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.t12 TSS g960.t12 7070835 7070835
chr_3 g960 g960.t12 isoform g960.t12 7070869 7072731
chr_3 g960 g960.t12 exon g960.t12.exon1 7070869 7070913
chr_3 g960 g960.t12 exon g960.t12.exon2 7071498 7071728
chr_3 g960 g960.t12 cds g960.t12.CDS1 7071533 7071728
chr_3 g960 g960.t12 exon g960.t12.exon3 7071790 7072013
chr_3 g960 g960.t12 cds g960.t12.CDS2 7071790 7072013
chr_3 g960 g960.t12 exon g960.t12.exon4 7072078 7072731
chr_3 g960 g960.t12 cds g960.t12.CDS3 7072078 7072323
chr_3 g960 g960.t12 TTS g960.t12 NA NA

Sequences

>g960.t12 Gene=g960 Length=1154
ACGCGCTTTCATATAAATTGAAAAAATTATTAAATATTCATTAAAAGAGGAATTTTAGTA
AATTCAACTGAAAAAGTACAATGGCAGCAGAACAAGATATTCCTACTTTCAAATGCGTTT
TAGTTGGAGATGGTGGTACTGGTAAGACAACATTTGTTAAACGTCATATGACTGGTGAAT
TTGAGAAGAAATACGTTGCAACTCTTGGTGTTGAAGTACATCCGCTAGTCTTTCATACTA
ATCGTGGCGCCATTCGTTTTAATGTCTGGGATACAGCTGGTCAAGAGAAATTCGGGGGTC
TTCGTGATGGTTATTATATTCAAGGGCAATGTGCTATTGTCATGTTTGATGTCACATCTC
GAATTACTTACAAGAATGTACCAAATTGGCATCGTGATTTAGTTCGTGTGTGTGAAAATA
TTCCAATTGTGTTATGTGGAAACAAGGTAGACATTAAGGATCGTAAAGTGAAAGCAAAGA
GCATCGTTTTTCATAGAAAGGGCTTGCTCGTAAATTGGTTGGAGACCCTAATTTGGAATT
TGTTGCGATGCCCGCACTTTTGCCACCAGAAGTCAAAATGGACAAAGCATGGCAAGATCA
ATTGGAGAGAGAAATGGAAGAAGCATCAAAGACTGCGCTGCCAGAAGACGACGAGGACTT
GTAAAATGTATTCGATCGCAACTGTCAGATGTTCTCAATGGGATTTTTATTTCAAACCAT
ATGTTCATAAAACACGATCTATTTAGTTAATTTATAAATAAGGCATTTGAAATTTTAATC
TTCTGGCACCTGAAAAAATTTGTATACCTACATCAATTTCATAAACTAAAACTAACACTT
TTTGTTCAAATACAATATTTGATTTGATATGCAGTAATTAGTTTAAGATTTGAAATGTTC
ACATATTAAAATACTTTTCCAATTTTTCAACAAAATTATTTTTGTATTTTTCTTATTATT
CCATTTTTATTGCACATTAAGTTTTTCTCATTTCTTTTTTTGCTATATTTTTGTTTGTTA
TTCCTGCTCTCATACTCTTATTTGACTTTTTTTATTCTTTCAAAATTCTTTCTGATGTGA
AGAAGTATGAAATGAGTAATAGAATTTAATAAAAATTGAAATCAATGATTAAGTAAAATA
AAATTTATATAAAA

>g960.t12 Gene=g960 Length=221
MAAEQDIPTFKCVLVGDGGTGKTTFVKRHMTGEFEKKYVATLGVEVHPLVFHTNRGAIRF
NVWDTAGQEKFGGLRDGYYIQGQCAIVMFDVTSRITYKNVPNWHRDLVRVCENIPIVLCG
NKVDIKDRKVKAKSIVFHRKGLLVNWLETLIWNLLRCPHFCHQKSKWTKHGKINWREKWK
KHQRLRCQKTTRTCKMYSIATVRCSQWDFYFKPYVHKTRSI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g960.t12 CDD cd00877 Ran 10 143 0.0000000
9 g960.t12 Gene3D G3DSA:3.40.50.300 - 2 195 0.0000000
2 g960.t12 PANTHER PTHR24071 RAN GTPASE 8 142 0.0000000
3 g960.t12 PANTHER PTHR24071:SF17 GTP-BINDING NUCLEAR PROTEIN RAN 8 142 0.0000000
5 g960.t12 PRINTS PR00627 GTP-binding nuclear protein Ran/Tc4 family signature 23 37 0.0000000
6 g960.t12 PRINTS PR00627 GTP-binding nuclear protein Ran/Tc4 family signature 70 88 0.0000000
7 g960.t12 PRINTS PR00627 GTP-binding nuclear protein Ran/Tc4 family signature 90 111 0.0000000
4 g960.t12 PRINTS PR00627 GTP-binding nuclear protein Ran/Tc4 family signature 126 144 0.0000000
1 g960.t12 Pfam PF00071 Ras family 11 134 0.0000000
16 g960.t12 ProSiteProfiles PS51418 small GTPase Ran family profile. 3 190 24.9340000
11 g960.t12 SMART SM00173 ras_sub_4 7 171 0.0000000
12 g960.t12 SMART SM00175 rab_sub_5 10 157 0.0000000
14 g960.t12 SMART SM00174 rho_sub_3 12 156 0.0000017
13 g960.t12 SMART SM00176 ran_sub_2 15 201 0.0000000
8 g960.t12 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 9 131 0.0000000
15 g960.t12 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 9 132 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

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