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.t16 TSS g14235.t16 35698312 35698312
chr_1 g14235 g14235.t16 isoform g14235.t16 35698390 35700309
chr_1 g14235 g14235.t16 exon g14235.t16.exon1 35698390 35698437
chr_1 g14235 g14235.t16 cds g14235.t16.CDS1 35698390 35698437
chr_1 g14235 g14235.t16 exon g14235.t16.exon2 35698566 35698644
chr_1 g14235 g14235.t16 cds g14235.t16.CDS2 35698566 35698644
chr_1 g14235 g14235.t16 exon g14235.t16.exon3 35699139 35699187
chr_1 g14235 g14235.t16 cds g14235.t16.CDS3 35699139 35699187
chr_1 g14235 g14235.t16 exon g14235.t16.exon4 35699327 35699564
chr_1 g14235 g14235.t16 cds g14235.t16.CDS4 35699327 35699564
chr_1 g14235 g14235.t16 exon g14235.t16.exon5 35699630 35700309
chr_1 g14235 g14235.t16 cds g14235.t16.CDS5 35699630 35699830
chr_1 g14235 g14235.t16 TTS g14235.t16 NA NA

Sequences

>g14235.t16 Gene=g14235 Length=1094
ATGTCTAAGAAGACTTACGATTTGCTGTTTAAATTATTATTGATTGGTGACTCGGGTGTC
GGAAAAACTTGCATTCTGTTTAGATTCAGTGATGATGCATTTACATCAACGTTTATATCT
ACCATAGGAATTGATTTCAAAATCAAAACAGTCGAGTTAAGAGGAAAGAAAATCAAATTT
TTTTTTAAGACCGCTGGTCAAGAAAGATTTCACACAATCACAACCTCTTATTATCGTGGA
GCTATGGGTATTATGTTGGTGTATGACATAACAAATGAAAAGAGTTTTGAGAATATAATA
AAGTGGCTTCGGAATATTGATGAACATGCTAATGAAGATGTTGAACGAATGATTCTTGGC
AATAAATGTGATATGACTGATAAACGAGTTGTCAGTAAAGAACGTGGTGAAAATATTGCT
CGCGAATATGGAATTCGCTTCATGGAAACATCAGCCAAAGCAAACATTAATATTGAAAAA
GCATTTAGCGAACTTGCAGAAGCAATTCTAGATCAAACAGCTGGAAAAGAAAATAATGAT
AATCAAGAGCGCGTTGTTGTAGATCGAAAAAATCAAGAAAAATCACCGGCTTACAGTAGA
TGTTGTACATCTTAAATACATACAGCCTAATCATGCTGTCTAAAAATAATCAATGTCATT
CTAACTACGCTCTTTCATTCTTCATCGCTTTAAAAGATGTATAATAAAAACAATTCTTGT
AAAAGATACTTAATAAAACTGCTTTACTAATTTTATTAAAAATGCAATTGAAATGTCTTG
GTTAAAAGCTCAAAAGAATCAACAATTTAATTGAATTTTATATTTTTCTATCATAGTTAA
AAATTTAAAACGCTTATGTTTAGCATGATTTGCTTAAAGCGCAAAAAAGCAGCTGAATAA
AGTCGACCAATCGCTAATCATCTTATCAAACAAATCTAGATCAATAAAACTTTTCACAAT
AATGCGTAAATGTATGAAAGAATATGTAGTTTCAAAAAAATTTTATTTTTATGTATTCAA
AAATTTTCATGATGATTTTACAATAAAATATGTGCATAATAAATAAACATTATTTAAATG
CAGTTGCACAATTT

>g14235.t16 Gene=g14235 Length=204
MSKKTYDLLFKLLLIGDSGVGKTCILFRFSDDAFTSTFISTIGIDFKIKTVELRGKKIKF
FFKTAGQERFHTITTSYYRGAMGIMLVYDITNEKSFENIIKWLRNIDEHANEDVERMILG
NKCDMTDKRVVSKERGENIAREYGIRFMETSAKANINIEKAFSELAEAILDQTAGKENND
NQERVVVDRKNQEKSPAYSRCCTS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g14235.t16 CDD cd01867 Rab8_Rab10_Rab13_like 7 172 4.53473E-109
10 g14235.t16 Gene3D G3DSA:3.40.50.300 - 3 202 3.9E-64
2 g14235.t16 PANTHER PTHR47980 LD44762P 1 192 7.6E-91
3 g14235.t16 PANTHER PTHR47980:SF36 RAS-RELATED PROTEIN RAB-10 1 192 7.6E-91
6 g14235.t16 PRINTS PR00449 Transforming protein P21 ras signature 10 31 1.5E-32
7 g14235.t16 PRINTS PR00449 Transforming protein P21 ras signature 33 49 1.5E-32
5 g14235.t16 PRINTS PR00449 Transforming protein P21 ras signature 50 72 1.5E-32
4 g14235.t16 PRINTS PR00449 Transforming protein P21 ras signature 112 125 1.5E-32
8 g14235.t16 PRINTS PR00449 Transforming protein P21 ras signature 147 169 1.5E-32
1 g14235.t16 Pfam PF00071 Ras family 11 170 2.3E-59
12 g14235.t16 Phobius SIGNAL_PEPTIDE Signal peptide region 1 21 -
13 g14235.t16 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 7 -
14 g14235.t16 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 8 16 -
15 g14235.t16 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 17 21 -
11 g14235.t16 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 22 204 -
22 g14235.t16 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 5 202 33.776
17 g14235.t16 SMART SM00173 ras_sub_4 7 172 8.7E-21
18 g14235.t16 SMART SM00175 rab_sub_5 10 172 2.0E-90
20 g14235.t16 SMART SM00174 rho_sub_3 12 172 7.6E-10
19 g14235.t16 SMART SM00176 ran_sub_2 15 198 5.4E-5
9 g14235.t16 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 5 182 1.12E-55
21 g14235.t16 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 10 164 2.3E-25

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