Gene loci information

Transcript annotation

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

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.t6 TSS g13385.t6 29622058 29622058
chr_1 g13385 g13385.t6 isoform g13385.t6 29622275 29623481
chr_1 g13385 g13385.t6 exon g13385.t6.exon1 29622275 29622379
chr_1 g13385 g13385.t6 cds g13385.t6.CDS1 29622363 29622379
chr_1 g13385 g13385.t6 exon g13385.t6.exon2 29622721 29622799
chr_1 g13385 g13385.t6 cds g13385.t6.CDS2 29622721 29622799
chr_1 g13385 g13385.t6 exon g13385.t6.exon3 29623026 29623481
chr_1 g13385 g13385.t6 cds g13385.t6.CDS3 29623026 29623481
chr_1 g13385 g13385.t6 TTS g13385.t6 29623602 29623602

Sequences

>g13385.t6 Gene=g13385 Length=640
ATGGATGTTTCATTTGATTATCAATTTAGATTGATATTAATCGGTGACAGTACAGTGGGA
AAGTCAAGTTTATTGAAATATTTCACAGATGGAAGATTTGCAGAGTGATCCAACGATCGG
TGTCGATTTTTTTGCTCACATGATGGAGGTCAAGGACGGCACAAGAATTAAATTGCAGGT
AGGAGAAAGATTTCGATCTATTACAAAATCCTACTATAGAAATTCAGTTGGTGTGCTTTT
GGTTTATGACATATGCAATCATGCAAGTTTTGAACATATTCCTCTATGGCTTTTGGAAGC
TAAACGACACATCGAACCTTATCATCCTGTATTTGCGCTTGTGGGTACAAAATTAGATTT
AGTAACTAATGGTGAGAACAGAGAAGTGAGTGTTGAGGAAGCAAAAAAATTTGCAGAACA
GCATGCATTGATCTTTGTTGAAACATCTGCACGAACTGGGATAAACGTGAGAGAGTCATT
TTCATTAGTCACACAAGAAATTTACAACAGAATCAAAAGCGGTGAATATAAAATAGAAAA
CGGTTGGGATGGCATTAAAACAGGATTTCCACGATCTAATTCATTGGATTTTAATAATTT
AGCAATGGCTGAACCAGTTCAAAAAAATTCATGCTGTTGA

>g13385.t6 Gene=g13385 Length=183
MEDLQSDPTIGVDFFAHMMEVKDGTRIKLQVGERFRSITKSYYRNSVGVLLVYDICNHAS
FEHIPLWLLEAKRHIEPYHPVFALVGTKLDLVTNGENREVSVEEAKKFAEQHALIFVETS
ARTGINVRESFSLVTQEIYNRIKSGEYKIENGWDGIKTGFPRSNSLDFNNLAMAEPVQKN
SCC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g13385.t6 Gene3D G3DSA:3.40.50.300 - 3 157 0.0000000
2 g13385.t6 PANTHER PTHR47979:SF53 FI07418P 5 181 0.0000000
3 g13385.t6 PANTHER PTHR47979 DRAB11-RELATED 5 181 0.0000000
6 g13385.t6 PRINTS PR00449 Transforming protein P21 ras signature 1 14 0.0000000
5 g13385.t6 PRINTS PR00449 Transforming protein P21 ras signature 78 91 0.0000000
4 g13385.t6 PRINTS PR00449 Transforming protein P21 ras signature 116 138 0.0000000
1 g13385.t6 Pfam PF00071 Ras family 5 139 0.0000000
12 g13385.t6 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 1 183 23.3350000
8 g13385.t6 SMART SM00173 ras_sub_4 1 141 0.0000022
9 g13385.t6 SMART SM00175 rab_sub_5 3 141 0.0000000
10 g13385.t6 SMART SM00174 rho_sub_3 10 141 0.0002100
7 g13385.t6 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 5 154 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. There were no conditions that were differentially expressed