General information for g2817.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Nuclear pore complex protein Nup58.
Parent gene
- The parent gene g2817 is located on chr_3: 20429339..20431083 (- 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 | g2817 | g2817.t1 | isoform | g2817.t1 | 20429339 | 20430934 |
| chr_3 | g2817 | g2817.t1 | exon | g2817.t1.exon1 | 20429339 | 20430782 |
| chr_3 | g2817 | g2817.t1 | cds | g2817.t1.CDS1 | 20429339 | 20430782 |
| chr_3 | g2817 | g2817.t1 | exon | g2817.t1.exon2 | 20430852 | 20430934 |
| chr_3 | g2817 | g2817.t1 | cds | g2817.t1.CDS2 | 20430852 | 20430934 |
| chr_3 | g2817 | g2817.t1 | TSS | g2817.t1 | 20431012 | 20431012 |
| chr_3 | g2817 | g2817.t1 | TTS | g2817.t1 | NA | NA |
Sequences
>g2817.t1 Gene=g2817 Length=1527
ATGTCTGGTTTCTCCTTTGGAACTCCTACACCAACAACAACATCATCAACAACAGGGTTC
TCATTTGGGACGCCTCAAACTAGCAATTCGCCTCAAGCTCAAAGTGGCTCTTCTTTTGGA
ATAGGCACAGGCACTGGATTGACTTTTGGCAGTGCTACACCATCAACTGGTTTAAATTTT
AGTTTTGGATCGTCTACTCCAGCTGCAGCTTCTTCTTCTTCTTCTTCAACGACCGTGGCA
CCGACTCTTGGCTTTCAAAATTCAGCAATAGCTGTAACAACAACTGCAAGTACACAATTT
AGTTTTGGTGGATTAAGTCAAACTGCAACAACAAATCCATCAACGAGTGTTGCAAATGTA
GTCCCAACATCTTCGACATTAACGTTTGGTGCACCTGCTTCATCAACGCTAACTTTTGGA
ACTCCCACTGTTTCATCTTCTTCTGCTGCCTCTTCAACTTTACAAACAAGAGCAGTTACA
ACATCATCTGCTTTAAATTTTTCAACAACAAATATCAATCCACAGCCTGCACCGACACTT
TTTGGAGCATCAGCAACAACTACAACTTCTTCGTTAAATTTATCAGCTGCAGCACCAGCT
ATGACGAGTGCAAGCACAAGTAACAATTTTGTTGGTTTAGGAGGAATCGATATGGCAACC
ACTGCCCAACAAATAGTTCCTCAAGGAAAAGTTGAAACGACTAAGGTGAAAGAAACACAA
GTTCCAGCACAAATTATTCAATCAGTTGAAGATTTTAAAACGTACGTTAAAAACCAAAAG
ACAATTTCATCAGAAATTACTCGTTCATCCGATAGAAAACAAAAAACTGTATCAGAAGAA
CTTCAAAGATTGAATAACAAGCTACAAGAATCATCAAATAATATAGATAACAATAGGCTA
GCATTAAGACATTTGCGGAATGAAACTTCAAAAGTGATTGAACATGCAGATATGGCTCAG
CGAACGCATGAAACTCCAAGTGGTCTCCAATTCGAAAATACAATGCCACAAGTTTATTTC
AAGGAACTTATTCAAAAGTATGAAACAGATTTATTAGGATTGAAGCATCAAGTTGAGTTG
ACTGAAAAGCATTTGCAATCATTAGTGACACCTCAAAATTTTACTGCTCAAGATTTAAAA
CGTGGGCTACAACAAATTCATGAAAATTTTATTGCACTTGCTGGAAGGCTGCAAGAGGCA
CATACAAAAGTAGAAAATCAAAAGACTCAATATTTGGAACTTAGAAAACTTATACTAAAA
GATTCAACTAATATATTTGAGATTGAAGAAAAGAGTCCTGAAATAGATAAAGCACAGGCC
AGCAGAGTTCAATATGGACCAAATACTTTTTCTTCATCATCAGTAAATCATAATTTCTTC
AATTCTGTAATGAATAGACAGCAGCAGCAACAACAGCTTCAACAACAATCATTTCAAATG
CCATTAAGTCAAACTCAACAACCAGCAGCAGCACCTCAGAATAGTTTCTTTGGTTCGAAT
ACACTGAGTTTTAATTTTAATAAGTAA
>g2817.t1 Gene=g2817 Length=508
MSGFSFGTPTPTTTSSTTGFSFGTPQTSNSPQAQSGSSFGIGTGTGLTFGSATPSTGLNF
SFGSSTPAAASSSSSSTTVAPTLGFQNSAIAVTTTASTQFSFGGLSQTATTNPSTSVANV
VPTSSTLTFGAPASSTLTFGTPTVSSSSAASSTLQTRAVTTSSALNFSTTNINPQPAPTL
FGASATTTTSSLNLSAAAPAMTSASTSNNFVGLGGIDMATTAQQIVPQGKVETTKVKETQ
VPAQIIQSVEDFKTYVKNQKTISSEITRSSDRKQKTVSEELQRLNNKLQESSNNIDNNRL
ALRHLRNETSKVIEHADMAQRTHETPSGLQFENTMPQVYFKELIQKYETDLLGLKHQVEL
TEKHLQSLVTPQNFTAQDLKRGLQQIHENFIALAGRLQEAHTKVENQKTQYLELRKLILK
DSTNIFEIEEKSPEIDKAQASRVQYGPNTFSSSSVNHNFFNSVMNRQQQQQQLQQQSFQM
PLSQTQQPAAAPQNSFFGSNTLSFNFNK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g2817.t1 | Coils | Coil | Coil | 274 | 308 | - |
| 5 | g2817.t1 | Coils | Coil | Coil | 397 | 417 | - |
| 4 | g2817.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 470 | 494 | - |
| 2 | g2817.t1 | PANTHER | PTHR13437 | NUCLEOPORIN P58/P45 NUCLEOPORIN-LIKE PROTEIN 1 | 60 | 501 | 2.8E-43 |
| 3 | g2817.t1 | PANTHER | PTHR13437:SF2 | NUCLEOPORIN P58/P45 | 60 | 501 | 2.8E-43 |
| 1 | g2817.t1 | Pfam | PF15967 | Nucleoporin FG repeated region | 1 | 472 | 1.8E-59 |
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:0006913 | nucleocytoplasmic transport | BP |
| GO:0017056 | structural constituent of nuclear pore | MF |
| GO:0008139 | nuclear localization sequence binding | MF |
KEGG
Orthology
- This transcript has been annotated with K14307 (nucleoporin p58/p45)
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.
