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.t25 TSS g11563.t25 17159420 17159420
chr_1 g11563 g11563.t25 isoform g11563.t25 17159511 17161973
chr_1 g11563 g11563.t25 exon g11563.t25.exon1 17159511 17159565
chr_1 g11563 g11563.t25 exon g11563.t25.exon2 17159662 17159733
chr_1 g11563 g11563.t25 exon g11563.t25.exon3 17160068 17160132
chr_1 g11563 g11563.t25 cds g11563.t25.CDS1 17160126 17160132
chr_1 g11563 g11563.t25 exon g11563.t25.exon4 17160668 17160709
chr_1 g11563 g11563.t25 cds g11563.t25.CDS2 17160668 17160709
chr_1 g11563 g11563.t25 exon g11563.t25.exon5 17161175 17161468
chr_1 g11563 g11563.t25 cds g11563.t25.CDS3 17161175 17161468
chr_1 g11563 g11563.t25 exon g11563.t25.exon6 17161525 17161973
chr_1 g11563 g11563.t25 cds g11563.t25.CDS4 17161525 17161535
chr_1 g11563 g11563.t25 TTS g11563.t25 17161974 17161974

Sequences

>g11563.t25 Gene=g11563 Length=977
ATGTCTACGAAGACCTACGATTATTTGTTTAAACTTCTTTTGATCGGCGATAGTGGTGTA
GGAAAAACCTGTATACTGTTCAGATTTTCGGAAAATAATTTCAACACAACATTTATATCA
ACAATTGGAATTGACTTCAAAATTCGAACAATAGAGCTGGATGGAAAGAAAATAAAACTG
CAGATATGGTGACTGGACAAGAACGGTTTCGTACAATCACTACAGCGTATTATCCAATGG
GTATCATGCTTGTATATGACATCACTCAAGAGAAGTCATTTGAAAATATTAAAAATTGGA
TAAGAAACATAGAAGAAAATGCTTCGACTGACGTTGAAAAGATGTTGTTAGGTAATAAGT
GTGAGTTAAATGAGAAGAGACAAGTCACAAAGGAACGAGGAGAGCAGTTAGCTGTTGAAT
ACGGAATCAAATTTCTTGAAACATCAGCGAAGAATAGCATCAATGTAGAAGAAGCATTCT
TTACATTAGCTCGAGATATAAAAATTAAAATGGAGAAGAGAATGGTAAGAAGCAAATAAT
CCACCGAAGGGCCATCAATTGAAAGCAAATGAACCGCCACGAAAACCTGGTCTCGGATGG
CTATCAAAGTGTAACTTCTTTTAGCCTTATTGCATTATATTGTGTAGTTATTCCATGATG
ATAACGATGTAAGGAAAATTCTCAAATTTTTTGCAAATTTTGTATACACACACACACACA
TACAAACATAAAAACGAATGAAAAATGACGAAATGCCCCTTTTAAAACTTTCAAATCTTT
ATTATTTATTTTCTTATTTTTCTTTATATTCTATGTATATATCAATCCTTTTTTTGTTGC
AATACAAATTGTGAGGAAAAGGTCAAATGAGTTTAAATAATTATGTCCATTCTATTTTAA
TTTTTTATTTCTTCAACTCCTATATCCTTGTTCTTATTTTTAATAAAATACTTTAAAATA
AAAGTAAAAAAATGGAA

>g11563.t25 Gene=g11563 Length=117
MVTGQERFRTITTAYYPMGIMLVYDITQEKSFENIKNWIRNIEENASTDVEKMLLGNKCE
LNEKRQVTKERGEQLAVEYGIKFLETSAKNSINVEEAFFTLARDIKIKMEKRMVRSK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g11563.t25 Gene3D G3DSA:3.40.50.300 - 2 117 0.0000000
2 g11563.t25 PANTHER PTHR47980 LD44762P 3 114 0.0000000
3 g11563.t25 PANTHER PTHR47980:SF33 RAS-RELATED PROTEIN RAB-8A 3 114 0.0000000
5 g11563.t25 PRINTS PR00449 Transforming protein P21 ras signature 48 61 0.0000000
4 g11563.t25 PRINTS PR00449 Transforming protein P21 ras signature 83 105 0.0000000
1 g11563.t25 Pfam PF00071 Ras family 4 106 0.0000000
10 g11563.t25 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 1 117 20.3990000
7 g11563.t25 SMART SM00173 ras_sub_4 3 108 0.0000001
8 g11563.t25 SMART SM00175 rab_sub_5 4 108 0.0000000
6 g11563.t25 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 4 110 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. There were no conditions that were differentially expressed