General information for g388.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Nuclear pore complex protein Nup98-Nup96.
Parent gene
- The parent gene g388 is located on chr_3: 3137879..3140347 (+ 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 | g388 | g388.t2 | TSS | g388.t2 | 3134462 | 3134462 |
| chr_3 | g388 | g388.t2 | isoform | g388.t2 | 3134679 | 3135535 |
| chr_3 | g388 | g388.t2 | exon | g388.t2.exon1 | 3134679 | 3134889 |
| chr_3 | g388 | g388.t2 | cds | g388.t2.CDS1 | 3134679 | 3134889 |
| chr_3 | g388 | g388.t2 | exon | g388.t2.exon2 | 3134949 | 3135535 |
| chr_3 | g388 | g388.t2 | cds | g388.t2.CDS2 | 3134949 | 3135535 |
| chr_3 | g388 | g388.t2 | TTS | g388.t2 | NA | NA |
Sequences
>g388.t2 Gene=g388 Length=798
ATGTTTGGCTCAAAAAATACTTTTGGACAACCCACGACTGGAACTTTTTCAGGCTTTGGA
CAAAGTGCATTCTCAAAGCCAGCAAATACATTCGGAACAAATACTTTTGGACAGCAAAAT
CAATCTGTCTTTGGTGCTCAACAGCAGCCGAGTTCTTCTGGACTTTTTGGCTCTGGCGCT
GCAGCTTCTACGCCTCAATCAGCATTTGGAAGTGCTTTTGGTCAACAAACATCAATTTTT
GGAAATACAAGCACGACTGGTACAACTTCACTTTTTGGTAATCAGCAGCAGCCGACATCT
GCATTTGGTGCTCCTAAGCAACAAATTTTCGGCCAAACACAACAACCAACAACTTCTCTT
TTTGGACAACCTCAACAACAACAAACAACATCACTTTTCGGTCAAACTCCCACTAATACG
GGAACTGGACTTTTTGGTTCAACAACAACTTCTGCTTTTGCTCAACCAACGACTTTAGGC
AATCAACAAACTGGAACAGCTATTGCAAAATTTCAAGCACAACAAGAAACTGATACTTTG
CTAAAAGGGTCAACAACATCTTATATCCAAACTAAGCAACAATGCATAACATTTATGAAA
GAATATGCAGATAAATCTCTTGAAGAATTAAGAGTTGAAGATTATATTGCAAATCGAAAA
GGTCCACAGCCAGCTTCTGCAGGTCTTTTTGGTGGAAGCAATCAAAGTAATTTCTTCAAT
TCAAATCCAACATCGACTTCAGGAGGATTTACTGGTTTTGGTCAGCAATCGACTGCTCAA
CCGATTTTTGGTCAAACA
>g388.t2 Gene=g388 Length=266
MFGSKNTFGQPTTGTFSGFGQSAFSKPANTFGTNTFGQQNQSVFGAQQQPSSSGLFGSGA
AASTPQSAFGSAFGQQTSIFGNTSTTGTTSLFGNQQQPTSAFGAPKQQIFGQTQQPTTSL
FGQPQQQQTTSLFGQTPTNTGTGLFGSTTTSAFAQPTTLGNQQTGTAIAKFQAQQETDTL
LKGSTTSYIQTKQQCITFMKEYADKSLEELRVEDYIANRKGPQPASAGLFGGSNQSNFFN
SNPTSTSGGFTGFGQQSTAQPIFGQT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g388.t2 | Gene3D | G3DSA:1.10.10.2360 | - | 164 | 220 | 1.6E-22 |
| 5 | g388.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 231 | 266 | - |
| 3 | g388.t2 | PANTHER | PTHR23198:SF17 | NUCLEAR PORE COMPLEX PROTEIN NUP98-NUP96 | 1 | 265 | 5.7E-18 |
| 4 | g388.t2 | PANTHER | PTHR23198 | NUCLEOPORIN | 1 | 265 | 5.7E-18 |
| 1 | g388.t2 | Pfam | PF13634 | Nucleoporin FG repeat region | 7 | 77 | 0.066 |
| 2 | g388.t2 | Pfam | PF13634 | Nucleoporin FG repeat region | 222 | 266 | 130.0 |
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:0005643 | nuclear pore | CC |
| GO:0017056 | structural constituent of nuclear pore | 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.
