAGCTTCCAA
GCAACTCAGGAATTTCGTGAACAAATTTTGCGTGTTAAAAATGACGAAAATATACCATTT
CTTTTGGTCGGTAATAAATGCGATTTAAACGATAAACGTAAGGTGCCATTGTCTGAATGT
CAGGCGAGAGCACAACAATGGGGAGGCGTTCCCTATGTAGAAACATCTGCAAAAACTCGT
GAGAATGTCGATAAGGTATTTTTTGATTTAATGCGCGAGATTCGATCAAGGAAAACAGAA
GATTCATCCAAAGCTAGCGGTCGTGCAAAAGAAAGAAAGAAGCGAAAGCTTAAATGCACA
CTACTGTAG

>g6250.t1 Gene=g6250 Length=202
MSKKPSSSPPSLHKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEV
QIDILDTAGQEDYAAIRDNYFRSGEGFLCVFSITDDESFQATQEFREQILRVKNDENIPF
LLVGNKCDLNDKRKVPLSECQARAQQWGGVPYVETSAKTRENVDKVFFDLMREIRSRKTE
DSSKASGRAKERKKRKLKCTLL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g6250.t1 CDD cd04139 RalA_RalB 13 176 0.0000
10 g6250.t1 Gene3D G3DSA:3.40.50.300 - 13 202 0.0000
2 g6250.t1 PANTHER PTHR24070:SF258 RAS-RELATED PROTEIN RAL-A 8 201 0.0000
3 g6250.t1 PANTHER PTHR24070 RAS, DI-RAS, AND RHEB FAMILY MEMBERS OF SMALL GTPASE SUPERFAMILY 8 201 0.0000
8 g6250.t1 PRINTS PR00449 Transforming protein P21 ras signature 13 34 0.0000
7 g6250.t1 PRINTS PR00449 Transforming protein P21 ras signature 36 52 0.0000
6 g6250.t1 PRINTS PR00449 Transforming protein P21 ras signature 53 75 0.0000
4 g6250.t1 PRINTS PR00449 Transforming protein P21 ras signature 116 129 0.0000
5 g6250.t1 PRINTS PR00449 Transforming protein P21 ras signature 152 174 0.0000
1 g6250.t1 Pfam PF00071 Ras family 14 175 0.0000
17 g6250.t1 ProSiteProfiles PS51421 small GTPase Ras family profile. 6 202 42.0810
12 g6250.t1 SMART SM00173 ras_sub_4 10 177 0.0000
13 g6250.t1 SMART SM00175 rab_sub_5 13 177 0.0000
15 g6250.t1 SMART SM00174 rho_sub_3 15 177 0.0000
14 g6250.t1 SMART SM00176 ran_sub_2 18 197 0.0024
9 g6250.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 10 181 0.0000
16 g6250.t1 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 14 167 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

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