Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t3 TTS g284.t3 2412808 2412808
chr_3 g284 g284.t3 isoform g284.t3 2413579 2415103
chr_3 g284 g284.t3 exon g284.t3.exon1 2413579 2414490
chr_3 g284 g284.t3 cds g284.t3.CDS1 2414357 2414490
chr_3 g284 g284.t3 exon g284.t3.exon2 2414572 2414884
chr_3 g284 g284.t3 cds g284.t3.CDS2 2414572 2414725
chr_3 g284 g284.t3 exon g284.t3.exon3 2414953 2415103
chr_3 g284 g284.t3 TSS g284.t3 2415508 2415508

Sequences

>g284.t3 Gene=g284 Length=1376
AATTGGAGATTCAGGCGTTGGAAAGTCGAATCTTCTTTCGCGATTCACACGTAATGAATT
CAATTTAGAATCGAAATCTACAATTGGAGTCGAATTTGCAACTCGTAGTATTGTTGTGGA
TAATAAAACTATCAAAGCTCAAATTTGGGATACTGCTGGTCAAGAAAGATATCGAGCGAT
TACATCTGCTTATTACCGTGGTGCTGTTGGTGCTCTTTTGGTTTATGATATTGCTAAACA
TCTCACATATGAGAATGTAGAGAGATGGCTTCGTGAATTGCGTGATCATGCAGATCAAAA
TATCGTGATAATGTTGGTTGGTAACAAGAGCGATTTGAGGCATTTGCGTGCTGTGCCAAC
GGATGAGGCAAAGACTTTTGCTGAACGTAATGGTCTCAGTTTCATCGAAACATCAGCACT
TGATTCAACAAATGTGGAAACGGCATTTCAAAATATACTCACAGAAATTTACCGAATCGT
CTCGCAAAAACAAATTCGCGATCCACCAGAAGGAGATGTGATTCGTCCATCGAATGTAGA
GCCGATTGATGTTAAACCGACAGTAACATCAGAAGTTAGAAAGCAATGTTGTCAGTGAGC
CAGTGATTCGCTTGTGTTTTTATTTCCATCATGTAATGCAATTATATATGCATTCAAATT
ATGAAAGCCCGAGAAAGAAAAACAATTTTCCATTTTATAATTTTCCTGCAAACGCTTCCC
TACTTTCCTTACATAAATCATTTACTTCATCATGCGATGAAATTTTTTTATAATGAATAT
TTTTCCAATATTCCCTTCTCATATTGAAGAATATAAATTTTTTTCATTGAAGAGAATTTG
ATTGTTACAATTATTACCTATTCCTCGCATATTTAATTGTGTCATAATAATCAATTTTGA
ATTCCTTAATTTTTTAATTTGTATTATTCTATGTCCTATTTCTTTATCCTTCATCCCATT
CCTTCTTTTCACTCGCATGCAAAACACACATCAAATTTGTTTAAGGTAAAATGAATATTA
ATAAAAAAGAATTAATATTAGAGCGCGATAATAAAAAAAAGGCTGTAGTTCAGTTATGTG
CTACTTATTCTCACTCTCTGTCTCTTGATGAATAAAAATGTTTGTTAAATTGATGCGCTT
CTTTGAAAAATTATTTGTATCTATATCTAAATCAAATAAACACATGCATATTCTCCATAA
GTTAATCAAATTAAACAAGAGAAAAAAATCGATTTTCCCATTGATAAACATTTATTTTCT
AAAGGACTAAATAAAAAAAGAATGAGTTTAAATTTGCTAAATGTATTAACTTTTCTTTTC
TTTCTTTTCTCGCACATATACACACATACATGCATTGGTAAACAAACGAAAAAAAG

>g284.t3 Gene=g284 Length=95
MLVGNKSDLRHLRAVPTDEAKTFAERNGLSFIETSALDSTNVETAFQNILTEIYRIVSQK
QIRDPPEGDVIRPSNVEPIDVKPTVTSEVRKQCCQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g284.t3 Gene3D G3DSA:3.40.50.300 - 1 70 0.000000
2 g284.t3 PANTHER PTHR47979:SF49 RAS-RELATED PROTEIN RAB-11A 1 95 0.000000
3 g284.t3 PANTHER PTHR47979 DRAB11-RELATED 1 95 0.000000
1 g284.t3 Pfam PF00071 Ras family 1 54 0.000000
7 g284.t3 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 1 94 12.148000
5 g284.t3 SMART SM00175 rab_sub_5 1 56 0.000036
4 g284.t3 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 1 67 0.000000

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