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.t11 TTS g11879.t11 18944415 18944415
chr_1 g11879 g11879.t11 isoform g11879.t11 18944610 18946630
chr_1 g11879 g11879.t11 exon g11879.t11.exon1 18944610 18945481
chr_1 g11879 g11879.t11 cds g11879.t11.CDS1 18945276 18945481
chr_1 g11879 g11879.t11 exon g11879.t11.exon2 18945547 18945664
chr_1 g11879 g11879.t11 cds g11879.t11.CDS2 18945547 18945664
chr_1 g11879 g11879.t11 exon g11879.t11.exon3 18945973 18946059
chr_1 g11879 g11879.t11 cds g11879.t11.CDS3 18945973 18946002
chr_1 g11879 g11879.t11 exon g11879.t11.exon4 18946119 18946234
chr_1 g11879 g11879.t11 exon g11879.t11.exon5 18946456 18946630
chr_1 g11879 g11879.t11 TSS g11879.t11 18946677 18946677

Sequences

>g11879.t11 Gene=g11879 Length=1368
CGTAAATTTAATTAATTTTAGTGGGTTAAAAGGCATAAAAAGAGCATTCTTGTTATTCTC
ATTGACACTCGCGGTTGTGTATACATATGAAGTTGTGTTGTGCAATTAAATTATATTGAA
AATCTTTACGAGAAAGTAAATAACTTGTTGCTTCAGAGTGAATTTAAGAAATAGTTGTTA
AATTATGAGACCGTTAAAGATTACAACAGTTGGTGATGGAGCTGTCGGAAAAACGTGCAT
GTTGATTTCATACACACAAAATGAATTTCCCGTAGAATATGTACCGACAGTATTTGATAA
TCATGCATGTACAATTACTGTGGATAATAAAGAGTACTCACTAACATTATGGTAAGTCTC
AAATATTATTTTACCAGTACTGATTGTTTTCTTTTGTGCTATTCTATGGACTCCAGAACC
TCTTTTGAGAATGTTTCTTCAAAATGGAATCCTGAAATAAGACACTTTTCGCCACATGTT
CCAATCGTCCTAGTCGGCACAAAATCAGATTTGAGAATTCAGGGATCAGAAAAATATGTA
ACTACACAAGAGGCAAAAAAATTATGCAAAAAGATTGGAGCATACACTTTAGTCGAGTGC
TCTGCAAAGAAGAAAACAAATTTAGTGACGGTATTTGAAGAGGCCGTCAGAGCGGTGGAA
AAGAAAAAACCGAGAACTAGAGAACCTTGTAAAATTCTCTAAATGTTTATTAACACACAT
ATGTATGTCTTCATAAATTAAAATCACAAAAAAAAACCTATTCCTCATACAATAAATGCT
GAGAATTTAATTATGTGAGTATAATTGGTACTTACAAATATTTGATAAAGAAAAAAAGTT
AAATTAAAAGTGCCATTAATTTTGCGTAATTTTTGTTAAACATTAAAAATCAATTTATAT
ATTTTTAAACTCACAATTTATCTAGTTCAAATTTCTTATAAAATATAACTTCAAAGACTA
ATCATTGATTATTTCAAAAACTTTATGAAAAATGGCAGAGTGAGAAAGACAAAAAATATA
TGTGTCTGTATCATATCAAAAATTAAAATATACTTATGCTGAAGTTAAGTAAACAATCAC
ACACAGCTGTGTAGATGGAATTTTTATAAGTGTTATTAAAAAATTGATATTTTAAATCAG
AGAAAAAACACAAAAATTCATCACAAACAAATCAATAGTTGCTCGGAAATTTAAAAAGTT
AAATAATAATTTTTGAGGAAACGATAATTTTTGAGTTTACCTACTTTTGTAGGACGAAAA
TACGCAATTAAAAAGCACAATTAGAGTTATGTGGAATCATTATTTTACTTATTGAAAAAA
AATTATTTTAAAAGAAATTAAAAATTTTTTATTGTTGCTCAGCTCTTT

>g11879.t11 Gene=g11879 Length=117
MVSLKYYFTSTDCFLLCYSMDSRTSFENVSSKWNPEIRHFSPHVPIVLVGTKSDLRIQGS
EKYVTTQEAKKLCKKIGAYTLVECSAKKKTNLVTVFEEAVRAVEKKKPRTREPCKIL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g11879.t11 Gene3D G3DSA:3.40.50.300 - 2 108 0.0000000
2 g11879.t11 PANTHER PTHR24072 RHO FAMILY GTPASE 8 114 0.0000000
3 g11879.t11 PANTHER PTHR24072:SF305 RAS-LIKE GTP-BINDING PROTEIN RHOL 8 114 0.0000000
5 g11879.t11 PRINTS PR00449 Transforming protein P21 ras signature 42 55 0.0000000
4 g11879.t11 PRINTS PR00449 Transforming protein P21 ras signature 81 103 0.0000000
1 g11879.t11 Pfam PF00071 Ras family 6 104 0.0000000
11 g11879.t11 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 1 117 12.7140000
7 g11879.t11 SMART SM00173 ras_sub_4 1 106 0.0000560
9 g11879.t11 SMART SM00174 rho_sub_3 1 106 0.0000000
8 g11879.t11 SMART SM00175 rab_sub_5 3 106 0.0000007
6 g11879.t11 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 5 103 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: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