Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Ras-related protein Rab-5B.

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_2 g5596 g5596.t17 TSS g5596.t17 10449274 10449274
chr_2 g5596 g5596.t17 isoform g5596.t17 10449831 10452059
chr_2 g5596 g5596.t17 exon g5596.t17.exon1 10449831 10450138
chr_2 g5596 g5596.t17 exon g5596.t17.exon2 10450750 10450991
chr_2 g5596 g5596.t17 exon g5596.t17.exon3 10451390 10451515
chr_2 g5596 g5596.t17 cds g5596.t17.CDS1 10451414 10451515
chr_2 g5596 g5596.t17 exon g5596.t17.exon4 10451581 10451749
chr_2 g5596 g5596.t17 cds g5596.t17.CDS2 10451581 10451749
chr_2 g5596 g5596.t17 exon g5596.t17.exon5 10451822 10451929
chr_2 g5596 g5596.t17 cds g5596.t17.CDS3 10451822 10451871
chr_2 g5596 g5596.t17 exon g5596.t17.exon6 10451989 10452059
chr_2 g5596 g5596.t17 TTS g5596.t17 10452771 10452771

Sequences

>g5596.t17 Gene=g5596 Length=1024
AAGTGCGTAAATAACTTTATTGAGTGCGAGCACTTTAGATTGCAAGTTTGCAAGATTTAA
TGCGTCGTAAAAAAATCTTTATCATTTTTGTTTTGCTTCCTTTATTGAGTGTTCGAAAAA
GAGAACTCATTTCTATCATGTGAATTATTATAAATGTTCATCAAGTAAGTGAGAGAAGAA
AGAAATGAATGTTTAGCGAATAAAAAACTTGTACAAATATTTGTCGGATGTATGTCAATA
TGAGAAAAAAGAGCAGAAAACTGTGGAAATATAATATAAAAATTTCATTTATACTTAAGA
AAAACTAGATAAATTATGGCAAATAATCAACGTGGAGGAGGAATTCAACGTCCAAATGGT
TCAACACAGAGCAAAATTTGCCAATTTAAGCTGGTACTTTTGGGCGAATCGGCTGTTGGA
AAATCATCACTCGTGCTAAGATTTGTCAAGGGTCAATTTCATGAATATCAAGAGAGTACC
ATTGGAGCCGCTTTTCTTACTCAGACCGTGCACATCGACGAGACTGCAGTCAAATTTGAA
ATTTGGATAAGAACGTTATCATAGTTTAGCTCCAATGTATTATCGAGGTGCTCAGGCGGC
TATTGTCGTGTATGACATTCAAAATCAGGACAGTTTTTCTCGTGCTCAGACGTGGGTCAA
AGAACTTCAACGACAGGCATCGCCAAATATCGTTATAGCCTTGGCTGGCAATAAAGCGGA
TCTTGCAGCAAGTCGAGCTGTTGACTATGAAGAAGCAAAACAATATGCTGACGAAAACGG
ATTACTATTCATGGAAACTTCGGCAAAGACAGCAGTCAATGTGAATGAGATATTTTTAGC
AATAGAAGAACGAAGGTACTGGGCAGCAAACAAATATACGTCCGCAAGCGGGTGAAACGA
ATAGAACTTCAGGGAATTGCTGTAATAAGTGATCACATGTTCTGGCATCGAAGATCAGTG
GAAGTCAGAAAAAAAATTCTATTATTGTCTTTTTTATTACTTTATAGAACAAAAAGAAAT
TTAA

>g5596.t17 Gene=g5596 Length=106
MYYRGAQAAIVVYDIQNQDSFSRAQTWVKELQRQASPNIVIALAGNKADLAASRAVDYEE
AKQYADENGLLFMETSAKTAVNVNEIFLAIEERRYWAANKYTSASG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g5596.t17 Gene3D G3DSA:3.40.50.300 - 1 104 0.000000
2 g5596.t17 PANTHER PTHR24073:SF1129 RAS-RELATED PROTEIN RAB-5A 1 94 0.000000
3 g5596.t17 PANTHER PTHR24073 DRAB5-RELATED 1 94 0.000000
1 g5596.t17 Pfam PF00071 Ras family 1 91 0.000000
8 g5596.t17 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 1 106 19.724000
6 g5596.t17 SMART SM00175 rab_sub_5 1 97 0.000000
5 g5596.t17 SMART SM00173 ras_sub_4 2 95 0.000039
4 g5596.t17 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 1 94 0.000000

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5596/g5596.t17; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5596.t17.fa.iupred3.txt does not exist

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