General information for g6600.t4
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 g6600 is located on chr_2: 17755615..17756483 (- 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 | g6600 | g6600.t4 | TTS | g6600.t4 | 17754056 | 17754056 |
| chr_2 | g6600 | g6600.t4 | isoform | g6600.t4 | 17754226 | 17755631 |
| chr_2 | g6600 | g6600.t4 | exon | g6600.t4.exon1 | 17754226 | 17754681 |
| chr_2 | g6600 | g6600.t4 | cds | g6600.t4.CDS1 | 17754226 | 17754681 |
| chr_2 | g6600 | g6600.t4 | exon | g6600.t4.exon2 | 17754763 | 17754910 |
| chr_2 | g6600 | g6600.t4 | cds | g6600.t4.CDS2 | 17754763 | 17754910 |
| chr_2 | g6600 | g6600.t4 | exon | g6600.t4.exon3 | 17754974 | 17755215 |
| chr_2 | g6600 | g6600.t4 | cds | g6600.t4.CDS3 | 17754974 | 17755215 |
| chr_2 | g6600 | g6600.t4 | exon | g6600.t4.exon4 | 17755270 | 17755631 |
| chr_2 | g6600 | g6600.t4 | cds | g6600.t4.CDS4 | 17755270 | 17755278 |
| chr_2 | g6600 | g6600.t4 | TSS | g6600.t4 | NA | NA |
Sequences
>g6600.t4 Gene=g6600 Length=1208
AGAGTACGGTAGAAAAAATCCAATACAATAATTAAAAAAATCATTTACTGCATAATTTCA
AAAAACTTTAAATGTATAAATGCAACGGATTTATACAATGAGCTTATTATAAATAAATGG
AAATGATTGAAGCAGGTTACATTGAAAATAAAATAAATTATTGTTACATATTTTAAAATT
TTAAATACTTTACTAAATAGAGTAAGAAGGGATTTAAAAAATGTTTAATTCATCAAAATT
GCCTCTATTTAAATTTTAAAACCAAAAAAAATCATAATGTTGAAGATTACATTCCATCGC
AAAAAAATTTAATTTCATTTCGCAGTGAAGTAAAAAGAAGATTTCCTAAATTAATGAAAT
TGGATGGAGTCGAATTGGGTCCTGTCATAGGTTTTGATGTATCCGAAGAATCGAAGAATC
TTCCATCATGGAAACAACTCTATTTTTGTAATGCATCAGGACAAGATTTAATTGCAAAAT
TCATCGAACAATATTTTGCCATTTATGATTCAGATAACAGACAACAGTTGCTAGATGCTT
ATCATGAAAATGCAATGTTGTCAATAACAGCCACAAATAATCAGCATTACACACAAGATG
AAAGATTATTTTCCTATTACAAATTCGGAAGAAATCTTATGCATCCAAAAGGTTTTGAGC
ATCGATTTGCAAGTTTAAAACGAGGAAAATTAGTTGTTGTTGCATTATTGAATGATTTAC
CACCAACAAAACATGATCCGCAATCTTTTGCTCCACAAATGATTGTTTTAACCATCACTG
GAATTTTTAAAGAAAGAAATCCTGATCCGAAATTGGAATTTATTCGAACGTTTCAAAAAA
CAATAACTATTGTCCCCAATAATGGTGGATTTTGCATTAGAAATGAATTACTACATGTTA
ATAACAGTAATCCCTCGCAAGCCAAAAAAGCTTTTAAAACAGTGGTTGTTGGAAACTTAA
ATGCACACAACAACAATGTTACATTAAATCCAGCTGCTTCAACTTCTCAACAACAACAGC
CAACGCAGCAACTTGATGAAGCAAGTAAATTTAAAATGATTGAAGAAATGTCAAGACTTT
CTCAAATGAATTTGGAATGGAGTAAAAAATGCTTAGAAGAGACAAATTGGGATTTTACTC
GTGCTGGTTTTGTTTTTCAAGAACTTTTTAAACAAAACAAAATACCACAAGAAGCTTTTG
CAAAATAG
>g6600.t4 Gene=g6600 Length=284
MKLDGVELGPVIGFDVSEESKNLPSWKQLYFCNASGQDLIAKFIEQYFAIYDSDNRQQLL
DAYHENAMLSITATNNQHYTQDERLFSYYKFGRNLMHPKGFEHRFASLKRGKLVVVALLN
DLPPTKHDPQSFAPQMIVLTITGIFKERNPDPKLEFIRTFQKTITIVPNNGGFCIRNELL
HVNNSNPSQAKKAFKTVVVGNLNAHNNNVTLNPAASTSQQQQPTQQLDEASKFKMIEEMS
RLSQMNLEWSKKCLEETNWDFTRAGFVFQELFKQNKIPQEAFAK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g6600.t4 | CDD | cd14342 | UBA_TAP-C | 235 | 282 | 0.000 |
| 8 | g6600.t4 | Gene3D | G3DSA:3.10.450.50 | - | 23 | 199 | 0.000 |
| 7 | g6600.t4 | Gene3D | G3DSA:1.10.8.10 | DNA helicase RuvA subunit | 215 | 284 | 0.000 |
| 3 | g6600.t4 | PANTHER | PTHR10662 | NUCLEAR RNA EXPORT FACTOR | 3 | 282 | 0.000 |
| 2 | g6600.t4 | Pfam | PF02136 | Nuclear transport factor 2 (NTF2) domain | 41 | 180 | 0.000 |
| 1 | g6600.t4 | Pfam | PF03943 | TAP C-terminal domain | 235 | 282 | 0.000 |
| 10 | g6600.t4 | ProSiteProfiles | PS50177 | Nuclear transport factor 2 domain profile. | 39 | 182 | 17.917 |
| 9 | g6600.t4 | ProSiteProfiles | PS51281 | TAP C-terminal (TAP-C) domain profile. | 230 | 284 | 25.684 |
| 6 | g6600.t4 | SMART | SM00804 | TAP_C_cls | 221 | 284 | 0.000 |
| 4 | g6600.t4 | SUPERFAMILY | SSF54427 | NTF2-like | 24 | 196 | 0.000 |
| 5 | g6600.t4 | SUPERFAMILY | SSF46934 | UBA-like | 226 | 283 | 0.000 |
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:0005634 | nucleus | CC |
| GO:0005515 | protein binding | MF |
| GO:0051028 | mRNA transport | BP |
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.
