General information for g2817.t2
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.t2 | isoform | g2817.t2 | 20429339 | 20431083 |
| chr_3 | g2817 | g2817.t2 | exon | g2817.t2.exon1 | 20429339 | 20431083 |
| chr_3 | g2817 | g2817.t2 | cds | g2817.t2.CDS1 | 20429339 | 20430265 |
| chr_3 | g2817 | g2817.t2 | TSS | g2817.t2 | NA | NA |
| chr_3 | g2817 | g2817.t2 | TTS | g2817.t2 | NA | NA |
Sequences
>g2817.t2 Gene=g2817 Length=1745
TTTTTCGCGATTTTACAATAACTCATGCCGCAAACTTGTTTTCTTTTAAAGCTGTGCTGC
AGCATTTTTTTAAGGTTAATTTTAAAAATTTCTTTTTTAAACGTAAACATAAATTTTATT
GGCATAAATATTAAAATCAATTAGTGAAAATGTCTGGTTTCTCCTTTGGAACTCCTACAC
CAACAACAACATCATCAACAACAGGGTTCTCATTTGGGACGCCTCAAACTAGGTAATTAA
TTTTAATATATAAAAATGGCATCATTCAAAAGAATTTTTTTTTTGATTTTAATAATTTAA
GCAATTCGCCTCAAGCTCAAAGTGGCTCTTCTTTTGGAATAGGCACAGGCACTGGATTGA
CTTTTGGCAGTGCTACACCATCAACTGGTTTAAATTTTAGTTTTGGATCGTCTACTCCAG
CTGCAGCTTCTTCTTCTTCTTCTTCAACGACCGTGGCACCGACTCTTGGCTTTCAAAATT
CAGCAATAGCTGTAACAACAACTGCAAGTACACAATTTAGTTTTGGTGGATTAAGTCAAA
CTGCAACAACAAATCCATCAACGAGTGTTGCAAATGTAGTCCCAACATCTTCGACATTAA
CGTTTGGTGCACCTGCTTCATCAACGCTAACTTTTGGAACTCCCACTGTTTCATCTTCTT
CTGCTGCCTCTTCAACTTTACAAACAAGAGCAGTTACAACATCATCTGCTTTAAATTTTT
CAACAACAAATATCAATCCACAGCCTGCACCGACACTTTTTGGAGCATCAGCAACAACTA
CAACTTCTTCGTTAAATTTATCAGCTGCAGCACCAGCTATGACGAGTGCAAGCACAAGTA
ACAATTTTGTTGGTTTAGGAGGAATCGATATGGCAACCACTGCCCAACAAATAGTTCCTC
AAGGAAAAGTTGAAACGACTAAGGTGAAAGAAACACAAGTTCCAGCACAAATTATTCAAT
CAGTTGAAGATTTTAAAACGTACGTTAAAAACCAAAAGACAATTTCATCAGAAATTACTC
GTTCATCCGATAGAAAACAAAAAACTGTATCAGAAGAACTTCAAAGATTGAATAACAAGC
TACAAGAATCATCAAATAATATAGATAACAATAGGCTAGCATTAAGACATTTGCGGAATG
AAACTTCAAAAGTGATTGAACATGCAGATATGGCTCAGCGAACGCATGAAACTCCAAGTG
GTCTCCAATTCGAAAATACAATGCCACAAGTTTATTTCAAGGAACTTATTCAAAAGTATG
AAACAGATTTATTAGGATTGAAGCATCAAGTTGAGTTGACTGAAAAGCATTTGCAATCAT
TAGTGACACCTCAAAATTTTACTGCTCAAGATTTAAAACGTGGGCTACAACAAATTCATG
AAAATTTTATTGCACTTGCTGGAAGGCTGCAAGAGGCACATACAAAAGTAGAAAATCAAA
AGACTCAATATTTGGAACTTAGAAAACTTATACTAAAAGATTCAACTAATATATTTGAGA
TTGAAGAAAAGAGTCCTGAAATAGATAAAGCACAGGCCAGCAGAGTTCAATATGGACCAA
ATACTTTTTCTTCATCATCAGTAAATCATAATTTCTTCAATTCTGTAATGAATAGACAGC
AGCAGCAACAACAGCTTCAACAACAATCATTTCAAATGCCATTAAGTCAAACTCAACAAC
CAGCAGCAGCACCTCAGAATAGTTTCTTTGGTTCGAATACACTGAGTTTTAATTTTAATA
AGTAA
>g2817.t2 Gene=g2817 Length=308
MTSASTSNNFVGLGGIDMATTAQQIVPQGKVETTKVKETQVPAQIIQSVEDFKTYVKNQK
TISSEITRSSDRKQKTVSEELQRLNNKLQESSNNIDNNRLALRHLRNETSKVIEHADMAQ
RTHETPSGLQFENTMPQVYFKELIQKYETDLLGLKHQVELTEKHLQSLVTPQNFTAQDLK
RGLQQIHENFIALAGRLQEAHTKVENQKTQYLELRKLILKDSTNIFEIEEKSPEIDKAQA
SRVQYGPNTFSSSSVNHNFFNSVMNRQQQQQQLQQQSFQMPLSQTQQPAAAPQNSFFGSN
TLSFNFNK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g2817.t2 | Coils | Coil | Coil | 74 | 108 | - |
| 6 | g2817.t2 | Coils | Coil | Coil | 197 | 217 | - |
| 4 | g2817.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 270 | 294 | - |
| 2 | g2817.t2 | PANTHER | PTHR13437 | NUCLEOPORIN P58/P45 NUCLEOPORIN-LIKE PROTEIN 1 | 6 | 301 | 1.6E-42 |
| 3 | g2817.t2 | PANTHER | PTHR13437:SF2 | NUCLEOPORIN P58/P45 | 6 | 301 | 1.6E-42 |
| 1 | g2817.t2 | Pfam | PF15967 | Nucleoporin FG repeated region | 4 | 272 | 2.7E-46 |
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.
