Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t20 TSS g14235.t20 35698312 35698312
chr_1 g14235 g14235.t20 isoform g14235.t20 35698390 35701706
chr_1 g14235 g14235.t20 exon g14235.t20.exon1 35698390 35698435
chr_1 g14235 g14235.t20 exon g14235.t20.exon2 35698566 35698644
chr_1 g14235 g14235.t20 exon g14235.t20.exon3 35699139 35699191
chr_1 g14235 g14235.t20 exon g14235.t20.exon4 35699340 35699564
chr_1 g14235 g14235.t20 cds g14235.t20.CDS1 35699394 35699564
chr_1 g14235 g14235.t20 exon g14235.t20.exon5 35699630 35699979
chr_1 g14235 g14235.t20 cds g14235.t20.CDS2 35699630 35699830
chr_1 g14235 g14235.t20 exon g14235.t20.exon6 35701699 35701706
chr_1 g14235 g14235.t20 TTS g14235.t20 NA NA

Sequences

>g14235.t20 Gene=g14235 Length=761
ATGTCTAAGAAGACTTACGATTTGCTGTTTAAATTATTATTGATTGGACTCGGGTGTCGG
AAAAACTTGCATTCTGTTTAGATTCAGTGATGATGCATTTACATCAACGTTTATATCTAC
CATAGGAATTGATTTCAAAATCAAAACAGTCGAGTTAAGAGGAAAGAAAATCAAGTATAC
CGCTGGTCAAGAAAGATTTCACACAATCACAACCTCTTATTATCGTGGAGCTATGGGTAT
TATGTTGGTGTATGACATAACAAATGAAAAGAGTTTTGAGAATATAATAAAGTGGCTTCG
GAATATTGATGAACATGCTAATGAAGATGTTGAACGAATGATTCTTGGCAATAAATGTGA
TATGACTGATAAACGAGTTGTCAGTAAAGAACGTGGTGAAAATATTGCTCGCGAATATGG
AATTCGCTTCATGGAAACATCAGCCAAAGCAAACATTAATATTGAAAAAGCATTTAGCGA
ACTTGCAGAAGCAATTCTAGATCAAACAGCTGGAAAAGAAAATAATGATAATCAAGAGCG
CGTTGTTGTAGATCGAAAAAATCAAGAAAAATCACCGGCTTACAGTAGATGTTGTACATC
TTAAATACATACAGCCTAATCATGCTGTCTAAAAATAATCAATGTCATTCTAACTACGCT
CTTTCATTCTTCATCGCTTTAAAAGATGTATAATAAAAACAATTCTTGTAAAAGATACTT
AATAAAACTGCTTTACTAATTTTATTAAAAATGCAAAAATT

>g14235.t20 Gene=g14235 Length=123
MGIMLVYDITNEKSFENIIKWLRNIDEHANEDVERMILGNKCDMTDKRVVSKERGENIAR
EYGIRFMETSAKANINIEKAFSELAEAILDQTAGKENNDNQERVVVDRKNQEKSPAYSRC
CTS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g14235.t20 Gene3D G3DSA:3.40.50.300 - 1 121 0.0000000
2 g14235.t20 PANTHER PTHR47980 LD44762P 1 112 0.0000000
3 g14235.t20 PANTHER PTHR47980:SF36 RAS-RELATED PROTEIN RAB-10 1 112 0.0000000
5 g14235.t20 PRINTS PR00449 Transforming protein P21 ras signature 31 44 0.0000000
4 g14235.t20 PRINTS PR00449 Transforming protein P21 ras signature 66 88 0.0000000
1 g14235.t20 Pfam PF00071 Ras family 2 89 0.0000000
11 g14235.t20 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 1 121 18.7160000
7 g14235.t20 SMART SM00173 ras_sub_4 1 91 0.0000081
8 g14235.t20 SMART SM00175 rab_sub_5 1 91 0.0000000
9 g14235.t20 SMART SM00174 rho_sub_3 1 91 0.0041000
6 g14235.t20 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 2 102 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