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 g11564 g11564.t2 TSS g11564.t2 17159420 17159420
chr_1 g11564 g11564.t2 isoform g11564.t2 17159661 17161973
chr_1 g11564 g11564.t2 exon g11564.t2.exon1 17159661 17159733
chr_1 g11564 g11564.t2 exon g11564.t2.exon2 17160068 17160159
chr_1 g11564 g11564.t2 cds g11564.t2.CDS1 17160126 17160159
chr_1 g11564 g11564.t2 exon g11564.t2.exon3 17161175 17161464
chr_1 g11564 g11564.t2 cds g11564.t2.CDS2 17161175 17161464
chr_1 g11564 g11564.t2 exon g11564.t2.exon4 17161525 17161973
chr_1 g11564 g11564.t2 cds g11564.t2.CDS3 17161525 17161620
chr_1 g11564 g11564.t2 TTS g11564.t2 17161974 17161974

Sequences

>g11564.t2 Gene=g11564 Length=904
GGTGTAGGAAAAACCTGTATACTGTTCAGATTTTCGGAAAATAATTTCAACACAACATTT
ATATCAACAATTGGAATTGACTTCAAAATTCGAACAATAGAGCTGGATGGAAAGAAAATA
AAACTGCAGATATGGTGAGTGACAAATGTTTCATTTTTGATGCTGCAATGGGTATCATGC
TTGTATATGACATCACTCAAGAGAAGTCATTTGAAAATATTAAAAATTGGATAAGAAACA
TAGAAGAAAATGCTTCGACTGACGTTGAAAAGATGTTGTTAGGTAATAAGTGTGAGTTAA
ATGAGAAGAGACAAGTCACAAAGGAACGAGGAGAGCAGTTAGCTGTTGAATACGGAATCA
AATTTCTTGAAACATCAGCGAAGAATAGCATCAATGTAGAAGAAGCATTCTTTACATTAG
CTCGAGATATAAAAATTAAAATGGAGAAGAGAATGGAAGCAAATAATCCACCGAAGGGCC
ATCAATTGAAAGCAAATGAACCGCCACGAAAACCTGGTCTCGGATGGCTATCAAAGTGTA
ACTTCTTTTAGCCTTATTGCATTATATTGTGTAGTTATTCCATGATGATAACGATGTAAG
GAAAATTCTCAAATTTTTTGCAAATTTTGTATACACACACACACACATACAAACATAAAA
ACGAATGAAAAATGACGAAATGCCCCTTTTAAAACTTTCAAATCTTTATTATTTATTTTC
TTATTTTTCTTTATATTCTATGTATATATCAATCCTTTTTTTGTTGCAATACAAATTGTG
AGGAAAAGGTCAAATGAGTTTAAATAATTATGTCCATTCTATTTTAATTTTTTATTTCTT
CAACTCCTATATCCTTGTTCTTATTTTTAATAAAATACTTTAAAATAAAAGTAAAAAAAT
GGAA

>g11564.t2 Gene=g11564 Length=139
MVSDKCFIFDAAMGIMLVYDITQEKSFENIKNWIRNIEENASTDVEKMLLGNKCELNEKR
QVTKERGEQLAVEYGIKFLETSAKNSINVEEAFFTLARDIKIKMEKRMEANNPPKGHQLK
ANEPPRKPGLGWLSKCNFF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g11564.t2 Gene3D G3DSA:3.40.50.300 - 6 127 0.0000000
2 g11564.t2 PANTHER PTHR47980 LD44762P 9 127 0.0000000
3 g11564.t2 PANTHER PTHR47980:SF33 RAS-RELATED PROTEIN RAB-8A 9 127 0.0000000
5 g11564.t2 PRINTS PR00449 Transforming protein P21 ras signature 43 56 0.0000000
4 g11564.t2 PRINTS PR00449 Transforming protein P21 ras signature 78 100 0.0000000
1 g11564.t2 Pfam PF00071 Ras family 9 101 0.0000000
10 g11564.t2 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 1 136 18.3880000
7 g11564.t2 SMART SM00173 ras_sub_4 2 103 0.0000001
8 g11564.t2 SMART SM00175 rab_sub_5 3 103 0.0000000
6 g11564.t2 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 9 130 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