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.t8 TSS g1674.t8 12384437 12384437
chr_3 g1674 g1674.t8 isoform g1674.t8 12384566 12386735
chr_3 g1674 g1674.t8 exon g1674.t8.exon1 12384566 12384588
chr_3 g1674 g1674.t8 cds g1674.t8.CDS1 12384566 12384588
chr_3 g1674 g1674.t8 exon g1674.t8.exon2 12385403 12385590
chr_3 g1674 g1674.t8 cds g1674.t8.CDS2 12385403 12385590
chr_3 g1674 g1674.t8 exon g1674.t8.exon3 12385719 12385924
chr_3 g1674 g1674.t8 cds g1674.t8.CDS3 12385719 12385924
chr_3 g1674 g1674.t8 exon g1674.t8.exon4 12385995 12386735
chr_3 g1674 g1674.t8 cds g1674.t8.CDS4 12385995 12386192
chr_3 g1674 g1674.t8 TTS g1674.t8 12386728 12386728

Sequences

>g1674.t8 Gene=g1674 Length=1158
ATGTCGGCAATGTCACCTGAATATGATTATTTGTTCAAATTGCTTTTGATTGGTGACTCA
GGTGTTGGAAAATCGTGCTTATTGTTAAGATTTGCAGATGACACCTACACAGAAAGCTAT
ATTAGTACTATTGGTGTTGACTTTAAAATCAGAACAATTGAATTGGATGGAAAGACCATA
AAACTTCAGGTAATTATTTCTAACAACAATAGATTTCGTACAATTACTTCCAGTTATTAT
CGTGGAGCGCATGGTATAATTGTAGTCTATGACTGCACGGATCAAGAGTCATTTAATAAT
GTGAAACAATGGCTTGAGGAAATTGAGCGTTATGCATGTGAAAATGTAAATAAACTTTTG
GTAGGCAACAAATGTGATCTTACGACAAAGAAAGTCGTAGATACCACGACCGCAACGGAA
TATGCCAATCAACTTGGAATACCATTCCTTGAAACATCAGCGAAAAATGCAACAAATGTT
GAGCAGGCCTTTATGACGATGGCAGCCGAAATTAAAAATCGCGTTGGACCACCATCAAGT
GCAACAGATACTGCGAGCAAAGTTAAAATCGATACTGGACGTCCTGTTGAAGGAAATAAG
AGTGGATGTTGTTAAATATTCATCCTCTCATAATTATTTTATTCCTCATACATCTACCAA
CCTAATTTCTGATCGTCCCTCCTTTTTTTTTCATAAACATGCATGCATCTTCCTTCGTTT
CTCCTCTCTAATTCTCTTTTTCCTCATCTATTCTCAAATTTTGTTTTGTGTTTTTGTATT
CTAATTATTAGAATCATACATATATGCATAATTATAATTTTTTCCTCGAAGATGTGCACA
TTTTTATGCGATATATAGATGAAAAGTGTTATCGTCTCTATGTGTATGTGGTAAAGAAAA
AGGTGATGAAAAAGTTGAAGATGAGATAAAAATTCATGCATGAACCAAAATTTAATAATC
GAGAACATTGTATTTTCTAAATACTTATATTAAAGAAAATTTCCTTTTCCTTCAACACAC
CATACACATAAAATTGTCTCTTTCTACTTTTATGAGTTGAGATGAAATTTCATACGAAGA
AATTACTTTGTATTTTTGTCGATTTATATTTCGTCTGTCTATTAAGCCGATTAAATATTT
GTATCTAAATGAATTGAA

>g1674.t8 Gene=g1674 Length=204
MSAMSPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTI
KLQVIISNNNRFRTITSSYYRGAHGIIVVYDCTDQESFNNVKQWLEEIERYACENVNKLL
VGNKCDLTTKKVVDTTTATEYANQLGIPFLETSAKNATNVEQAFMTMAAEIKNRVGPPSS
ATDTASKVKIDTGRPVEGNKSGCC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g1674.t8 CDD cd01869 Rab1_Ypt1 10 174 3.92724E-114
9 g1674.t8 Gene3D G3DSA:3.40.50.300 - 5 204 9.7E-65
15 g1674.t8 MobiDBLite mobidb-lite consensus disorder prediction 175 204 -
2 g1674.t8 PANTHER PTHR47977 LD21953P-RELATED 8 204 5.7E-112
3 g1674.t8 PANTHER PTHR47977:SF6 RAS-RELATED PROTEIN RABD2A-LIKE 8 204 5.7E-112
4 g1674.t8 PRINTS PR00449 Transforming protein P21 ras signature 12 33 8.0E-35
5 g1674.t8 PRINTS PR00449 Transforming protein P21 ras signature 35 51 8.0E-35
6 g1674.t8 PRINTS PR00449 Transforming protein P21 ras signature 114 127 8.0E-35
7 g1674.t8 PRINTS PR00449 Transforming protein P21 ras signature 149 171 8.0E-35
1 g1674.t8 Pfam PF00071 Ras family 13 172 2.0E-55
17 g1674.t8 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 7 204 34.832
11 g1674.t8 SMART SM00173 ras_sub_4 9 174 5.3E-22
12 g1674.t8 SMART SM00175 rab_sub_5 12 174 2.0E-83
14 g1674.t8 SMART SM00174 rho_sub_3 14 172 1.2E-10
13 g1674.t8 SMART SM00176 ran_sub_2 17 204 0.0017
8 g1674.t8 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 7 179 2.72E-57
16 g1674.t8 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 10 167 1.7E-25

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