Gene loci information

Transcript annotation

  • This transcript has been annotated as Ras-related protein Rab-1A.

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_3 g1674 g1674.t1 TSS g1674.t1 12384437 12384437
chr_3 g1674 g1674.t1 isoform g1674.t1 12384566 12386192
chr_3 g1674 g1674.t1 exon g1674.t1.exon1 12384566 12384588
chr_3 g1674 g1674.t1 cds g1674.t1.CDS1 12384566 12384588
chr_3 g1674 g1674.t1 exon g1674.t1.exon2 12385403 12385568
chr_3 g1674 g1674.t1 cds g1674.t1.CDS2 12385403 12385568
chr_3 g1674 g1674.t1 exon g1674.t1.exon3 12385636 12385660
chr_3 g1674 g1674.t1 cds g1674.t1.CDS3 12385636 12385660
chr_3 g1674 g1674.t1 exon g1674.t1.exon4 12385719 12385924
chr_3 g1674 g1674.t1 cds g1674.t1.CDS4 12385719 12385924
chr_3 g1674 g1674.t1 exon g1674.t1.exon5 12385995 12386192
chr_3 g1674 g1674.t1 cds g1674.t1.CDS5 12385995 12386192
chr_3 g1674 g1674.t1 TTS g1674.t1 12386728 12386728

Sequences

>g1674.t1 Gene=g1674 Length=618
ATGTCGGCAATGTCACCTGAATATGATTATTTGTTCAAATTGCTTTTGATTGGTGACTCA
GGTGTTGGAAAATCGTGCTTATTGTTAAGATTTGCAGATGACACCTACACAGAAAGCTAT
ATTAGTACTATTGGTGTTGACTTTAAAATCAGAACAATTGAATTGGATGGAAAGACCATA
AAACTTCAGATTTGGGATACAGCGGGTCAAGAGAGATTTCGTACAATTACTTCCAGTTAT
TATCGTGGAGCGCATGGTATAATTGTAGTCTATGACTGCACGGATCAAGAGTCATTTAAT
AATGTGAAACAATGGCTTGAGGAAATTGAGCGTTATGCATGTGAAAATGTAAATAAACTT
TTGGTAGGCAACAAATGTGATCTTACGACAAAGAAAGTCGTAGATACCACGACCGCAACG
GAATATGCCAATCAACTTGGAATACCATTCCTTGAAACATCAGCGAAAAATGCAACAAAT
GTTGAGCAGGCCTTTATGACGATGGCAGCCGAAATTAAAAATCGCGTTGGACCACCATCA
AGTGCAACAGATACTGCGAGCAAAGTTAAAATCGATACTGGACGTCCTGTTGAAGGAAAT
AAGAGTGGATGTTGTTAA

>g1674.t1 Gene=g1674 Length=205
MSAMSPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTI
KLQIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQESFNNVKQWLEEIERYACENVNKL
LVGNKCDLTTKKVVDTTTATEYANQLGIPFLETSAKNATNVEQAFMTMAAEIKNRVGPPS
SATDTASKVKIDTGRPVEGNKSGCC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g1674.t1 CDD cd01869 Rab1_Ypt1 10 175 2.75473E-126
10 g1674.t1 Gene3D G3DSA:3.40.50.300 - 5 205 4.7E-74
17 g1674.t1 MobiDBLite mobidb-lite consensus disorder prediction 176 205 -
2 g1674.t1 PANTHER PTHR47977 LD21953P-RELATED 8 205 1.0E-123
3 g1674.t1 PANTHER PTHR47977:SF6 RAS-RELATED PROTEIN RABD2A-LIKE 8 205 1.0E-123
4 g1674.t1 PRINTS PR00449 Transforming protein P21 ras signature 12 33 3.1E-48
7 g1674.t1 PRINTS PR00449 Transforming protein P21 ras signature 35 51 3.1E-48
8 g1674.t1 PRINTS PR00449 Transforming protein P21 ras signature 53 75 3.1E-48
6 g1674.t1 PRINTS PR00449 Transforming protein P21 ras signature 115 128 3.1E-48
5 g1674.t1 PRINTS PR00449 Transforming protein P21 ras signature 150 172 3.1E-48
1 g1674.t1 Pfam PF00071 Ras family 13 173 2.5E-66
19 g1674.t1 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 7 205 38.381
13 g1674.t1 SMART SM00177 arf_sub_2 2 176 0.0012
12 g1674.t1 SMART SM00173 ras_sub_4 9 175 8.9E-36
14 g1674.t1 SMART SM00175 rab_sub_5 12 175 8.5E-105
16 g1674.t1 SMART SM00174 rho_sub_3 14 173 7.7E-17
15 g1674.t1 SMART SM00176 ran_sub_2 17 205 2.1E-6
9 g1674.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 7 180 3.0E-67
18 g1674.t1 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 10 168 8.6E-36

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

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