Gene loci information

Transcript annotation

  • This transcript has been annotated as Ras-related protein Rab-11A.

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_3 g284 g284.t6 TTS g284.t6 2413823 2413823
chr_3 g284 g284.t6 isoform g284.t6 2414323 2415331
chr_3 g284 g284.t6 exon g284.t6.exon1 2414323 2415331
chr_3 g284 g284.t6 cds g284.t6.CDS1 2414561 2414935
chr_3 g284 g284.t6 TSS g284.t6 2415508 2415508

Sequences

>g284.t6 Gene=g284 Length=1009
ACTGTTGTATGGTAAGGAAAATTTTTAATGCAATCAAAGTTTATGAATATGCGAAAGGGA
TACAAATTAAATTGAATTACAATATATTGCACTGTATACATCCTATCTCGCTTTTATAAG
TGTGAAAAATTGATAATGATAAATTATGTGAAAAGAATGCCTTATTGATTTATTATCAAA
TATGATACTAACAATGGTTCTTACTTTTTTTTTATTTTTAGTGGTTTTAATTGGAGATTC
AGGCGTTGGAAAGTCGAATCTTCTTTCGCGATTCACACGTAATGAATTCAATTTAGAATC
GAAATCTACAATTGGAGTCGAATTTGCAACTCGTAGTATTGTTGTGGATAATAAAACTAT
CAAAGCTCAAATTTGGGATGTAAGTACATTTTGAACATGACAATTGCATGTCATCACTAT
GTATCATTTTTAATTATTTCAATTCAGACTGCTGGTCAAGAAAGATATCGAGCGATTACA
TCTGCTTATTACCGTGGTGCTGTTGGTGCTCTTTTGGTTTATGATATTGCTAAACATCTC
ACATATGAGAATGTAGAGAGATGGCTTCGTGAATTGCGTGATCATGCAGATCAAAATATC
GTGATAATGTTGGTTGGTAACAAGAGCGATTTGAGGCATTTGCGTGCTGTGCCAACGGAT
GAGGCAAAGACTTTTGCTGAACGTAATGGTCTCAGTTTCATCGAAACATCAGCACTTGAT
TCAACAAATGTGGAAACGGCATTTCAAAATATACTCACAGGTAAACATTAATGATTTATT
GCCGGACTTTTACACTCATATTTTATTTCTTATCAATCAATGTCTGAAATTATATTTTTA
GAAATTTACCGAATCGTCTCGCAAAAACAAATTCGCGATCCACCAGAAGGAGATGTGATT
CGTCCATCGAATGTAGAGCCGATTGATGTTAAACCGACAGTAACATCAGAAGTTAGAAAG
CAATGTTGTCAGTGAGCCAGTGATTCGCTTGTGTTTTTATTTCCATCAT

>g284.t6 Gene=g284 Length=124
MTIACHHYVSFLIISIQTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLREL
RDHADQNIVIMLVGNKSDLRHLRAVPTDEAKTFAERNGLSFIETSALDSTNVETAFQNIL
TGKH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g284.t6 Gene3D G3DSA:3.40.50.300 - 5 123 0.0000000
2 g284.t6 PANTHER PTHR47979:SF49 RAS-RELATED PROTEIN RAB-11A 17 121 0.0000000
3 g284.t6 PANTHER PTHR47979 DRAB11-RELATED 17 121 0.0000000
5 g284.t6 PRINTS PR00449 Transforming protein P21 ras signature 4 26 0.0000000
4 g284.t6 PRINTS PR00449 Transforming protein P21 ras signature 66 79 0.0000000
6 g284.t6 PRINTS PR00449 Transforming protein P21 ras signature 101 123 0.0000000
1 g284.t6 Pfam PF00071 Ras family 17 120 0.0000000
12 g284.t6 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 1 124 22.1560000
9 g284.t6 SMART SM00173 ras_sub_4 2 124 0.0000002
11 g284.t6 SMART SM00174 rho_sub_3 2 122 0.0000670
10 g284.t6 SMART SM00175 rab_sub_5 3 123 0.0000000
7 g284.t6 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 12 120 0.0000000
13 g284.t6 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 12 119 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