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.t13 TSS g1674.t13 12384437 12384437
chr_3 g1674 g1674.t13 isoform g1674.t13 12384566 12387219
chr_3 g1674 g1674.t13 exon g1674.t13.exon1 12384566 12384588
chr_3 g1674 g1674.t13 cds g1674.t13.CDS1 12384566 12384588
chr_3 g1674 g1674.t13 exon g1674.t13.exon2 12385403 12385568
chr_3 g1674 g1674.t13 cds g1674.t13.CDS2 12385403 12385568
chr_3 g1674 g1674.t13 exon g1674.t13.exon3 12385636 12385660
chr_3 g1674 g1674.t13 cds g1674.t13.CDS3 12385636 12385660
chr_3 g1674 g1674.t13 exon g1674.t13.exon4 12385719 12385924
chr_3 g1674 g1674.t13 cds g1674.t13.CDS4 12385719 12385924
chr_3 g1674 g1674.t13 exon g1674.t13.exon5 12385995 12386054
chr_3 g1674 g1674.t13 cds g1674.t13.CDS5 12385995 12386054
chr_3 g1674 g1674.t13 exon g1674.t13.exon6 12386180 12387219
chr_3 g1674 g1674.t13 cds g1674.t13.CDS6 12386180 12386242
chr_3 g1674 g1674.t13 TTS g1674.t13 12387182 12387182

Sequences

>g1674.t13 Gene=g1674 Length=1520
ATGTCGGCAATGTCACCTGAATATGATTATTTGTTCAAATTGCTTTTGATTGGTGACTCA
GGTGTTGGAAAATCGTGCTTATTGTTAAGATTTGCAGATGACACCTACACAGAAAGCTAT
ATTAGTACTATTGGTGTTGACTTTAAAATCAGAACAATTGAATTGGATGGAAAGACCATA
AAACTTCAGATTTGGGATACAGCGGGTCAAGAGAGATTTCGTACAATTACTTCCAGTTAT
TATCGTGGAGCGCATGGTATAATTGTAGTCTATGACTGCACGGATCAAGAGTCATTTAAT
AATGTGAAACAATGGCTTGAGGAAATTGAGCGTTATGCATGTGAAAATGTAAATAAACTT
TTGGTAGGCAACAAATGTGATCTTACGACAAAGAAAGTCGTAGATACCACGACCGCAACG
GAATATGCCAATCAACTTGGAATACCATTCCTTGAAACATCAGCGAAAAATGCAACAAAT
TGGATGTTGTTAAATATTCATCCTCTCATAATTATTTTATTCCTCATACATCTACCAACC
TAATTTCTGATCGTCCCTCCTTTTTTTTTCATAAACATGCATGCATCTTCCTTCGTTTCT
CCTCTCTAATTCTCTTTTTCCTCATCTATTCTCAAATTTTGTTTTGTGTTTTTGTATTCT
AATTATTAGAATCATACATATATGCATAATTATAATTTTTTCCTCGAAGATGTGCACATT
TTTATGCGATATATAGATGAAAAGTGTTATCGTCTCTATGTGTATGTGGTAAAGAAAAAG
GTGATGAAAAAGTTGAAGATGAGATAAAAATTCATGCATGAACCAAAATTTAATAATCGA
GAACATTGTATTTTCTAAATACTTATATTAAAGAAAATTTCCTTTTCCTTCAACACACCA
TACACATAAAATTGTCTCTTTCTACTTTTATGAGTTGAGATGAAATTTCATACGAAGAAA
TTACTTTGTATTTTTGTCGATTTATATTTCGTCTGTCTATTAAGCCGATTAAATATTTGT
ATCTAAATGAATTGAATGAATGATGATTTTATTTAGTTTAGATTTTGGATTTTTTGTTCT
TTCTGTTTTCCTGCACACACACACACATACCAATCAGCAGCAAAAACCATAATTAAACTA
TCTACATATAAAAATATTTAATATTAAACAACACAAAAAACCAATGGTTTAAAATGATGG
TGAAGAATTTTTTTGAATAAAAAAGAAACAATCCTTTTTTAAGGCGTTAGGCAAAGTTAA
ATATCTTTAATTACAGAAAAATGATTAGACAGCAACTGACGCGAATTATTAAAGTATAAA
AAATGATTCCAATAAAAAAATAAATTTATATTATGGAGCATAAATAAATTAATTAATGCT
TAGCGATTTATCAAAAATAAGTTTTATGTTTTAAAATATCTTCTCGCTTTGGTTTCTTTT
ACTCTCATTGTATAGACAATTTTTTTCTCCAAAAAAAATAATAAAAAAAATATTTGAAAA
AATTGCTAGAATGTCTTGTG

>g1674.t13 Gene=g1674 Length=180
MSAMSPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTI
KLQIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQESFNNVKQWLEEIERYACENVNKL
LVGNKCDLTTKKVVDTTTATEYANQLGIPFLETSAKNATNWMLLNIHPLIIILFLIHLPT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g1674.t13 CDD cd01869 Rab1_Ypt1 10 160 3.26879E-114
10 g1674.t13 Gene3D G3DSA:3.40.50.300 - 1 165 1.9E-68
2 g1674.t13 PANTHER PTHR47977 LD21953P-RELATED 8 160 1.8E-111
3 g1674.t13 PANTHER PTHR47977:SF6 RAS-RELATED PROTEIN RABD2A-LIKE 8 160 1.8E-111
4 g1674.t13 PRINTS PR00449 Transforming protein P21 ras signature 12 33 4.2E-39
7 g1674.t13 PRINTS PR00449 Transforming protein P21 ras signature 35 51 4.2E-39
8 g1674.t13 PRINTS PR00449 Transforming protein P21 ras signature 53 75 4.2E-39
6 g1674.t13 PRINTS PR00449 Transforming protein P21 ras signature 115 128 4.2E-39
5 g1674.t13 PRINTS PR00449 Transforming protein P21 ras signature 150 172 4.2E-39
1 g1674.t13 Pfam PF00071 Ras family 13 160 7.0E-62
11 g1674.t13 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 160 -
13 g1674.t13 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 161 178 -
12 g1674.t13 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 179 180 -
21 g1674.t13 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 7 180 34.609
16 g1674.t13 SMART SM00177 arf_sub_2 2 170 0.0064
15 g1674.t13 SMART SM00173 ras_sub_4 9 175 6.5E-24
17 g1674.t13 SMART SM00175 rab_sub_5 12 170 5.9E-90
19 g1674.t13 SMART SM00174 rho_sub_3 14 165 1.8E-13
18 g1674.t13 SMART SM00176 ran_sub_2 17 180 0.0028
9 g1674.t13 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 7 162 1.79E-62
20 g1674.t13 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 10 161 4.4E-34

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