Gene loci information

Transcript annotation

  • This transcript has been annotated as Ras-related protein Rab-10.

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 g14235 g14235.t15 TSS g14235.t15 35698312 35698312
chr_1 g14235 g14235.t15 isoform g14235.t15 35698390 35700309
chr_1 g14235 g14235.t15 exon g14235.t15.exon1 35698390 35698437
chr_1 g14235 g14235.t15 cds g14235.t15.CDS1 35698390 35698437
chr_1 g14235 g14235.t15 exon g14235.t15.exon2 35698566 35698644
chr_1 g14235 g14235.t15 cds g14235.t15.CDS2 35698566 35698644
chr_1 g14235 g14235.t15 exon g14235.t15.exon3 35699139 35699191
chr_1 g14235 g14235.t15 cds g14235.t15.CDS3 35699139 35699191
chr_1 g14235 g14235.t15 exon g14235.t15.exon4 35699340 35699556
chr_1 g14235 g14235.t15 cds g14235.t15.CDS4 35699340 35699556
chr_1 g14235 g14235.t15 exon g14235.t15.exon5 35699630 35700309
chr_1 g14235 g14235.t15 cds g14235.t15.CDS5 35699630 35699685
chr_1 g14235 g14235.t15 TTS g14235.t15 NA NA

Sequences

>g14235.t15 Gene=g14235 Length=1077
ATGTCTAAGAAGACTTACGATTTGCTGTTTAAATTATTATTGATTGGTGACTCGGGTGTC
GGAAAAACTTGCATTCTGTTTAGATTCAGTGATGATGCATTTACATCAACGTTTATATCT
ACCATAGGAATTGATTTCAAAATCAAAACAGTCGAGTTAAGAGGAAAGAAAATCAAGTAT
ACCGCTGGTCAAGAAAGATTTCACACAATCACAACCTCTTATTATCGTGGAGCTATGGGT
ATTATGTTGGTGTATGACATAACAAATGAAAAGAGTTTTGAGAATATAATAAAGTGGCTT
CGGAATATTGATGAACATGCTAATGAAGATGTTGAACGAATGATTCTTGGCAATAAATGT
GATATGACTGATAAACGAGTTGTCAGTAAAGAACGTGATTGCTCGCGAATATGGAATTCG
CTTCATGGAAACATCAGCCAAAGCAAACATTAATATTGAAAAAGCATTTAGCGAACTTGC
AGAAGCAATTCTAGATCAAACAGCTGGAAAAGAAAATAATGATAATCAAGAGCGCGTTGT
TGTAGATCGAAAAAATCAAGAAAAATCACCGGCTTACAGTAGATGTTGTACATCTTAAAT
ACATACAGCCTAATCATGCTGTCTAAAAATAATCAATGTCATTCTAACTACGCTCTTTCA
TTCTTCATCGCTTTAAAAGATGTATAATAAAAACAATTCTTGTAAAAGATACTTAATAAA
ACTGCTTTACTAATTTTATTAAAAATGCAATTGAAATGTCTTGGTTAAAAGCTCAAAAGA
ATCAACAATTTAATTGAATTTTATATTTTTCTATCATAGTTAAAAATTTAAAACGCTTAT
GTTTAGCATGATTTGCTTAAAGCGCAAAAAAGCAGCTGAATAAAGTCGACCAATCGCTAA
TCATCTTATCAAACAAATCTAGATCAATAAAACTTTTCACAATAATGCGTAAATGTATGA
AAGAATATGTAGTTTCAAAAAAATTTTATTTTTATGTATTCAAAAATTTTCATGATGATT
TTACAATAAAATATGTGCATAATAAATAAACATTATTTAAATGCAGTTGCACAATTT

>g14235.t15 Gene=g14235 Length=150
MSKKTYDLLFKLLLIGDSGVGKTCILFRFSDDAFTSTFISTIGIDFKIKTVELRGKKIKY
TAGQERFHTITTSYYRGAMGIMLVYDITNEKSFENIIKWLRNIDEHANEDVERMILGNKC
DMTDKRVVSKERDCSRIWNSLHGNISQSKH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g14235.t15 Gene3D G3DSA:3.40.50.300 - 1 143 5.8E-46
2 g14235.t15 PANTHER PTHR47980:SF6 RAS-RELATED PROTEIN RAB-8B 4 133 4.2E-70
3 g14235.t15 PANTHER PTHR47980 LD44762P 4 133 4.2E-70
4 g14235.t15 PRINTS PR00449 Transforming protein P21 ras signature 10 31 1.6E-20
5 g14235.t15 PRINTS PR00449 Transforming protein P21 ras signature 33 49 1.6E-20
6 g14235.t15 PRINTS PR00449 Transforming protein P21 ras signature 109 122 1.6E-20
1 g14235.t15 Pfam PF00071 Ras family 11 132 1.7E-44
10 g14235.t15 Phobius SIGNAL_PEPTIDE Signal peptide region 1 21 -
11 g14235.t15 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 7 -
12 g14235.t15 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 8 16 -
13 g14235.t15 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 17 21 -
9 g14235.t15 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 22 150 -
18 g14235.t15 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 5 150 25.679
14 g14235.t15 SMART SM00173 ras_sub_4 7 148 1.8E-7
15 g14235.t15 SMART SM00175 rab_sub_5 10 148 4.8E-59
16 g14235.t15 SMART SM00174 rho_sub_3 12 149 8.2E-5
7 g14235.t15 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 5 132 4.33E-42
17 g14235.t15 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 10 132 3.1E-20

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