Gene loci information

Transcript annotation

  • This transcript has been annotated as Ras-related protein Rab-35.

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 g11236 g11236.t4 TSS g11236.t4 14842856 14842856
chr_1 g11236 g11236.t4 isoform g11236.t4 14843314 14846675
chr_1 g11236 g11236.t4 exon g11236.t4.exon1 14843314 14843365
chr_1 g11236 g11236.t4 cds g11236.t4.CDS1 14843314 14843365
chr_1 g11236 g11236.t4 exon g11236.t4.exon2 14845575 14845711
chr_1 g11236 g11236.t4 cds g11236.t4.CDS2 14845575 14845711
chr_1 g11236 g11236.t4 exon g11236.t4.exon3 14845770 14845807
chr_1 g11236 g11236.t4 cds g11236.t4.CDS3 14845770 14845807
chr_1 g11236 g11236.t4 exon g11236.t4.exon4 14845914 14846042
chr_1 g11236 g11236.t4 cds g11236.t4.CDS4 14845914 14846042
chr_1 g11236 g11236.t4 exon g11236.t4.exon5 14846104 14846675
chr_1 g11236 g11236.t4 cds g11236.t4.CDS5 14846104 14846119
chr_1 g11236 g11236.t4 TTS g11236.t4 14847140 14847140

Sequences

>g11236.t4 Gene=g11236 Length=928
ATGGCAAGAGACTATGATCATTTATTTAAGTTACTGATAATAGGCGATAGCGGTGTCGGA
AAGTCATCATTACTCATACGGTTTAGCGACAATACTTTTAGCGGTAGCTACATTACAACA
ATCGGTGTTGATTTCAAAATACGAACAGTTGTCATCGGTGGTGAACGAGTAAAACTTCAG
ATTTGGGACACTGCTGGACAAGAGCGATTCAGAACAATAACAAACACATATTACAGAGGA
ACACACGGTGTGATTGTTGTGTACGATGTTACAAATGGCGAATCGTTTGCTAATGTAAAG
AGGTGGCTTCAAGAAATTGACTCTAATTGTGAAGTTGTAAATAAAGTGCTTGGTATTTGG
AAACAAAAATGATGATCCGCAGAGGAAGGTTGTTCTAACCGAAGACGCACAACGATTTGC
CGAGCAAATGGGAATACCATTATATGAGACATCCGCCAAAGATAATTTGAATGTAGAAGA
AATGTTCTTAGCAATAACGGAAAAAGTTCTGCGTCATAAAAAACAGACTCAGCGTCAACA
GAATGATCAGAACGATGATCGAATTAAAATAAATAATACAAGTGGCATTAAGAAGAAGAA
AAAATGTTGCTAGTGAAATTGATTCTTTTGTCTTCAACATACATTTAAACAATATAAACA
TATATTTTTATGAGAAAACGAGCAGCGAGAAGCAGAAAATAACTATTGGCATGCAAAGAT
GAGTGTGTGATTATCATATATGATATTTAATAGTAGTGATGAGCTAGCCGCCATACTGGG
TGGATGCATCATATTTCAAATGCAGCATTACAAACAAAAATTATCTCATACTTGATGACT
TTATTTCAATTTTTGCGACTGTAAACAATTTTTCCCCTGTGTTTGTCTATATACATTTAA
TAAATACTTTGATAATTGTTTAAAATTA

>g11236.t4 Gene=g11236 Length=123
MARDYDHLFKLLIIGDSGVGKSSLLIRFSDNTFSGSYITTIGVDFKIRTVVIGGERVKLQ
IWDTAGQERFRTITNTYYRGTHGVIVVYDVTNGESFANVKRWLQEIDSNCEVVNKVLGIW
KQK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g11236.t4 Gene3D G3DSA:3.40.50.300 - 2 121 0.0000000
2 g11236.t4 PANTHER PTHR47977 LD21953P-RELATED 1 118 0.0000000
3 g11236.t4 PANTHER PTHR47977:SF11 SI:DKEY-16L2.16 1 118 0.0000000
4 g11236.t4 PRINTS PR00449 Transforming protein P21 ras signature 9 30 0.0000000
6 g11236.t4 PRINTS PR00449 Transforming protein P21 ras signature 32 48 0.0000000
5 g11236.t4 PRINTS PR00449 Transforming protein P21 ras signature 50 72 0.0000000
1 g11236.t4 Pfam PF00071 Ras family 10 116 0.0000000
12 g11236.t4 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 4 123 26.2270000
9 g11236.t4 SMART SM00173 ras_sub_4 6 123 0.0000020
10 g11236.t4 SMART SM00175 rab_sub_5 9 123 0.0000000
11 g11236.t4 SMART SM00174 rho_sub_3 11 123 0.0000006
7 g11236.t4 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 4 115 0.0000000
13 g11236.t4 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 9 116 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.

Raw TPM values