General information for g6600.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t6 | TTS | g6600.t6 | 17754056 | 17754056 |
| chr_2 | g6600 | g6600.t6 | isoform | g6600.t6 | 17754763 | 17756483 |
| chr_2 | g6600 | g6600.t6 | exon | g6600.t6.exon1 | 17754763 | 17754910 |
| chr_2 | g6600 | g6600.t6 | cds | g6600.t6.CDS1 | 17754763 | 17754910 |
| chr_2 | g6600 | g6600.t6 | exon | g6600.t6.exon2 | 17754974 | 17755215 |
| chr_2 | g6600 | g6600.t6 | cds | g6600.t6.CDS2 | 17754974 | 17755215 |
| chr_2 | g6600 | g6600.t6 | exon | g6600.t6.exon3 | 17755270 | 17755306 |
| chr_2 | g6600 | g6600.t6 | cds | g6600.t6.CDS3 | 17755270 | 17755306 |
| chr_2 | g6600 | g6600.t6 | exon | g6600.t6.exon4 | 17756162 | 17756271 |
| chr_2 | g6600 | g6600.t6 | cds | g6600.t6.CDS4 | 17756162 | 17756271 |
| chr_2 | g6600 | g6600.t6 | exon | g6600.t6.exon5 | 17756334 | 17756483 |
| chr_2 | g6600 | g6600.t6 | cds | g6600.t6.CDS5 | 17756334 | 17756483 |
| chr_2 | g6600 | g6600.t6 | TSS | g6600.t6 | NA | NA |
Sequences
>g6600.t6 Gene=g6600 Length=687
ATGGCAGCCGTTATTGATATAATAGCCGAAAATATTCCTGATCTTGAAGCTCTCAATCTC
AATGATAATAAACTTAACATGATTGACCATATGAAAGTTTTGTCATCGAAATTACCTCAA
TTGAAAATCATATATCTTGCAAATAATAGGATTGTTATGCTGAGTTCTTTAGATGCTTTT
AAGAATTTGCCGATAGTAGAATTATTTTTAGATGGAAATCCATGCAAAAAACGTTTTAAG
GACAACAGTCATTATGTCAGTGAAGTAAAAAGAAGATTTCCTAAATTAATGAAATTGGAT
GGAGTCGAATTGGGTCCTGTCATAGGTTTTGATGTATCCGAAGAATCGAAGAATCTTCCA
TCATGGAAACAACTCTATTTTTGTAATGCATCAGGACAAGATTTAATTGCAAAATTCATC
GAACAATATTTTGCCATTTATGATTCAGATAACAGACAACAGTTGCTAGATGCTTATCAT
GAAAATGCAATGTTGTCAATAACAGCCACAAATAATCAGCATTACACACAAGATGAAAGA
TTATTTTCCTATTACAAATTCGGAAGAAATCTTATGCATCCAAAAGGTTTTGAGCATCGA
TTTGCAAGTTTAAAACGAGGAAAATTAGTTGTTGTTGCATTATTGAATGATTTACCACCA
ACAAAACATGATCCGCAATCTTTTGCT
>g6600.t6 Gene=g6600 Length=229
MAAVIDIIAENIPDLEALNLNDNKLNMIDHMKVLSSKLPQLKIIYLANNRIVMLSSLDAF
KNLPIVELFLDGNPCKKRFKDNSHYVSEVKRRFPKLMKLDGVELGPVIGFDVSEESKNLP
SWKQLYFCNASGQDLIAKFIEQYFAIYDSDNRQQLLDAYHENAMLSITATNNQHYTQDER
LFSYYKFGRNLMHPKGFEHRFASLKRGKLVVVALLNDLPPTKHDPQSFA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g6600.t6 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 1 | 110 | 0.00000 |
| 6 | g6600.t6 | Gene3D | G3DSA:3.10.450.50 | - | 119 | 229 | 0.00000 |
| 2 | g6600.t6 | PANTHER | PTHR10662 | NUCLEAR RNA EXPORT FACTOR | 1 | 228 | 0.00000 |
| 1 | g6600.t6 | Pfam | PF02136 | Nuclear transport factor 2 (NTF2) domain | 137 | 206 | 0.00014 |
| 7 | g6600.t6 | ProSiteProfiles | PS50177 | Nuclear transport factor 2 domain profile. | 135 | 229 | 10.57000 |
| 4 | g6600.t6 | SUPERFAMILY | SSF52058 | L domain-like | 4 | 103 | 0.00000 |
| 3 | g6600.t6 | SUPERFAMILY | SSF54427 | NTF2-like | 120 | 228 | 0.00000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
