Gene loci information

Transcript annotation

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

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.t5 isoform g5596.t5 10449252 10452059
chr_2 g5596 g5596.t5 exon g5596.t5.exon1 10449252 10449411
chr_2 g5596 g5596.t5 TSS g5596.t5 10449274 10449274
chr_2 g5596 g5596.t5 exon g5596.t5.exon2 10450750 10450991
chr_2 g5596 g5596.t5 exon g5596.t5.exon3 10451390 10451515
chr_2 g5596 g5596.t5 cds g5596.t5.CDS1 10451414 10451515
chr_2 g5596 g5596.t5 exon g5596.t5.exon4 10451581 10451749
chr_2 g5596 g5596.t5 cds g5596.t5.CDS2 10451581 10451749
chr_2 g5596 g5596.t5 exon g5596.t5.exon5 10451808 10451929
chr_2 g5596 g5596.t5 cds g5596.t5.CDS3 10451808 10451908
chr_2 g5596 g5596.t5 exon g5596.t5.exon6 10451994 10452059
chr_2 g5596 g5596.t5 TTS g5596.t5 10452771 10452771

Sequences

>g5596.t5 Gene=g5596 Length=885
CTTCTTGCTCACTCTCTAAATTTGAGTGATTGAATTTTTATAATAAAAGAAGATCCAAGT
TGAAAATTTGTCGACAATTTTAGTAAAAAATATTGAATTTTAAGCCAAGTAAAGTTGATT
ATTGTGTGTATTAAGACATCTTTAAAGTGAATAAAATAAAATAAATTATGGCAAATAATC
AACGTGGAGGAGGAATTCAACGTCCAAATGGTTCAACACAGAGCAAAATTTGCCAATTTA
AGCTGGTACTTTTGGGCGAATCGGCTGTTGGAAAATCATCACTCGTGCTAAGATTTGTCA
AGGGTCAATTTCATGAATATCAAGAGAGTACCATTGGAGCCGCTTTTCTTACTCAGACCG
TGCACATCGACGAGACTGCAGTCAAATTTGAAATTTGGATAAGAACGTTATCATAGTTTA
GCTCCAATGTATTATCGAGGTGCTCAGGCGGCTATTGTCGTGTATGACATTCAAAATCAG
GACAGTTTTTCTCGTGCTCAGACGTGGGTCAAAGAACTTCAACGACAGGCATCGCCAAAT
ATCGTTATAGCCTTGGCTGGCAATAAAGCGGATCTTGCAGCAAGTCGAGCTGTTGACTAT
GAAGAAGCAAAACAATATGCTGACGAAAACGGATTACTATTCATGGAAACTTCGGCAAAG
ACAGCAGTCAATGTGAATGAGATATTTTTAGCAATAGCAAAAAAACTTCCCAAGAACGAA
GGTACTGGGCAGCAAACAAATATACGTCCGCAAGCGGGTGAAACGAATAGAACTTCAGGG
AATTGCTGTAATAAGTGATCACATGTTCTGGCATCGAAGTGGAAGTCAGAAAAAAAATTC
TATTATTGTCTTTTTTATTACTTTATAGAACAAAAAGAAATTTAA

>g5596.t5 Gene=g5596 Length=123
MYYRGAQAAIVVYDIQNQDSFSRAQTWVKELQRQASPNIVIALAGNKADLAASRAVDYEE
AKQYADENGLLFMETSAKTAVNVNEIFLAIAKKLPKNEGTGQQTNIRPQAGETNRTSGNC
CNK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g5596.t5 Gene3D G3DSA:3.40.50.300 - 1 121 9.4E-36
7 g5596.t5 MobiDBLite mobidb-lite consensus disorder prediction 97 123 -
2 g5596.t5 PANTHER PTHR24073:SF366 RAS-RELATED PROTEIN RAB-5C 1 105 3.4E-51
3 g5596.t5 PANTHER PTHR24073 DRAB5-RELATED 1 105 3.4E-51
1 g5596.t5 Pfam PF00071 Ras family 1 94 1.4E-30
9 g5596.t5 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 1 123 21.275
6 g5596.t5 SMART SM00175 rab_sub_5 1 97 2.0E-20
5 g5596.t5 SMART SM00173 ras_sub_4 2 97 2.4E-5
4 g5596.t5 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 1 102 4.56E-29

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5596/g5596.t5; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5596.t5.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