Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Ras-related protein Rab-8B.

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 g11564 g11564.t5 TSS g11564.t5 17160438 17160438
chr_1 g11564 g11564.t5 isoform g11564.t5 17160667 17161973
chr_1 g11564 g11564.t5 exon g11564.t5.exon1 17160667 17160713
chr_1 g11564 g11564.t5 exon g11564.t5.exon2 17161175 17161446
chr_1 g11564 g11564.t5 cds g11564.t5.CDS1 17161177 17161446
chr_1 g11564 g11564.t5 exon g11564.t5.exon3 17161525 17161973
chr_1 g11564 g11564.t5 cds g11564.t5.CDS2 17161525 17161620
chr_1 g11564 g11564.t5 TTS g11564.t5 17161974 17161974

Sequences

>g11564.t5 Gene=g11564 Length=768
GCTGGACAAGAACGGTTTCGTACAATCACTACAGCGTATTATCGTAACAATGGGTATCAT
GCTTGTATATGACATCACTCAAGAGAAGTCATTTGAAAATATTAAAAATTGGATAAGAAA
CATAGAAGAAAATGCTTCGACTGACGTTGAAAAGATGTTGTTAGGTAATAAGTGTGAGTT
AAATGAGAAGAGACAAGTCACAAAGGAACGAGGAGAGCAGTTAGCTGTTGAATACGGAAT
CAAATTTCTTGAAACATCAGCGAAGAATAGCATCAATGTAGAAGAAGCATTCTTTACATT
AGCTCGAGATATAAAAATTGAAGCAAATAATCCACCGAAGGGCCATCAATTGAAAGCAAA
TGAACCGCCACGAAAACCTGGTCTCGGATGGCTATCAAAGTGTAACTTCTTTTAGCCTTA
TTGCATTATATTGTGTAGTTATTCCATGATGATAACGATGTAAGGAAAATTCTCAAATTT
TTTGCAAATTTTGTATACACACACACACACATACAAACATAAAAACGAATGAAAAATGAC
GAAATGCCCCTTTTAAAACTTTCAAATCTTTATTATTTATTTTCTTATTTTTCTTTATAT
TCTATGTATATATCAATCCTTTTTTTGTTGCAATACAAATTGTGAGGAAAAGGTCAAATG
AGTTTAAATAATTATGTCCATTCTATTTTAATTTTTTATTTCTTCAACTCCTATATCCTT
GTTCTTATTTTTAATAAAATACTTTAAAATAAAAGTAAAAAAATGGAA

>g11564.t5 Gene=g11564 Length=121
MGIMLVYDITQEKSFENIKNWIRNIEENASTDVEKMLLGNKCELNEKRQVTKERGEQLAV
EYGIKFLETSAKNSINVEEAFFTLARDIKIEANNPPKGHQLKANEPPRKPGLGWLSKCNF
F

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g11564.t5 Gene3D G3DSA:3.40.50.300 - 1 108 0.0000000
2 g11564.t5 PANTHER PTHR47980:SF6 RAS-RELATED PROTEIN RAB-8B 1 93 0.0000000
3 g11564.t5 PANTHER PTHR47980 LD44762P 1 93 0.0000000
5 g11564.t5 PRINTS PR00449 Transforming protein P21 ras signature 31 44 0.0000000
4 g11564.t5 PRINTS PR00449 Transforming protein P21 ras signature 66 88 0.0000000
1 g11564.t5 Pfam PF00071 Ras family 2 89 0.0000000
10 g11564.t5 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 1 119 18.9920000
7 g11564.t5 SMART SM00173 ras_sub_4 1 91 0.0000005
8 g11564.t5 SMART SM00175 rab_sub_5 1 91 0.0000000
6 g11564.t5 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 2 92 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