Gene loci information

Transcript annotation

  • This transcript has been annotated as Ras-like GTP-binding protein Rho1.

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 g8352 g8352.t14 TTS g8352.t14 29902698 29902698
chr_2 g8352 g8352.t14 isoform g8352.t14 29902801 29907331
chr_2 g8352 g8352.t14 exon g8352.t14.exon1 29902801 29903713
chr_2 g8352 g8352.t14 cds g8352.t14.CDS1 29903441 29903713
chr_2 g8352 g8352.t14 exon g8352.t14.exon2 29903789 29903913
chr_2 g8352 g8352.t14 cds g8352.t14.CDS2 29903789 29903913
chr_2 g8352 g8352.t14 exon g8352.t14.exon3 29904016 29904040
chr_2 g8352 g8352.t14 cds g8352.t14.CDS3 29904016 29904040
chr_2 g8352 g8352.t14 exon g8352.t14.exon4 29905754 29905914
chr_2 g8352 g8352.t14 cds g8352.t14.CDS4 29905754 29905914
chr_2 g8352 g8352.t14 exon g8352.t14.exon5 29907251 29907331
chr_2 g8352 g8352.t14 cds g8352.t14.CDS5 29907251 29907287
chr_2 g8352 g8352.t14 TSS g8352.t14 29907400 29907400

Sequences

>g8352.t14 Gene=g8352 Length=1305
CAAGTAGGTATTTCGAAATTTTATGTGGTGGTGAGGTTTTTAATATGTTCAACTGTTTCT
CTACTGATGAAAGCTATCAAGAACCAATGGCAGCAATTCGGAAAAAATTAGTTATTGTCG
GAGACGGAGCATGTGGCAAAACTTGTCTGCTAATCGTATTCAGTAAAGATCAATTCCCTG
AAGTCTATGTGCCAACAGTGTTTGAGAATTATGTGGCTGATATCGAAGTAGATGGAAAGC
AGGTTGAATTAGCACTATGGGATACCGCTGGACAAGAAGATTATGACAGATTGCGTCCAT
TGAGTTATCCAGATACAGATGTTATTTTGATGTGCTTTTCTGTAGATTCACCTGACTCAT
TGGAAAATATTCCAGAAAAGTGGACGCCTGAGGTAAAACATTTTTGCCCAAATGTACCCA
TCATTTTAGTCGGTAATAAAAAAGATCTCAGAAATGATCCGCACACTATTAAAGAATTGG
CAAAAATGAAGCAAGAGCCGGTAAAAACATCGGAAGGCAAGGCGATGTTTGAGAAAATAA
ACGCATTTGCTTATTTGGAATGTTCCGCTAAATCAAAGGAAGGTGTACGCGAAGTGTTTG
AGACGGCAACAAGAGCTGCATTGCAAGTGAAAAAGAAGAAGAAGAATCGATGTATTATGC
TTTAAATTTGCCTTCTCTTCTTCTTCTTTTACGACTTCCTTCCTTCCCGATGCTCCTCTC
CCCTTTTTACTACGAACATTATATACATGCATAAACACACAAATACACATCTCCTTTTAA
ACAACAACAACTTCAACTTTGTTTCTTTCGTGGAATTTCAACGAGCTACAATATGTACAC
ACACAACAACAAAACAAGAAAATATATATTCGATAATATTATATTAATAATCAAACTAAC
ATTCAATCTATTCGCCAACCAGCAGAAAAATAGCAAAACAAAAAATTGTCCATCTTTAAA
AACAATAACGAAAACTAAATGAAAAGAAAAAAGTTTTTACTCGATTTTTTTTTATTGAAA
GAAAAAAAGAAATTAAAGAGAAAATTACGTATTACAAACAGTTTAGCAATTTTTTCTTGT
GTGGATAAATTTCCGCGAAATTTTTGTATTGTTGAAGCTCCTCTTGAGTCTTGATGAAGC
TTCGCCTTTTAAAAAACGAAAAACACAAAAAAAAATTTGGAATAATAATGGGTGAAAGAT
GTGAGAAATTTTTTTAATGAGAGAATCTTAATGCTAGAATTATCTTTAGAAACAACATGT
TTTTGAATTGATTCATGGGTTTTTTTGTTAAGAGTAACAGCTACA

>g8352.t14 Gene=g8352 Length=206
MFNCFSTDESYQEPMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADI
EVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSVDSPDSLENIPEKWTPEVKHF
CPNVPIILVGNKKDLRNDPHTIKELAKMKQEPVKTSEGKAMFEKINAFAYLECSAKSKEG
VREVFETATRAALQVKKKKKNRCIML

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g8352.t14 CDD cd01870 RhoA_like 19 193 0.0000
10 g8352.t14 Gene3D G3DSA:3.40.50.300 - 15 206 0.0000
2 g8352.t14 PANTHER PTHR24072:SF100 RHO-RELATED GTP-BINDING PROTEIN RHOC 17 204 0.0000
3 g8352.t14 PANTHER PTHR24072 RHO FAMILY GTPASE 17 204 0.0000
4 g8352.t14 PRINTS PR00449 Transforming protein P21 ras signature 20 41 0.0000
7 g8352.t14 PRINTS PR00449 Transforming protein P21 ras signature 43 59 0.0000
6 g8352.t14 PRINTS PR00449 Transforming protein P21 ras signature 60 82 0.0000
5 g8352.t14 PRINTS PR00449 Transforming protein P21 ras signature 122 135 0.0000
8 g8352.t14 PRINTS PR00449 Transforming protein P21 ras signature 170 192 0.0000
1 g8352.t14 Pfam PF00071 Ras family 21 193 0.0000
17 g8352.t14 ProSiteProfiles PS51420 small GTPase Rho family profile. 13 192 27.8560
12 g8352.t14 SMART SM00173 ras_sub_4 21 195 0.0000
13 g8352.t14 SMART SM00175 rab_sub_5 21 195 0.0000
15 g8352.t14 SMART SM00174 rho_sub_3 22 195 0.0000
14 g8352.t14 SMART SM00176 ran_sub_2 25 206 0.0071
9 g8352.t14 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 20 193 0.0000
16 g8352.t14 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 19 172 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:0007264 small GTPase mediated 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