Gene loci information

Transcript annotation

  • This transcript has been annotated as GTP-binding nuclear protein Ran.

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 g960 g960.t4 isoform g960.t4 7070813 7072241
chr_3 g960 g960.t4 exon g960.t4.exon1 7070813 7070869
chr_3 g960 g960.t4 TSS g960.t4 7070835 7070835
chr_3 g960 g960.t4 exon g960.t4.exon2 7071498 7071728
chr_3 g960 g960.t4 cds g960.t4.CDS1 7071533 7071728
chr_3 g960 g960.t4 exon g960.t4.exon3 7071790 7072241
chr_3 g960 g960.t4 cds g960.t4.CDS2 7071790 7072241
chr_3 g960 g960.t4 TTS g960.t4 7072508 7072508

Sequences

>g960.t4 Gene=g960 Length=740
AGTCCCCTGTATACACTTACATTAGTATTAGTAAAAATTTCTTTGCGAGCAAAAACAAGA
GGAATTTTAGTAAATTCAACTGAAAAAGTACAATGGCAGCAGAACAAGATATTCCTACTT
TCAAATGCGTTTTAGTTGGAGATGGTGGTACTGGTAAGACAACATTTGTTAAACGTCATA
TGACTGGTGAATTTGAGAAGAAATACGTTGCAACTCTTGGTGTTGAAGTACATCCGCTAG
TCTTTCATACTAATCGTGGCGCCATTCGTTTTAATGTCTGGGATACAGCTGGTCAAGAGA
AATTCGGGGGTCTTCGTGATGGTTATTATATTCAAGGGCAATGTGCTATTGTCATGTTTG
ATGTCACATCTCGAATTACTTACAAGAATGTACCAAATTGGCATCGTGATTTAGTTCGTG
TGTGTGAAAATATTCCAATTGTGTTATGTGGAAACAAGGTAGACATTAAGGATCGTAAAG
TGAAAGCAAAGAGCATCGTTTTTCATAGAAAGAAGAACTTGCAATACTATGACATCTCAG
CTAAATCAAATTACAACTTTGAAAAACCTTTCTTATGGCTTGCTCGTAAATTGGTTGGAG
ACCCTAATTTGGAATTTGTTGCGATGCCCGCACTTTTGCCACCAGAAGTCAAAATGGACA
AAGCATGGCAAGATCAATTGGAGAGAGAAATGGAAGAAGCATCAAAGACTGCGCTGCCAG
AAGACGACGAGGACTTGTAA

>g960.t4 Gene=g960 Length=215
MAAEQDIPTFKCVLVGDGGTGKTTFVKRHMTGEFEKKYVATLGVEVHPLVFHTNRGAIRF
NVWDTAGQEKFGGLRDGYYIQGQCAIVMFDVTSRITYKNVPNWHRDLVRVCENIPIVLCG
NKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLVGDPNLEFVAMPA
LLPPEVKMDKAWQDQLEREMEEASKTALPEDDEDL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g960.t4 CDD cd00877 Ran 10 175 0.0000000
10 g960.t4 Gene3D G3DSA:3.40.50.300 - 2 215 0.0000000
2 g960.t4 PANTHER PTHR24071 RAN GTPASE 8 215 0.0000000
3 g960.t4 PANTHER PTHR24071:SF17 GTP-BINDING NUCLEAR PROTEIN RAN 8 215 0.0000000
5 g960.t4 PRINTS PR00627 GTP-binding nuclear protein Ran/Tc4 family signature 23 37 0.0000000
6 g960.t4 PRINTS PR00627 GTP-binding nuclear protein Ran/Tc4 family signature 70 88 0.0000000
7 g960.t4 PRINTS PR00627 GTP-binding nuclear protein Ran/Tc4 family signature 90 111 0.0000000
4 g960.t4 PRINTS PR00627 GTP-binding nuclear protein Ran/Tc4 family signature 126 144 0.0000000
8 g960.t4 PRINTS PR00627 GTP-binding nuclear protein Ran/Tc4 family signature 164 186 0.0000000
1 g960.t4 Pfam PF00071 Ras family 11 167 0.0000000
17 g960.t4 ProSiteProfiles PS51418 small GTPase Ran family profile. 3 167 30.6470000
12 g960.t4 SMART SM00173 ras_sub_4 7 170 0.0000000
13 g960.t4 SMART SM00175 rab_sub_5 10 170 0.0000000
15 g960.t4 SMART SM00174 rho_sub_3 12 170 0.0000001
14 g960.t4 SMART SM00176 ran_sub_2 15 215 0.0000000
9 g960.t4 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 9 195 0.0000000
16 g960.t4 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 9 158 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:0006913 nucleocytoplasmic transport BP
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