General information for g960.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as GTP-binding nuclear protein Ran.
Parent gene
- The parent gene g960 is located on chr_3: 7071533..7072842 (+ strand)
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.t2 | isoform | g960.t2 | 7070813 | 7072241 |
| chr_3 | g960 | g960.t2 | exon | g960.t2.exon1 | 7070813 | 7070913 |
| chr_3 | g960 | g960.t2 | TSS | g960.t2 | 7070835 | 7070835 |
| chr_3 | g960 | g960.t2 | exon | g960.t2.exon2 | 7071498 | 7071593 |
| chr_3 | g960 | g960.t2 | exon | g960.t2.exon3 | 7071729 | 7072241 |
| chr_3 | g960 | g960.t2 | cds | g960.t2.CDS1 | 7071855 | 7072241 |
| chr_3 | g960 | g960.t2 | TTS | g960.t2 | 7072508 | 7072508 |
Sequences
>g960.t2 Gene=g960 Length=710
AGTCCCCTGTATACACTTACATTAGTATTAGTAAAAATTTCTTTGCGAGCAAAAACACGC
GCTTTCATATAAATTGAAAAAATTATTAAATATTCATTAAAAGAGGAATTTTAGTAAATT
CAACTGAAAAAGTACAATGGCAGCAGAACAAGATATTCCTACTTTCAAATGCGTTTTAGT
TGGAGATGGTGGTACTGGTAAATCATAAAATTTATTAAAATCTAAAAGTTTTTACATATG
AAAATTATTGTATTATAGCTGGTCAAGAGAAATTCGGGGGTCTTCGTGATGGTTATTATA
TTCAAGGGCAATGTGCTATTGTCATGTTTGATGTCACATCTCGAATTACTTACAAGAATG
TACCAAATTGGCATCGTGATTTAGTTCGTGTGTGTGAAAATATTCCAATTGTGTTATGTG
GAAACAAGGTAGACATTAAGGATCGTAAAGTGAAAGCAAAGAGCATCGTTTTTCATAGAA
AGAAGAACTTGCAATACTATGACATCTCAGCTAAATCAAATTACAACTTTGAAAAACCTT
TCTTATGGCTTGCTCGTAAATTGGTTGGAGACCCTAATTTGGAATTTGTTGCGATGCCCG
CACTTTTGCCACCAGAAGTCAAAATGGACAAAGCATGGCAAGATCAATTGGAGAGAGAAA
TGGAAGAAGCATCAAAGACTGCGCTGCCAGAAGACGACGAGGACTTGTAA
>g960.t2 Gene=g960 Length=128
MFDVTSRITYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYD
ISAKSNYNFEKPFLWLARKLVGDPNLEFVAMPALLPPEVKMDKAWQDQLEREMEEASKTA
LPEDDEDL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g960.t2 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 128 | 0.0000 |
| 2 | g960.t2 | PANTHER | PTHR24071 | RAN GTPASE | 1 | 128 | 0.0000 |
| 3 | g960.t2 | PANTHER | PTHR24071:SF17 | GTP-BINDING NUCLEAR PROTEIN RAN | 1 | 128 | 0.0000 |
| 5 | g960.t2 | PRINTS | PR00627 | GTP-binding nuclear protein Ran/Tc4 family signature | 3 | 24 | 0.0000 |
| 4 | g960.t2 | PRINTS | PR00627 | GTP-binding nuclear protein Ran/Tc4 family signature | 39 | 57 | 0.0000 |
| 6 | g960.t2 | PRINTS | PR00627 | GTP-binding nuclear protein Ran/Tc4 family signature | 77 | 99 | 0.0000 |
| 1 | g960.t2 | Pfam | PF00071 | Ras family | 1 | 80 | 0.0000 |
| 11 | g960.t2 | ProSiteProfiles | PS51418 | small GTPase Ran family profile. | 1 | 80 | 12.5550 |
| 8 | g960.t2 | SMART | SM00175 | rab_sub_5 | 1 | 83 | 0.0013 |
| 9 | g960.t2 | SMART | SM00176 | ran_sub_2 | 1 | 128 | 0.0000 |
| 7 | g960.t2 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 1 | 108 | 0.0000 |
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.
