Gene loci information

Transcript annotation

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

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_1 g11879 g11879.t5 isoform g11879.t5 18944405 18946496
chr_1 g11879 g11879.t5 exon g11879.t5.exon1 18944405 18945481
chr_1 g11879 g11879.t5 TTS g11879.t5 18944415 18944415
chr_1 g11879 g11879.t5 cds g11879.t5.CDS1 18945276 18945481
chr_1 g11879 g11879.t5 exon g11879.t5.exon2 18945547 18945664
chr_1 g11879 g11879.t5 cds g11879.t5.CDS2 18945547 18945664
chr_1 g11879 g11879.t5 exon g11879.t5.exon3 18945723 18945768
chr_1 g11879 g11879.t5 cds g11879.t5.CDS3 18945723 18945768
chr_1 g11879 g11879.t5 exon g11879.t5.exon4 18946000 18946059
chr_1 g11879 g11879.t5 cds g11879.t5.CDS4 18946000 18946059
chr_1 g11879 g11879.t5 exon g11879.t5.exon5 18946119 18946234
chr_1 g11879 g11879.t5 cds g11879.t5.CDS5 18946119 18946225
chr_1 g11879 g11879.t5 exon g11879.t5.exon6 18946456 18946496
chr_1 g11879 g11879.t5 TSS g11879.t5 18946677 18946677

Sequences

>g11879.t5 Gene=g11879 Length=1458
AGTAAATAACTTGTTGCTTCAGAGTGAATTTAAGAAATAGTTGTTAAATTATGAGACCGT
TAAAGATTACAACAGTTGGTGATGGAGCTGTCGGAAAAACGTGCATGTTGATTTCATACA
CACAAAATGAATTTCCCGTAGAATATGTACCGACAGTATTTGATAATCATGCATGTACAA
TTACTGTGGATAATAAAGAGTACTCACTAACATTATGCTTTAAAAAAGACTATGAGAGGC
TGCGCCCATTAAGTTACCCGAATACTGATTGTTTTCTTTTGTGCTATTCTATGGACTCCA
GAACCTCTTTTGAGAATGTTTCTTCAAAATGGAATCCTGAAATAAGACACTTTTCGCCAC
ATGTTCCAATCGTCCTAGTCGGCACAAAATCAGATTTGAGAATTCAGGGATCAGAAAAAT
ATGTAACTACACAAGAGGCAAAAAAATTATGCAAAAAGATTGGAGCATACACTTTAGTCG
AGTGCTCTGCAAAGAAGAAAACAAATTTAGTGACGGTATTTGAAGAGGCCGTCAGAGCGG
TGGAAAAGAAAAAACCGAGAACTAGAGAACCTTGTAAAATTCTCTAAATGTTTATTAACA
CACATATGTATGTCTTCATAAATTAAAATCACAAAAAAAAACCTATTCCTCATACAATAA
ATGCTGAGAATTTAATTATGTGAGTATAATTGGTACTTACAAATATTTGATAAAGAAAAA
AAGTTAAATTAAAAGTGCCATTAATTTTGCGTAATTTTTGTTAAACATTAAAAATCAATT
TATATATTTTTAAACTCACAATTTATCTAGTTCAAATTTCTTATAAAATATAACTTCAAA
GACTAATCATTGATTATTTCAAAAACTTTATGAAAAATGGCAGAGTGAGAAAGACAAAAA
ATATATGTGTCTGTATCATATCAAAAATTAAAATATACTTATGCTGAAGTTAAGTAAACA
ATCACACACAGCTGTGTAGATGGAATTTTTATAAGTGTTATTAAAAAATTGATATTTTAA
ATCAGAGAAAAAACACAAAAATTCATCACAAACAAATCAATAGTTGCTCGGAAATTTAAA
AAGTTAAATAATAATTTTTGAGGAAACGATAATTTTTGAGTTTACCTACTTTTGTAGGAC
GAAAATACGCAATTAAAAAGCACAATTAGAGTTATGTGGAATCATTATTTTACTTATTGA
AAAAAAATTATTTTAAAAGAAATTAAAAATTTTTTATTGTTGCTCAGCTCTTTAAATAAC
TCCAAAATATGTAGAAACTATGATGACTTAGGTATTTTATAAAAGTATTCTTCCCGTAAT
ACATCATGTATTCGGATTGTATTCACAAAAATGTTATAGTCAAGTTTAACAGGTATTGTA
ATTTTTTAGAAAGATTTCATCTTTAATAATCAAGAAAATAAAATATATTTTATGAAAGAA
ATTTTAACAAAAAGAAAT

>g11879.t5 Gene=g11879 Length=178
MRPLKITTVGDGAVGKTCMLISYTQNEFPVEYVPTVFDNHACTITVDNKEYSLTLCFKKD
YERLRPLSYPNTDCFLLCYSMDSRTSFENVSSKWNPEIRHFSPHVPIVLVGTKSDLRIQG
SEKYVTTQEAKKLCKKIGAYTLVECSAKKKTNLVTVFEEAVRAVEKKKPRTREPCKIL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g11879.t5 CDD cd00157 Rho 4 163 0.000
9 g11879.t5 Gene3D G3DSA:3.40.50.300 - 1 169 0.000
2 g11879.t5 PANTHER PTHR24072 RHO FAMILY GTPASE 2 175 0.000
3 g11879.t5 PANTHER PTHR24072:SF305 RAS-LIKE GTP-BINDING PROTEIN RHOL 2 175 0.000
7 g11879.t5 PRINTS PR00449 Transforming protein P21 ras signature 4 25 0.000
4 g11879.t5 PRINTS PR00449 Transforming protein P21 ras signature 27 43 0.000
6 g11879.t5 PRINTS PR00449 Transforming protein P21 ras signature 103 116 0.000
5 g11879.t5 PRINTS PR00449 Transforming protein P21 ras signature 142 164 0.000
1 g11879.t5 Pfam PF00071 Ras family 5 165 0.000
15 g11879.t5 ProSiteProfiles PS51420 small GTPase Rho family profile. 1 164 21.125
11 g11879.t5 SMART SM00173 ras_sub_4 1 167 0.000
12 g11879.t5 SMART SM00175 rab_sub_5 4 167 0.000
13 g11879.t5 SMART SM00174 rho_sub_3 6 167 0.000
8 g11879.t5 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 3 164 0.000
14 g11879.t5 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 1 159 0.000

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

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