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.t3 TSS g1674.t3 12384437 12384437
chr_3 g1674 g1674.t3 isoform g1674.t3 12384566 12386721
chr_3 g1674 g1674.t3 exon g1674.t3.exon1 12384566 12384588
chr_3 g1674 g1674.t3 cds g1674.t3.CDS1 12384566 12384588
chr_3 g1674 g1674.t3 exon g1674.t3.exon2 12385403 12385568
chr_3 g1674 g1674.t3 cds g1674.t3.CDS2 12385403 12385568
chr_3 g1674 g1674.t3 exon g1674.t3.exon3 12385706 12385924
chr_3 g1674 g1674.t3 cds g1674.t3.CDS3 12385706 12385924
chr_3 g1674 g1674.t3 exon g1674.t3.exon4 12385995 12386721
chr_3 g1674 g1674.t3 cds g1674.t3.CDS4 12385995 12386192
chr_3 g1674 g1674.t3 TTS g1674.t3 12386728 12386728

Sequences

>g1674.t3 Gene=g1674 Length=1135
ATGTCGGCAATGTCACCTGAATATGATTATTTGTTCAAATTGCTTTTGATTGGTGACTCA
GGTGTTGGAAAATCGTGCTTATTGTTAAGATTTGCAGATGACACCTACACAGAAAGCTAT
ATTAGTACTATTGGTGTTGACTTTAAAATCAGAACAATTGAATTGGATGGAAAGACCATA
AAACTTCAGTTAAAAATTTCAGGATTTCGTACAATTACTTCCAGTTATTATCGTGGAGCG
CATGGTATAATTGTAGTCTATGACTGCACGGATCAAGAGTCATTTAATAATGTGAAACAA
TGGCTTGAGGAAATTGAGCGTTATGCATGTGAAAATGTAAATAAACTTTTGGTAGGCAAC
AAATGTGATCTTACGACAAAGAAAGTCGTAGATACCACGACCGCAACGGAATATGCCAAT
CAACTTGGAATACCATTCCTTGAAACATCAGCGAAAAATGCAACAAATGTTGAGCAGGCC
TTTATGACGATGGCAGCCGAAATTAAAAATCGCGTTGGACCACCATCAAGTGCAACAGAT
ACTGCGAGCAAAGTTAAAATCGATACTGGACGTCCTGTTGAAGGAAATAAGAGTGGATGT
TGTTAAATATTCATCCTCTCATAATTATTTTATTCCTCATACATCTACCAACCTAATTTC
TGATCGTCCCTCCTTTTTTTTTCATAAACATGCATGCATCTTCCTTCGTTTCTCCTCTCT
AATTCTCTTTTTCCTCATCTATTCTCAAATTTTGTTTTGTGTTTTTGTATTCTAATTATT
AGAATCATACATATATGCATAATTATAATTTTTTCCTCGAAGATGTGCACATTTTTATGC
GATATATAGATGAAAAGTGTTATCGTCTCTATGTGTATGTGGTAAAGAAAAAGGTGATGA
AAAAGTTGAAGATGAGATAAAAATTCATGCATGAACCAAAATTTAATAATCGAGAACATT
GTATTTTCTAAATACTTATATTAAAGAAAATTTCCTTTTCCTTCAACACACCATACACAT
AAAATTGTCTCTTTCTACTTTTATGAGTTGAGATGAAATTTCATACGAAGAAATTACTTT
GTATTTTTGTCGATTTATATTTCGTCTGTCTATTAAGCCGATTAAATATTTGTAT

>g1674.t3 Gene=g1674 Length=201
MSAMSPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTI
KLQLKISGFRTITSSYYRGAHGIIVVYDCTDQESFNNVKQWLEEIERYACENVNKLLVGN
KCDLTTKKVVDTTTATEYANQLGIPFLETSAKNATNVEQAFMTMAAEIKNRVGPPSSATD
TASKVKIDTGRPVEGNKSGCC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g1674.t3 CDD cd01869 Rab1_Ypt1 10 171 8.47707E-113
10 g1674.t3 Gene3D G3DSA:3.40.50.300 - 5 201 3.1E-62
16 g1674.t3 MobiDBLite mobidb-lite consensus disorder prediction 172 201 -
2 g1674.t3 PANTHER PTHR47977 LD21953P-RELATED 8 201 1.4E-109
3 g1674.t3 PANTHER PTHR47977:SF6 RAS-RELATED PROTEIN RABD2A-LIKE 8 201 1.4E-109
4 g1674.t3 PRINTS PR00449 Transforming protein P21 ras signature 12 33 3.0E-36
5 g1674.t3 PRINTS PR00449 Transforming protein P21 ras signature 35 51 3.0E-36
6 g1674.t3 PRINTS PR00449 Transforming protein P21 ras signature 53 75 3.0E-36
7 g1674.t3 PRINTS PR00449 Transforming protein P21 ras signature 111 124 3.0E-36
8 g1674.t3 PRINTS PR00449 Transforming protein P21 ras signature 146 168 3.0E-36
1 g1674.t3 Pfam PF00071 Ras family 13 169 1.3E-53
18 g1674.t3 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 7 201 33.855
12 g1674.t3 SMART SM00173 ras_sub_4 9 171 1.3E-22
13 g1674.t3 SMART SM00175 rab_sub_5 12 171 2.8E-84
15 g1674.t3 SMART SM00174 rho_sub_3 14 169 5.8E-11
14 g1674.t3 SMART SM00176 ran_sub_2 17 201 0.0052
9 g1674.t3 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 7 176 2.81E-56
17 g1674.t3 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 10 164 5.2E-24

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