Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t6 isoform g5596.t6 10449252 10452059
chr_2 g5596 g5596.t6 exon g5596.t6.exon1 10449252 10449411
chr_2 g5596 g5596.t6 TSS g5596.t6 10449274 10449274
chr_2 g5596 g5596.t6 exon g5596.t6.exon2 10450750 10450991
chr_2 g5596 g5596.t6 cds g5596.t6.CDS1 10450757 10450991
chr_2 g5596 g5596.t6 exon g5596.t6.exon3 10451145 10451191
chr_2 g5596 g5596.t6 cds g5596.t6.CDS2 10451145 10451191
chr_2 g5596 g5596.t6 exon g5596.t6.exon4 10451390 10451515
chr_2 g5596 g5596.t6 cds g5596.t6.CDS3 10451390 10451515
chr_2 g5596 g5596.t6 exon g5596.t6.exon5 10451581 10451749
chr_2 g5596 g5596.t6 cds g5596.t6.CDS4 10451581 10451749
chr_2 g5596 g5596.t6 exon g5596.t6.exon6 10451808 10451929
chr_2 g5596 g5596.t6 cds g5596.t6.CDS5 10451808 10451908
chr_2 g5596 g5596.t6 exon g5596.t6.exon7 10451989 10452059
chr_2 g5596 g5596.t6 TTS g5596.t6 10452771 10452771

Sequences

>g5596.t6 Gene=g5596 Length=937
CTTCTTGCTCACTCTCTAAATTTGAGTGATTGAATTTTTATAATAAAAGAAGATCCAAGT
TGAAAATTTGTCGACAATTTTAGTAAAAAATATTGAATTTTAAGCCAAGTAAAGTTGATT
ATTGTGTGTATTAAGACATCTTTAAAGTGAATAAAATAAAATAAATTATGGCAAATAATC
AACGTGGAGGAGGAATTCAACGTCCAAATGGTTCAACACAGAGCAAAATTTGCCAATTTA
AGCTGGTACTTTTGGGCGAATCGGCTGTTGGAAAATCATCACTCGTGCTAAGATTTGTCA
AGGGTCAATTTCATGAATATCAAGAGAGTACCATTGGAGCCGCTTTTCTTACTCAGACCG
TGCACATCGACGAGACTGCAGTCAAATTTGAAATTTGGATAATTATCTTTCTTTCTATTC
ACGGATCAAATATACGATACAGCTGGAAAGAACGTTATCATAGTTTAGCTCCAATGTATT
ATCGAGGTGCTCAGGCGGCTATTGTCGTGTATGACATTCAAAATCAGGACAGTTTTTCTC
GTGCTCAGACGTGGGTCAAAGAACTTCAACGACAGGCATCGCCAAATATCGTTATAGCCT
TGGCTGGCAATAAAGCGGATCTTGCAGCAAGTCGAGCTGTTGACTATGAAGAAGCAAAAC
AATATGCTGACGAAAACGGATTACTATTCATGGAAACTTCGGCAAAGACAGCAGTCAATG
TGAATGAGATATTTTTAGCAATAGCAAAAAAACTTCCCAAGAACGAAGGTACTGGGCAGC
AAACAAATATACGTCCGCAAGCGGGTGAAACGAATAGAACTTCAGGGAATTGCTGTAATA
AGTGATCACATGTTCTGGCATCGAAGATCAGTGGAAGTCAGAAAAAAAATTCTATTATTG
TCTTTTTTATTACTTTATAGAACAAAAAGAAATTTAA

>g5596.t6 Gene=g5596 Length=225
MANNQRGGGIQRPNGSTQSKICQFKLVLLGESAVGKSSLVLRFVKGQFHEYQESTIGAAF
LTQTVHIDETAVKFEIWIIIFLSIHGSNIRYSWKERYHSLAPMYYRGAQAAIVVYDIQNQ
DSFSRAQTWVKELQRQASPNIVIALAGNKADLAASRAVDYEEAKQYADENGLLFMETSAK
TAVNVNEIFLAIAKKLPKNEGTGQQTNIRPQAGETNRTSGNCCNK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g5596.t6 CDD cd01860 Rab5_related 23 197 1.74951E-112
10 g5596.t6 Gene3D G3DSA:3.40.50.300 - 18 223 9.4E-59
15 g5596.t6 MobiDBLite mobidb-lite consensus disorder prediction 200 225 -
3 g5596.t6 PANTHER PTHR24073:SF366 RAS-RELATED PROTEIN RAB-5C 8 206 6.5E-97
4 g5596.t6 PANTHER PTHR24073 DRAB5-RELATED 8 206 6.5E-97
8 g5596.t6 PRINTS PR00449 Transforming protein P21 ras signature 24 45 3.9E-28
6 g5596.t6 PRINTS PR00449 Transforming protein P21 ras signature 47 63 3.9E-28
7 g5596.t6 PRINTS PR00449 Transforming protein P21 ras signature 139 152 3.9E-28
5 g5596.t6 PRINTS PR00449 Transforming protein P21 ras signature 174 196 3.9E-28
1 g5596.t6 Pfam PF00071 Ras family 25 77 2.6E-15
2 g5596.t6 Pfam PF00071 Ras family 94 196 1.1E-33
17 g5596.t6 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 17 225 31.949
12 g5596.t6 SMART SM00173 ras_sub_4 21 199 6.2E-16
13 g5596.t6 SMART SM00175 rab_sub_5 24 199 1.0E-70
14 g5596.t6 SMART SM00174 rho_sub_3 26 198 8.2E-6
9 g5596.t6 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 23 204 2.97E-46
16 g5596.t6 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 24 189 6.6E-18

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5596/g5596.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5596.t6.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

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