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 g11563 g11563.t1 TSS g11563.t1 17159420 17159420
chr_1 g11563 g11563.t1 isoform g11563.t1 17159511 17161199
chr_1 g11563 g11563.t1 exon g11563.t1.exon1 17159511 17159565
chr_1 g11563 g11563.t1 cds g11563.t1.CDS1 17159511 17159565
chr_1 g11563 g11563.t1 exon g11563.t1.exon2 17159662 17159733
chr_1 g11563 g11563.t1 cds g11563.t1.CDS2 17159662 17159733
chr_1 g11563 g11563.t1 exon g11563.t1.exon3 17160068 17160128
chr_1 g11563 g11563.t1 cds g11563.t1.CDS3 17160068 17160128
chr_1 g11563 g11563.t1 exon g11563.t1.exon4 17160242 17160249
chr_1 g11563 g11563.t1 cds g11563.t1.CDS4 17160242 17160249
chr_1 g11563 g11563.t1 exon g11563.t1.exon5 17160668 17160709
chr_1 g11563 g11563.t1 cds g11563.t1.CDS5 17160668 17160709
chr_1 g11563 g11563.t1 exon g11563.t1.exon6 17160799 17160850
chr_1 g11563 g11563.t1 cds g11563.t1.CDS6 17160799 17160850
chr_1 g11563 g11563.t1 exon g11563.t1.exon7 17161175 17161199
chr_1 g11563 g11563.t1 cds g11563.t1.CDS7 17161175 17161199
chr_1 g11563 g11563.t1 TTS g11563.t1 17161974 17161974

Sequences

>g11563.t1 Gene=g11563 Length=315
ATGTCTACGAAGACCTACGATTATTTGTTTAAACTTCTTTTGATCGGCGATAGTGGTGTA
GGAAAAACCTGTATACTGTTCAGATTTTCGGAAAATAATTTCAACACAACATTTATATCA
ACAATTGGAATTGACTTCAAAATTCGAACAATAGAGCTGGATGGAAAGAAAATAAAACTG
CAGATATGGGACACTGCTGGACAAGAACGGTTTCGTACAATCACTACAGCGTATTATCAA
TTTTATTCATCATTCTTTGGTTTTCATAATAATTCTCCACAATTTAGGAGCAATGGGTAT
CATGCTTGTATATGA

>g11563.t1 Gene=g11563 Length=104
MSTKTYDYLFKLLLIGDSGVGKTCILFRFSENNFNTTFISTIGIDFKIRTIELDGKKIKL
QIWDTAGQERFRTITTAYYQFYSSFFGFHNNSPQFRSNGYHACI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g11563.t1 Gene3D G3DSA:3.40.50.300 - 1 91 0.000
2 g11563.t1 PANTHER PTHR47980:SF6 RAS-RELATED PROTEIN RAB-8B 3 80 0.000
3 g11563.t1 PANTHER PTHR47980 LD44762P 3 80 0.000
4 g11563.t1 PRINTS PR00449 Transforming protein P21 ras signature 10 31 0.000
5 g11563.t1 PRINTS PR00449 Transforming protein P21 ras signature 33 49 0.000
6 g11563.t1 PRINTS PR00449 Transforming protein P21 ras signature 51 73 0.000
1 g11563.t1 Pfam PF00071 Ras family 11 81 0.000
10 g11563.t1 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 5 104 17.279
9 g11563.t1 SMART SM00175 rab_sub_5 10 102 0.000
7 g11563.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 5 80 0.000
11 g11563.t1 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 8 80 0.000

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