Gene loci information

Transcript annotation

  • This transcript has been annotated as Ras-related protein Rab-39B.

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 g13385 g13385.t1 TSS g13385.t1 29622058 29622058
chr_1 g13385 g13385.t1 isoform g13385.t1 29622275 29623481
chr_1 g13385 g13385.t1 exon g13385.t1.exon1 29622275 29622379
chr_1 g13385 g13385.t1 cds g13385.t1.CDS1 29622275 29622379
chr_1 g13385 g13385.t1 exon g13385.t1.exon2 29622716 29622793
chr_1 g13385 g13385.t1 cds g13385.t1.CDS2 29622716 29622793
chr_1 g13385 g13385.t1 exon g13385.t1.exon3 29622861 29622881
chr_1 g13385 g13385.t1 cds g13385.t1.CDS3 29622861 29622881
chr_1 g13385 g13385.t1 exon g13385.t1.exon4 29623026 29623481
chr_1 g13385 g13385.t1 cds g13385.t1.CDS4 29623026 29623481
chr_1 g13385 g13385.t1 TTS g13385.t1 29623602 29623602

Sequences

>g13385.t1 Gene=g13385 Length=660
ATGGATGTTTCATTTGATTATCAATTTAGATTGATATTAATCGGTGACAGTACAGTGGGA
AAGTCAAGTTTATTGAAATATTTCACAGATGGAAGATTTGCAGAGATCAGTGATCCAACG
ATCGGTGTCGATTTTTTTGCTCACATGATGGAGGTCAAGGACGGCACAAGAATTAAATTG
CAGCTTTGGGATACAGCTGGCCAGGAAAGATTTCGATCTATTACAAAATCCTACTATAGA
AATTCAGTTGGTGTGCTTTTGGTTTATGACATATGCAATCATGCAAGTTTTGAACATATT
CCTCTATGGCTTTTGGAAGCTAAACGACACATCGAACCTTATCATCCTGTATTTGCGCTT
GTGGGTACAAAATTAGATTTAGTAACTAATGGTGAGAACAGAGAAGTGAGTGTTGAGGAA
GCAAAAAAATTTGCAGAACAGCATGCATTGATCTTTGTTGAAACATCTGCACGAACTGGG
ATAAACGTGAGAGAGTCATTTTCATTAGTCACACAAGAAATTTACAACAGAATCAAAAGC
GGTGAATATAAAATAGAAAACGGTTGGGATGGCATTAAAACAGGATTTCCACGATCTAAT
TCATTGGATTTTAATAATTTAGCAATGGCTGAACCAGTTCAAAAAAATTCATGCTGTTGA

>g13385.t1 Gene=g13385 Length=219
MDVSFDYQFRLILIGDSTVGKSSLLKYFTDGRFAEISDPTIGVDFFAHMMEVKDGTRIKL
QLWDTAGQERFRSITKSYYRNSVGVLLVYDICNHASFEHIPLWLLEAKRHIEPYHPVFAL
VGTKLDLVTNGENREVSVEEAKKFAEQHALIFVETSARTGINVRESFSLVTQEIYNRIKS
GEYKIENGWDGIKTGFPRSNSLDFNNLAMAEPVQKNSCC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g13385.t1 CDD cd04111 Rab39 7 219 0.0000
10 g13385.t1 Gene3D G3DSA:3.40.50.300 - 2 193 0.0000
2 g13385.t1 PANTHER PTHR47979:SF53 FI07418P 3 217 0.0000
3 g13385.t1 PANTHER PTHR47979 DRAB11-RELATED 3 217 0.0000
4 g13385.t1 PRINTS PR00449 Transforming protein P21 ras signature 9 30 0.0000
8 g13385.t1 PRINTS PR00449 Transforming protein P21 ras signature 32 48 0.0000
7 g13385.t1 PRINTS PR00449 Transforming protein P21 ras signature 51 73 0.0000
6 g13385.t1 PRINTS PR00449 Transforming protein P21 ras signature 114 127 0.0000
5 g13385.t1 PRINTS PR00449 Transforming protein P21 ras signature 152 174 0.0000
1 g13385.t1 Pfam PF00071 Ras family 10 175 0.0000
17 g13385.t1 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 4 219 32.6670
12 g13385.t1 SMART SM00173 ras_sub_4 6 177 0.0000
13 g13385.t1 SMART SM00175 rab_sub_5 9 177 0.0000
15 g13385.t1 SMART SM00174 rho_sub_3 11 177 0.0000
14 g13385.t1 SMART SM00176 ran_sub_2 14 218 0.0042
9 g13385.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 6 190 0.0000
16 g13385.t1 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 7 170 0.0000

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:0032482 Rab protein signal transduction BP
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