General information for g6601.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Nuclear RNA export factor 1.
Parent gene
- The parent gene g6601 is located on chr_2: 17757206..17758650 (- 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_2 | g6601 | g6601.t1 | TTS | g6601.t1 | 17755573 | 17755573 |
| chr_2 | g6601 | g6601.t1 | isoform | g6601.t1 | 17756552 | 17757353 |
| chr_2 | g6601 | g6601.t1 | exon | g6601.t1.exon1 | 17756552 | 17756943 |
| chr_2 | g6601 | g6601.t1 | cds | g6601.t1.CDS1 | 17756552 | 17756943 |
| chr_2 | g6601 | g6601.t1 | exon | g6601.t1.exon2 | 17757012 | 17757206 |
| chr_2 | g6601 | g6601.t1 | cds | g6601.t1.CDS2 | 17757012 | 17757206 |
| chr_2 | g6601 | g6601.t1 | exon | g6601.t1.exon3 | 17757275 | 17757353 |
| chr_2 | g6601 | g6601.t1 | cds | g6601.t1.CDS3 | 17757275 | 17757353 |
| chr_2 | g6601 | g6601.t1 | TSS | g6601.t1 | 17757604 | 17757604 |
Sequences
>g6601.t1 Gene=g6601 Length=666
ATGATGCAAGGAAGGCGAGGAGGTGGCAAATTTAGAGGAACTAATAGAAATAATCAATCA
GGAGATCGATATCAGGATGATCATGATAACCGTGCAAGCAATAATTTCAAAACAAATCGC
CGTGTTAGTTTCAAAACTTCACATAGACATGCAAAAAACTTAAATGATGTAAAGATTAAA
GCATTTCTTGATGATGAGGAAATGAGTGGTGATTTAGGGCAAAATACATCAGGTGAAATA
AAGAGAAGAGGAAAATTTCGTAATATGCGTAAAGGTTCTCCAATACCTCGCAGCGGTATC
AGCATCGGAGGTGGTGGAAAATTAATGCAACATCCTGCAGGATGGTACCTTGTCACAATT
AATTTTGGCTGCAAATATGAAAAAGATGTCTTGCTAAAGCTATTAATGAATGCTCTTTCA
CCAACAACTTTCAATGCTCATTACTACAAAATAGATACCGACAACAATTTTTCACAATTT
TACGTTGACGACTATGATGTTGCTGAAAAAATTTTGCTGCAAGATAAACGTATTGAGCTT
CCAGATGGATTTAAAATGCAAATCAAAATTAGGGGAAATTTACCTCAAATAAAAATTGAT
CAAGCTCTAAAAGACAGAATGAAACATGCTATGGCAAAAAGATATAATCACAAACAAAAG
CATTAG
>g6601.t1 Gene=g6601 Length=221
MMQGRRGGGKFRGTNRNNQSGDRYQDDHDNRASNNFKTNRRVSFKTSHRHAKNLNDVKIK
AFLDDEEMSGDLGQNTSGEIKRRGKFRNMRKGSPIPRSGISIGGGGKLMQHPAGWYLVTI
NFGCKYEKDVLLKLLMNALSPTTFNAHYYKIDTDNNFSQFYVDDYDVAEKILLQDKRIEL
PDGFKMQIKIRGNLPQIKIDQALKDRMKHAMAKRYNHKQKH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g6601.t1 | Gene3D | G3DSA:3.30.70.330 | - | 113 | 200 | 7.7E-15 |
| 4 | g6601.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 49 | - |
| 3 | g6601.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 21 | 35 | - |
| 1 | g6601.t1 | Pfam | PF09162 | Tap, RNA-binding | 114 | 195 | 9.2E-17 |
| 2 | g6601.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 104 | 197 | 1.79E-16 |
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:0006406 | mRNA export from nucleus | BP |
| GO:0003723 | RNA binding | MF |
| GO:0005737 | cytoplasm | CC |
| GO:0003676 | nucleic acid binding | 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.
