General information for g3199.t1
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.t1 | TSS | g3199.t1 | 23616969 | 23616969 |
| chr_3 | g3199 | g3199.t1 | isoform | g3199.t1 | 23617033 | 23619533 |
| chr_3 | g3199 | g3199.t1 | exon | g3199.t1.exon1 | 23617033 | 23617474 |
| chr_3 | g3199 | g3199.t1 | cds | g3199.t1.CDS1 | 23617033 | 23617474 |
| chr_3 | g3199 | g3199.t1 | exon | g3199.t1.exon2 | 23617534 | 23619533 |
| chr_3 | g3199 | g3199.t1 | cds | g3199.t1.CDS2 | 23617534 | 23619533 |
| chr_3 | g3199 | g3199.t1 | TTS | g3199.t1 | 23619708 | 23619708 |
Sequences
>g3199.t1 Gene=g3199 Length=2442
ATGGAGCAGTCATTTTCACAATTTGAAGACTCATTAGCTAAGAAAAGTTTGTTAAGGTCG
CGAGGCAATGTTTTCCGAGACGATGCAAGTATTATTTCAAATACTACAAGCATTTTAGGA
AGCGGACAAACTAGCGTGCTAATCAAAGAAAAAACAGATCAATTGTATACTCATTTTCTG
GCTATAATTCAATCAAGCACAGATGATATTTTTGAAACTGTACAGAACTTATGGCAAGTA
CTTCAAAATACAGTCGATGAAATGCAAACAGGCGCTAAGAAACAAATTGGTGTAAATAAT
TGGATTCGACAGGAAATGAATACTTGGAGTCTTATTCACTGCCTCTATAAAGATAGATTA
ATAACTCAAAGAGAGGAAATGGAACAAGATGATTTGCCTTTAGTAAATAGTGAAAAACTA
ATTGTTGAGAATCTTTATATGAATAATGCAACACTTCGAGAGCATCAATTAATTCTTGAT
TGGCTTGAGCAAACGTCTTATGAAGCAAATCCTATTCAAGTTGCACATTATGGAGATCGC
AGTGCAATGGCTTGGGAAAATACTTTACATCATCTTCAAAATGTTGGTCGAACAGTTTTT
GGTGGTCGTCGTGAGCTCGTTAAAAGTTTAGATCCAGATGCACCACATAGAGAGAATTTG
CCACTTCATGATTTAGATATGGATGATCAACGTAGATTAGTAAAGCACATTTTTAATTGC
ATTAGACAAGGAAAGATTGATGAAGCTCAAAGCTTATGTGAACATTGCGGTCAGCCATGG
CAAGCTGCTTTATTGGAAGGATGGAGATTGTTTCATGATCCAAATTATTATACAAATGAA
ACAAAAGCTGTAAAGTTACCGATTGAAGGCAATCCTCGTCGAGATTTATGGAAAAAATGC
GCATATGCAATGGCAGATAGCAAAAAACTAGATGATTTTACCAGAGCTGTTGCTGGATCA
CTGTGTGGTAATCTTGATTCACTTTTAAATGTATGTGGTGAATCATGGTGGGATTTATTG
TGGGCATATCTCAAAGTGAATATTGATATTCGTGTTGAATCTGAAATTCGTTCATGCTGT
GCAAAAACTTATTGTGAAATGCCTGAAAAGTATTGGGATTCAAAAATGTCATTAGAAAGA
ATTTTTTCTGAACTTGATGGAAATAAGAATTTGAATGTCAAGACTACTGCCAAATCATGT
TTTGCAATGATTCAAAAATTCTTAATTTTAGATGATATAAAATCACTATTTGATCATATG
AACGAAATTATTGATACTGATGAAGTTACACCTCAAATTATGAGACTATTTGCACATTTA
GTGCTATTCATAAGACAAATCGGAAAAAGTCATCAGGAAGAAATAGGAGATAGAATTATA
CGTTCCTATGTTCAATGCTTGATGAAAATGGGTGATGCTCAGCTTGTTGCTTTCTATACA
GCAGCATTGCCGAGTGCACAGCAAATTCAAATTTATTCCGAATTTCTCGAAAATGTACCA
GAATCATCTCGTCGTTCTTGTATGGAAGAAGCACAAAGTCATGGACTCGATATTGCTCAA
ATTGCAAAAGTGACTGTCGAAAGAGTTCAAAGAATGATAGAAGATCCAGACAATGCAAAA
CTCTTGACTGGTGAAATGTCCGATTTAGATAGAAAGAAAATTTCGTCACTTGAATTTCTC
GTCTTTTTAAAAGATCAACGTGATGAACTTTTATGGCAAGCTAATGCGATGATGAGATAT
