General information for g3199.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Nuclear pore complex protein Nup107.
Parent gene
- The parent gene g3199 is located on chr_3: 23617797..23619533 (+ 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 | g3199 | g3199.t2 | TSS | g3199.t2 | 23616969 | 23616969 |
| chr_3 | g3199 | g3199.t2 | isoform | g3199.t2 | 23617797 | 23619533 |
| chr_3 | g3199 | g3199.t2 | exon | g3199.t2.exon1 | 23617797 | 23619533 |
| chr_3 | g3199 | g3199.t2 | cds | g3199.t2.CDS1 | 23618001 | 23619533 |
| chr_3 | g3199 | g3199.t2 | TTS | g3199.t2 | 23619708 | 23619708 |
Sequences
>g3199.t2 Gene=g3199 Length=1737
CACATTTTTAATTGCATTAGACAAGGAAAGATTGATGAAGCTCAAAGCTTATGTGAACAT
TGCGGTCAGCCATGGCAAGCTGCTTTATTGGAAGGATGGAGATTGTTTCATGATCCAAAT
TATTATACAAATGAAACAAAAGCTGTAAAGTTACCGATTGAAGGCAATCCTCGTCGAGAT
TTATGGAAAAAATGCGCATATGCAATGGCAGATAGCAAAAAACTAGATGATTTTACCAGA
GCTGTTGCTGGATCACTGTGTGGTAATCTTGATTCACTTTTAAATGTATGTGGTGAATCA
TGGTGGGATTTATTGTGGGCATATCTCAAAGTGAATATTGATATTCGTGTTGAATCTGAA
ATTCGTTCATGCTGTGCAAAAACTTATTGTGAAATGCCTGAAAAGTATTGGGATTCAAAA
ATGTCATTAGAAAGAATTTTTTCTGAACTTGATGGAAATAAGAATTTGAATGTCAAGACT
ACTGCCAAATCATGTTTTGCAATGATTCAAAAATTCTTAATTTTAGATGATATAAAATCA
CTATTTGATCATATGAACGAAATTATTGATACTGATGAAGTTACACCTCAAATTATGAGA
CTATTTGCACATTTAGTGCTATTCATAAGACAAATCGGAAAAAGTCATCAGGAAGAAATA
GGAGATAGAATTATACGTTCCTATGTTCAATGCTTGATGAAAATGGGTGATGCTCAGCTT
GTTGCTTTCTATACAGCAGCATTGCCGAGTGCACAGCAAATTCAAATTTATTCCGAATTT
CTCGAAAATGTACCAGAATCATCTCGTCGTTCTTGTATGGAAGAAGCACAAAGTCATGGA
CTCGATATTGCTCAAATTGCAAAAGTGACTGTCGAAAGAGTTCAAAGAATGATAGAAGAT
CCAGACAATGCAAAACTCTTGACTGGTGAAATGTCCGATTTAGATAGAAAGAAAATTTCG
TCACTTGAATTTCTCGTCTTTTTAAAAGATCAACGTGATGAACTTTTATGGCAAGCTAAT
GCGATGATGAGATATTTTATGGCTCAACGAAAAATTGAAGCTGTCAAGAAAGCTTTTACG
ATGATTCCAACAGATTCGATTCAAGTTCTAATTCAGCAATTTGGCGGGAAAAATAATTTG
TCAGTAAAAGCAGAATGCTCAATTAGAGAATATTTATGTCATCAAGCTTATTTAGCTGCA
ATTGATGGTTATAATGATTGGGTTGAATTCTTTTATAATAAGAAACCACGTCCACCAAAT
ACAGCTCAAGGAAAAAATTTCCAAGAGAAAGCTGCTTCAGAACATCAAGAACAAATTTAT
CAACAAGACTTAGAGCGATGGAAGAATCTTTTGAAAGAGCAAACATTCGCCACAAAGGAT
CTTTTTTATAATGTACTTTTATTTCCCGAAAAAGGATGGTTAATGGATGCAGAAGATTTA
AAAATGGAATTCTCAACTGAGGAGAATGCTAATGCTTGGGAAAATCGAAAAGTTCAAATG
GATAACTTGAGAAAACTTCATATTCCCGATATCGCACTACTTTTGCATAAAATTCTTACA
CTTGCAGAAGAACATCGAGAATGCATGAAATTGAGCATTGAATTGGCTGCTGAACAGAAT
CAATTATTTGACGTTTTCTCAAAGCACAAGATGAGTGAACTTCTTTCAAAAATGGCAGAG
TCATCACTTGCTTTAATGAATGAAAATATGGATCCATTTGGATTTTCTACTAATTAA
>g3199.t2 Gene=g3199 Length=510
MADSKKLDDFTRAVAGSLCGNLDSLLNVCGESWWDLLWAYLKVNIDIRVESEIRSCCAKT
YCEMPEKYWDSKMSLERIFSELDGNKNLNVKTTAKSCFAMIQKFLILDDIKSLFDHMNEI
IDTDEVTPQIMRLFAHLVLFIRQIGKSHQEEIGDRIIRSYVQCLMKMGDAQLVAFYTAAL
PSAQQIQIYSEFLENVPESSRRSCMEEAQSHGLDIAQIAKVTVERVQRMIEDPDNAKLLT
GEMSDLDRKKISSLEFLVFLKDQRDELLWQANAMMRYFMAQRKIEAVKKAFTMIPTDSIQ
VLIQQFGGKNNLSVKAECSIREYLCHQAYLAAIDGYNDWVEFFYNKKPRPPNTAQGKNFQ
EKAASEHQEQIYQQDLERWKNLLKEQTFATKDLFYNVLLFPEKGWLMDAEDLKMEFSTEE
NANAWENRKVQMDNLRKLHIPDIALLLHKILTLAEEHRECMKLSIELAAEQNQLFDVFSK
HKMSELLSKMAESSLALMNENMDPFGFSTN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g3199.t2 | Coils | Coil | Coil | 453 | 473 | - |
| 4 | g3199.t2 | Gene3D | G3DSA:1.20.190.50 | - | 236 | 510 | 8.7E-88 |
| 2 | g3199.t2 | PANTHER | PTHR13003 | NUP107-RELATED | 1 | 501 | 6.2E-103 |
| 3 | g3199.t2 | PANTHER | PTHR13003:SF2 | NUCLEAR PORE COMPLEX PROTEIN NUP107 | 1 | 501 | 6.2E-103 |
| 1 | g3199.t2 | Pfam | PF04121 | Nuclear pore protein 84 / 107 | 1 | 494 | 2.5E-120 |
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.
