Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t6 isoform g11879.t6 18944405 18946630
chr_1 g11879 g11879.t6 exon g11879.t6.exon1 18944405 18945481
chr_1 g11879 g11879.t6 TTS g11879.t6 18944415 18944415
chr_1 g11879 g11879.t6 cds g11879.t6.CDS1 18945276 18945481
chr_1 g11879 g11879.t6 exon g11879.t6.exon2 18945547 18945664
chr_1 g11879 g11879.t6 cds g11879.t6.CDS2 18945547 18945664
chr_1 g11879 g11879.t6 exon g11879.t6.exon3 18945723 18945769
chr_1 g11879 g11879.t6 cds g11879.t6.CDS3 18945723 18945769
chr_1 g11879 g11879.t6 exon g11879.t6.exon4 18945996 18946059
chr_1 g11879 g11879.t6 cds g11879.t6.CDS4 18945996 18946002
chr_1 g11879 g11879.t6 exon g11879.t6.exon5 18946119 18946234
chr_1 g11879 g11879.t6 exon g11879.t6.exon6 18946456 18946630
chr_1 g11879 g11879.t6 TSS g11879.t6 18946677 18946677

Sequences

>g11879.t6 Gene=g11879 Length=1597
CGTAAATTTAATTAATTTTAGTGGGTTAAAAGGCATAAAAAGAGCATTCTTGTTATTCTC
ATTGACACTCGCGGTTGTGTATACATATGAAGTTGTGTTGTGCAATTAAATTATATTGAA
AATCTTTACGAGAAAGTAAATAACTTGTTGCTTCAGAGTGAATTTAAGAAATAGTTGTTA
AATTATGAGACCGTTAAAGATTACAACAGTTGGTGATGGAGCTGTCGGAAAAACGTGCAT
GTTGATTTCATACACACAAAATGAATTTCCCGTAGAATATGTACCGACAGTATTTGATAA
TCATGCATGTACAATTACTGTGGATAATAAAGAGTACTCACTAACATTATGGTAATCTTT
AAAAAAGACTATGAGAGGCTGCGCCCATTAAGTTACCCGAATACTGATTGTTTTCTTTTG
TGCTATTCTATGGACTCCAGAACCTCTTTTGAGAATGTTTCTTCAAAATGGAATCCTGAA
ATAAGACACTTTTCGCCACATGTTCCAATCGTCCTAGTCGGCACAAAATCAGATTTGAGA
ATTCAGGGATCAGAAAAATATGTAACTACACAAGAGGCAAAAAAATTATGCAAAAAGATT
GGAGCATACACTTTAGTCGAGTGCTCTGCAAAGAAGAAAACAAATTTAGTGACGGTATTT
GAAGAGGCCGTCAGAGCGGTGGAAAAGAAAAAACCGAGAACTAGAGAACCTTGTAAAATT
CTCTAAATGTTTATTAACACACATATGTATGTCTTCATAAATTAAAATCACAAAAAAAAA
CCTATTCCTCATACAATAAATGCTGAGAATTTAATTATGTGAGTATAATTGGTACTTACA
AATATTTGATAAAGAAAAAAAGTTAAATTAAAAGTGCCATTAATTTTGCGTAATTTTTGT
TAAACATTAAAAATCAATTTATATATTTTTAAACTCACAATTTATCTAGTTCAAATTTCT
TATAAAATATAACTTCAAAGACTAATCATTGATTATTTCAAAAACTTTATGAAAAATGGC
AGAGTGAGAAAGACAAAAAATATATGTGTCTGTATCATATCAAAAATTAAAATATACTTA
TGCTGAAGTTAAGTAAACAATCACACACAGCTGTGTAGATGGAATTTTTATAAGTGTTAT
TAAAAAATTGATATTTTAAATCAGAGAAAAAACACAAAAATTCATCACAAACAAATCAAT
AGTTGCTCGGAAATTTAAAAAGTTAAATAATAATTTTTGAGGAAACGATAATTTTTGAGT
TTACCTACTTTTGTAGGACGAAAATACGCAATTAAAAAGCACAATTAGAGTTATGTGGAA
TCATTATTTTACTTATTGAAAAAAAATTATTTTAAAAGAAATTAAAAATTTTTTATTGTT
GCTCAGCTCTTTAAATAACTCCAAAATATGTAGAAACTATGATGACTTAGGTATTTTATA
AAAGTATTCTTCCCGTAATACATCATGTATTCGGATTGTATTCACAAAAATGTTATAGTC
AAGTTTAACAGGTATTGTAATTTTTTAGAAAGATTTCATCTTTAATAATCAAGAAAATAA
AATATATTTTATGAAAGAAATTTTAACAAAAAGAAAT

>g11879.t6 Gene=g11879 Length=125
MVIFKKDYERLRPLSYPNTDCFLLCYSMDSRTSFENVSSKWNPEIRHFSPHVPIVLVGTK
SDLRIQGSEKYVTTQEAKKLCKKIGAYTLVECSAKKKTNLVTVFEEAVRAVEKKKPRTRE
PCKIL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g11879.t6 CDD cd00157 Rho 7 110 0.0000000
7 g11879.t6 Gene3D G3DSA:3.40.50.300 - 4 125 0.0000000
2 g11879.t6 PANTHER PTHR24072 RHO FAMILY GTPASE 4 122 0.0000000
3 g11879.t6 PANTHER PTHR24072:SF305 RAS-LIKE GTP-BINDING PROTEIN RHOL 4 122 0.0000000
5 g11879.t6 PRINTS PR00449 Transforming protein P21 ras signature 50 63 0.0000000
4 g11879.t6 PRINTS PR00449 Transforming protein P21 ras signature 89 111 0.0000000
1 g11879.t6 Pfam PF00071 Ras family 7 112 0.0000000
13 g11879.t6 ProSiteProfiles PS51420 small GTPase Rho family profile. 1 111 13.1550000
11 g11879.t6 SMART SM00174 rho_sub_3 1 114 0.0000000
9 g11879.t6 SMART SM00173 ras_sub_4 3 114 0.0000240
10 g11879.t6 SMART SM00175 rab_sub_5 4 114 0.0000003
6 g11879.t6 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 7 111 0.0000000
12 g11879.t6 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 6 106 0.0000000

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