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.t1 TTS g284.t1 2413823 2413823
chr_3 g284 g284.t1 isoform g284.t1 2414357 2416849
chr_3 g284 g284.t1 exon g284.t1.exon1 2414357 2414490
chr_3 g284 g284.t1 cds g284.t1.CDS1 2414357 2414490
chr_3 g284 g284.t1 exon g284.t1.exon2 2414572 2414884
chr_3 g284 g284.t1 cds g284.t1.CDS2 2414572 2414884
chr_3 g284 g284.t1 exon g284.t1.exon3 2414953 2415110
chr_3 g284 g284.t1 cds g284.t1.CDS3 2414953 2415110
chr_3 g284 g284.t1 exon g284.t1.exon4 2416810 2416849
chr_3 g284 g284.t1 cds g284.t1.CDS4 2416810 2416849
chr_3 g284 g284.t1 TSS g284.t1 2416887 2416887

Sequences

>g284.t1 Gene=g284 Length=645
ATGGGAACCCGAGACGATGAATATGATTATTTATTTAAAGTGGTTTTAATTGGAGATTCA
GGCGTTGGAAAGTCGAATCTTCTTTCGCGATTCACACGTAATGAATTCAATTTAGAATCG
AAATCTACAATTGGAGTCGAATTTGCAACTCGTAGTATTGTTGTGGATAATAAAACTATC
AAAGCTCAAATTTGGGATACTGCTGGTCAAGAAAGATATCGAGCGATTACATCTGCTTAT
TACCGTGGTGCTGTTGGTGCTCTTTTGGTTTATGATATTGCTAAACATCTCACATATGAG
AATGTAGAGAGATGGCTTCGTGAATTGCGTGATCATGCAGATCAAAATATCGTGATAATG
TTGGTTGGTAACAAGAGCGATTTGAGGCATTTGCGTGCTGTGCCAACGGATGAGGCAAAG
ACTTTTGCTGAACGTAATGGTCTCAGTTTCATCGAAACATCAGCACTTGATTCAACAAAT
GTGGAAACGGCATTTCAAAATATACTCACAGAAATTTACCGAATCGTCTCGCAAAAACAA
ATTCGCGATCCACCAGAAGGAGATGTGATTCGTCCATCGAATGTAGAGCCGATTGATGTT
AAACCGACAGTAACATCAGAAGTTAGAAAGCAATGTTGTCAGTGA

>g284.t1 Gene=g284 Length=214
MGTRDDEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIVVDNKTI
KAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIM
LVGNKSDLRHLRAVPTDEAKTFAERNGLSFIETSALDSTNVETAFQNILTEIYRIVSQKQ
IRDPPEGDVIRPSNVEPIDVKPTVTSEVRKQCCQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g284.t1 CDD cd01868 Rab11_like 9 173 0.0000000
10 g284.t1 Gene3D G3DSA:3.40.50.300 - 9 188 0.0000000
2 g284.t1 PANTHER PTHR47979:SF49 RAS-RELATED PROTEIN RAB-11A 3 214 0.0000000
3 g284.t1 PANTHER PTHR47979 DRAB11-RELATED 3 214 0.0000000
4 g284.t1 PRINTS PR00449 Transforming protein P21 ras signature 12 33 0.0000000
7 g284.t1 PRINTS PR00449 Transforming protein P21 ras signature 35 51 0.0000000
8 g284.t1 PRINTS PR00449 Transforming protein P21 ras signature 53 75 0.0000000
6 g284.t1 PRINTS PR00449 Transforming protein P21 ras signature 115 128 0.0000000
5 g284.t1 PRINTS PR00449 Transforming protein P21 ras signature 150 172 0.0000000
1 g284.t1 Pfam PF00071 Ras family 13 173 0.0000000
17 g284.t1 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 7 213 36.5450000
12 g284.t1 SMART SM00173 ras_sub_4 9 175 0.0000000
13 g284.t1 SMART SM00175 rab_sub_5 12 175 0.0000000
15 g284.t1 SMART SM00174 rho_sub_3 14 174 0.0000000
14 g284.t1 SMART SM00176 ran_sub_2 17 212 0.0000005
9 g284.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 7 185 0.0000000
16 g284.t1 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 10 168 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

Pathway

  • This transcript belongs to the following pathways

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