Gene loci information

Transcript annotation

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

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.t6 TSS g11563.t6 17159420 17159420
chr_1 g11563 g11563.t6 isoform g11563.t6 17159426 17161973
chr_1 g11563 g11563.t6 exon g11563.t6.exon1 17159426 17159565
chr_1 g11563 g11563.t6 exon g11563.t6.exon2 17159662 17159737
chr_1 g11563 g11563.t6 exon g11563.t6.exon3 17160068 17160150
chr_1 g11563 g11563.t6 cds g11563.t6.CDS1 17160126 17160150
chr_1 g11563 g11563.t6 exon g11563.t6.exon4 17161175 17161464
chr_1 g11563 g11563.t6 cds g11563.t6.CDS2 17161175 17161464
chr_1 g11563 g11563.t6 exon g11563.t6.exon5 17161525 17161973
chr_1 g11563 g11563.t6 cds g11563.t6.CDS3 17161525 17161620
chr_1 g11563 g11563.t6 TTS g11563.t6 17161974 17161974

Sequences

>g11563.t6 Gene=g11563 Length=1038
AGAAGAAAAGGAATCTATCAATCAGATATTTAAAAAAAATAATTTTCATTTTTCGGGCAC
TACATTCAATATTGATTAGTTTGATATGTCTACGAAGACCTACGATTATTTGTTTAAACT
TCTTTTGATCGGCGATAGTGGTGTAGGAAAAACCTGTATACTGTTCAGATTTTCGGAAAA
TAATTTCAACACAACATTTATATCAACAATTGGTAAGAATTGACTTCAAAATTCGAACAA
TAGAGCTGGATGGAAAGAAAATAAAACTGCAGATATGGTGAGTGACAAATGTTTCATTTC
AATGGGTATCATGCTTGTATATGACATCACTCAAGAGAAGTCATTTGAAAATATTAAAAA
TTGGATAAGAAACATAGAAGAAAATGCTTCGACTGACGTTGAAAAGATGTTGTTAGGTAA
TAAGTGTGAGTTAAATGAGAAGAGACAAGTCACAAAGGAACGAGGAGAGCAGTTAGCTGT
TGAATACGGAATCAAATTTCTTGAAACATCAGCGAAGAATAGCATCAATGTAGAAGAAGC
ATTCTTTACATTAGCTCGAGATATAAAAATTAAAATGGAGAAGAGAATGGAAGCAAATAA
TCCACCGAAGGGCCATCAATTGAAAGCAAATGAACCGCCACGAAAACCTGGTCTCGGATG
GCTATCAAAGTGTAACTTCTTTTAGCCTTATTGCATTATATTGTGTAGTTATTCCATGAT
GATAACGATGTAAGGAAAATTCTCAAATTTTTTGCAAATTTTGTATACACACACACACAC
ATACAAACATAAAAACGAATGAAAAATGACGAAATGCCCCTTTTAAAACTTTCAAATCTT
TATTATTTATTTTCTTATTTTTCTTTATATTCTATGTATATATCAATCCTTTTTTTGTTG
CAATACAAATTGTGAGGAAAAGGTCAAATGAGTTTAAATAATTATGTCCATTCTATTTTA
ATTTTTTATTTCTTCAACTCCTATATCCTTGTTCTTATTTTTAATAAAATACTTTAAAAT
AAAAGTAAAAAAATGGAA

>g11563.t6 Gene=g11563 Length=136
MVSDKCFISMGIMLVYDITQEKSFENIKNWIRNIEENASTDVEKMLLGNKCELNEKRQVT
KERGEQLAVEYGIKFLETSAKNSINVEEAFFTLARDIKIKMEKRMEANNPPKGHQLKANE
PPRKPGLGWLSKCNFF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g11563.t6 Gene3D G3DSA:3.40.50.300 - 7 124 0.000e+00
2 g11563.t6 PANTHER PTHR47980 LD44762P 9 124 0.000e+00
3 g11563.t6 PANTHER PTHR47980:SF33 RAS-RELATED PROTEIN RAB-8A 9 124 0.000e+00
5 g11563.t6 PRINTS PR00449 Transforming protein P21 ras signature 40 53 0.000e+00
4 g11563.t6 PRINTS PR00449 Transforming protein P21 ras signature 75 97 0.000e+00
1 g11563.t6 Pfam PF00071 Ras family 9 98 0.000e+00
10 g11563.t6 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 1 133 1.837e+01
8 g11563.t6 SMART SM00175 rab_sub_5 3 100 0.000e+00
7 g11563.t6 SMART SM00173 ras_sub_4 4 100 2.000e-07
6 g11563.t6 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 10 127 0.000e+00

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