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.t19 TSS g14235.t19 35698312 35698312
chr_1 g14235 g14235.t19 isoform g14235.t19 35698390 35701673
chr_1 g14235 g14235.t19 exon g14235.t19.exon1 35698390 35698437
chr_1 g14235 g14235.t19 cds g14235.t19.CDS1 35698390 35698437
chr_1 g14235 g14235.t19 exon g14235.t19.exon2 35698566 35698644
chr_1 g14235 g14235.t19 cds g14235.t19.CDS2 35698566 35698644
chr_1 g14235 g14235.t19 exon g14235.t19.exon3 35699139 35699191
chr_1 g14235 g14235.t19 cds g14235.t19.CDS3 35699139 35699191
chr_1 g14235 g14235.t19 exon g14235.t19.exon4 35699340 35699564
chr_1 g14235 g14235.t19 cds g14235.t19.CDS4 35699340 35699564
chr_1 g14235 g14235.t19 exon g14235.t19.exon5 35699630 35700227
chr_1 g14235 g14235.t19 cds g14235.t19.CDS5 35699630 35699830
chr_1 g14235 g14235.t19 exon g14235.t19.exon6 35701588 35701673
chr_1 g14235 g14235.t19 TTS g14235.t19 NA NA

Sequences

>g14235.t19 Gene=g14235 Length=1089
ATGTCTAAGAAGACTTACGATTTGCTGTTTAAATTATTATTGATTGGTGACTCGGGTGTC
GGAAAAACTTGCATTCTGTTTAGATTCAGTGATGATGCATTTACATCAACGTTTATATCT
ACCATAGGAATTGATTTCAAAATCAAAACAGTCGAGTTAAGAGGAAAGAAAATCAAGTAT
ACCGCTGGTCAAGAAAGATTTCACACAATCACAACCTCTTATTATCGTGGAGCTATGGGT
ATTATGTTGGTGTATGACATAACAAATGAAAAGAGTTTTGAGAATATAATAAAGTGGCTT
CGGAATATTGATGAACATGCTAATGAAGATGTTGAACGAATGATTCTTGGCAATAAATGT
GATATGACTGATAAACGAGTTGTCAGTAAAGAACGTGGTGAAAATATTGCTCGCGAATAT
GGAATTCGCTTCATGGAAACATCAGCCAAAGCAAACATTAATATTGAAAAAGCATTTAGC
GAACTTGCAGAAGCAATTCTAGATCAAACAGCTGGAAAAGAAAATAATGATAATCAAGAG
CGCGTTGTTGTAGATCGAAAAAATCAAGAAAAATCACCGGCTTACAGTAGATGTTGTACA
TCTTAAATACATACAGCCTAATCATGCTGTCTAAAAATAATCAATGTCATTCTAACTACG
CTCTTTCATTCTTCATCGCTTTAAAAGATGTATAATAAAAACAATTCTTGTAAAAGATAC
TTAATAAAACTGCTTTACTAATTTTATTAAAAATGCAATTGAAATGTCTTGGTTAAAAGC
TCAAAAGAATCAACAATTTAATTGAATTTTATATTTTTCTATCATAGTTAAAAATTTAAA
ACGCTTATGTTTAGCATGATTTGCTTAAAGCGCAAAAAAGCAGCTGAATAAAGTCGACCA
ATCGCTAATCATCTTATCAAACAAATCTAGATCAATAAAACTTTTCACAATAATGCGTAA
ATGTATGAAAGAATATGTAGTTTCAAAAAAATTTTATTTTTATTCAAAATTTTCATGTGA
TTATAAATTGATTTGATCGCACCAACGATTGCATGTCAATAAGTCATAAAAATTGAATAC
ATTTTTGAT

>g14235.t19 Gene=g14235 Length=201
MSKKTYDLLFKLLLIGDSGVGKTCILFRFSDDAFTSTFISTIGIDFKIKTVELRGKKIKY
TAGQERFHTITTSYYRGAMGIMLVYDITNEKSFENIIKWLRNIDEHANEDVERMILGNKC
DMTDKRVVSKERGENIAREYGIRFMETSAKANINIEKAFSELAEAILDQTAGKENNDNQE
RVVVDRKNQEKSPAYSRCCTS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g14235.t19 CDD cd01867 Rab8_Rab10_Rab13_like 7 169 1.76931E-109
9 g14235.t19 Gene3D G3DSA:3.40.50.300 - 3 199 1.1E-62
2 g14235.t19 PANTHER PTHR47980 LD44762P 1 189 1.4E-89
3 g14235.t19 PANTHER PTHR47980:SF36 RAS-RELATED PROTEIN RAB-10 1 189 1.4E-89
4 g14235.t19 PRINTS PR00449 Transforming protein P21 ras signature 10 31 2.5E-31
5 g14235.t19 PRINTS PR00449 Transforming protein P21 ras signature 33 49 2.5E-31
6 g14235.t19 PRINTS PR00449 Transforming protein P21 ras signature 109 122 2.5E-31
7 g14235.t19 PRINTS PR00449 Transforming protein P21 ras signature 144 166 2.5E-31
1 g14235.t19 Pfam PF00071 Ras family 11 167 6.3E-58
11 g14235.t19 Phobius SIGNAL_PEPTIDE Signal peptide region 1 21 -
12 g14235.t19 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 7 -
13 g14235.t19 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 8 16 -
14 g14235.t19 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 17 21 -
10 g14235.t19 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 22 201 -
21 g14235.t19 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 5 199 33.702
16 g14235.t19 SMART SM00173 ras_sub_4 7 169 1.7E-21
17 g14235.t19 SMART SM00175 rab_sub_5 10 169 5.6E-93
19 g14235.t19 SMART SM00174 rho_sub_3 12 169 7.6E-10
18 g14235.t19 SMART SM00176 ran_sub_2 15 195 1.5E-4
8 g14235.t19 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 5 179 3.17E-55
20 g14235.t19 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 10 161 3.2E-24

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

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