TTTATGGCTCAACGAAAAATTGAAGCTGTCAAGAAAGCTTTTACGATGATTCCAACAGAT
TCGATTCAAGTTCTAATTCAGCAATTTGGCGGGAAAAATAATTTGTCAGTAAAAGCAGAA
TGCTCAATTAGAGAATATTTATGTCATCAAGCTTATTTAGCTGCAATTGATGGTTATAAT
GATTGGGTTGAATTCTTTTATAATAAGAAACCACGTCCACCAAATACAGCTCAAGGAAAA
AATTTCCAAGAGAAAGCTGCTTCAGAACATCAAGAACAAATTTATCAACAAGACTTAGAG
CGATGGAAGAATCTTTTGAAAGAGCAAACATTCGCCACAAAGGATCTTTTTTATAATGTA
CTTTTATTTCCCGAAAAAGGATGGTTAATGGATGCAGAAGATTTAAAAATGGAATTCTCA
ACTGAGGAGAATGCTAATGCTTGGGAAAATCGAAAAGTTCAAATGGATAACTTGAGAAAA
CTTCATATTCCCGATATCGCACTACTTTTGCATAAAATTCTTACACTTGCAGAAGAACAT
CGAGAATGCATGAAATTGAGCATTGAATTGGCTGCTGAACAGAATCAATTATTTGACGTT
TTCTCAAAGCACAAGATGAGTGAACTTCTTTCAAAAATGGCAGAGTCATCACTTGCTTTA
ATGAATGAAAATATGGATCCATTTGGATTTTCTACTAATTAA
>g3199.t1 Gene=g3199 Length=813
MEQSFSQFEDSLAKKSLLRSRGNVFRDDASIISNTTSILGSGQTSVLIKEKTDQLYTHFL
AIIQSSTDDIFETVQNLWQVLQNTVDEMQTGAKKQIGVNNWIRQEMNTWSLIHCLYKDRL
ITQREEMEQDDLPLVNSEKLIVENLYMNNATLREHQLILDWLEQTSYEANPIQVAHYGDR
SAMAWENTLHHLQNVGRTVFGGRRELVKSLDPDAPHRENLPLHDLDMDDQRRLVKHIFNC
IRQGKIDEAQSLCEHCGQPWQAALLEGWRLFHDPNYYTNETKAVKLPIEGNPRRDLWKKC
AYAMADSKKLDDFTRAVAGSLCGNLDSLLNVCGESWWDLLWAYLKVNIDIRVESEIRSCC
AKTYCEMPEKYWDSKMSLERIFSELDGNKNLNVKTTAKSCFAMIQKFLILDDIKSLFDHM
NEIIDTDEVTPQIMRLFAHLVLFIRQIGKSHQEEIGDRIIRSYVQCLMKMGDAQLVAFYT
AALPSAQQIQIYSEFLENVPESSRRSCMEEAQSHGLDIAQIAKVTVERVQRMIEDPDNAK
LLTGEMSDLDRKKISSLEFLVFLKDQRDELLWQANAMMRYFMAQRKIEAVKKAFTMIPTD
SIQVLIQQFGGKNNLSVKAECSIREYLCHQAYLAAIDGYNDWVEFFYNKKPRPPNTAQGK
NFQEKAASEHQEQIYQQDLERWKNLLKEQTFATKDLFYNVLLFPEKGWLMDAEDLKMEFS
TEENANAWENRKVQMDNLRKLHIPDIALLLHKILTLAEEHRECMKLSIELAAEQNQLFDV
FSKHKMSELLSKMAESSLALMNENMDPFGFSTN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g3199.t1 | Coils | Coil | Coil | 756 | 776 | - |
| 4 | g3199.t1 | Gene3D | G3DSA:1.10.3450.20 | - | 194 | 330 | 2.2E-26 |
| 5 | g3199.t1 | Gene3D | G3DSA:1.20.190.50 | - | 539 | 813 | 2.6E-87 |
| 2 | g3199.t1 | PANTHER | PTHR13003 | NUP107-RELATED | 49 | 804 | 7.1E-168 |
| 3 | g3199.t1 | PANTHER | PTHR13003:SF2 | NUCLEAR PORE COMPLEX PROTEIN NUP107 | 49 | 804 | 7.1E-168 |
| 1 | g3199.t1 | Pfam | PF04121 | Nuclear pore protein 84 / 107 | 100 | 797 | 1.1E-188 |
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 transcript has been annotated with K14301 (nuclear pore complex protein Nup107)
Pathway
- This transcript belongs to the following pathways
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.
