General information for g10576.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Nuclear pore complex protein Nup88.
Parent gene
- The parent gene g10576 is located on chr_1: 10513695..10515922 (+ 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_1 | g10576 | g10576.t1 | TSS | g10576.t1 | 10511481 | 10511481 |
| chr_1 | g10576 | g10576.t1 | isoform | g10576.t1 | 10511532 | 10513695 |
| chr_1 | g10576 | g10576.t1 | exon | g10576.t1.exon1 | 10511532 | 10511720 |
| chr_1 | g10576 | g10576.t1 | cds | g10576.t1.CDS1 | 10511532 | 10511720 |
| chr_1 | g10576 | g10576.t1 | exon | g10576.t1.exon2 | 10511779 | 10513695 |
| chr_1 | g10576 | g10576.t1 | cds | g10576.t1.CDS2 | 10511779 | 10513695 |
| chr_1 | g10576 | g10576.t1 | TTS | g10576.t1 | 10513765 | 10513765 |
Sequences
>g10576.t1 Gene=g10576 Length=2106
ATGACAGAAATTGATGTTTTTAAATTTTCACAGCTCAAAATATTTGATGGACTCAAGGAT
AATTTACCTGAAGAGTCGCGAGAAATTGCTACAGTATATGAAGATCTTCTTTTTGCTTGG
AATTTCAAAGAAAATAATTTGCAAGTTGTAAATTGGAGAGCGGCACAAAATAAAGAACCG
AAAATTCAAAAGTTGATTTTATCAGCAATACCTAATTTTACAATCTCAAAAGTTGCAATT
TCTTATGGAGGTTCATTTGCATTTGTAAGCGGTTCAAAAGGGATCATTATGATTGAAATG
CCGACTCGATGGGGATCTGATGGAATTTATCAAGATGGAAAAGCTCAAATTACTTGTAAA
ACTATAAATATATATGAGCATTCACTTCAGGCAGAAGTTATGCAAGCTCGTTGGCATCCT
AATTCACCAACAGACTCACATTTGCTCGTATTACTTTCTGATAATTCACTTAGAATTTAT
GATGAAGGAACATTGAAACATACATGGAGAGTTGGACCGTTGCCCACAGGAAACAATCTA
TCTTATCTCAAAGGACTTGGTGATACAGCTATTGATTTTGACATAGCGCCTGCTCAGGTC
AGCAACGATTTACAATCACCTAATAGTACTTTTGCCCTAGACATTAATGAAAGCAATAAA
AGTTTGACTACACATTCATTTTCAAACAAACGAAATCAAGAGCAAAAGAAAGTTGCATGG
CCCATTGTAATTTTACGTGGAAATGGAAGTGTTTATGTACTAACTGCTGGACTTAATACT
GAAAAACCTCGATTGCAAGGTCCATTGACTATGATTCCATCTCAAAAAGACAATTATGGC
GATGATTCTTGTTCGTTGATTGTTATTCCTACTCTACCAGTCACAATTGTCATTGCAGAG
AACTCGGGAGTTTTGCATCATGCATTAATGCTCGAAAATCAAATGAATCAAGATACTTTC
TTTGATGAATCAACAACTTTAGTTCCTAATGATTGGAATCTTTATGTTATAGAAAACATT
GAACTAGAATTGGGATTACAAGAAAACAATAACAAGTCAGATTTAACAACATGTCCTCTT
TATTTACATAGAGATCCAATAAATGAGCAAAGATATTTCTGTTATCATGATGCTGGACTT
CATGGTATAACTTTTGGATTTGTTCAACAGCTTCAAAAATATACTGATGATCAAACAAAT
GAAGATGAAATCAATATGAACGTACCATCTAGAATCGAATACATTCTCAGCACAAAAGCT
TTTAATAACGCAAAAATTAATGCAGTAGTGGGTTTTGGAATTCTTCAATTACCATCGGGA
GTGTTTGCTGTATTAAGCAGTGGACAAGTTATTAGTTTGAGTACTGTTAAAACAATGCTT
CCACTTGTGACTGATTTAAGTGCACATCAACCAAGTCTCGATTATTTCAAAACTAATGTA
CAAGACCAACAGTTGAAAGTTCCTTTTGATCAACATATTAGAGCTTTACTAAAATCTGAT
GTGTCACAACCAATTTTTCAGCTTGATAAAAGCAAACCACCATCATCTCAGGAAACTTTT
CAATTACTTATGAATTCAATACAAATTATGCGCGACAAACAATTTGCACGGCATGATAAA
GTACGTCAAGAACTTATTAAAAGAATTAAAATATTAAGTCTCATGAAGAATCAACAGAAA
GATGAAATTGCACTTTTATTTGAGAGTAAGGAGCAAATTCAAGAAAATGCTTATAAACTT
GCAGATATGCATGAAGATATCATTGATCGTCAGCAATTGTTGCAAAAACGTATTCAAGAC
ATCTCTCGTTTATCATCATTAAGATTACCTGCTATTTCATCGAACGAAAAAGAATTTGCT
GACACTATTAAGAAATTCAAATCATGCATTGACAAATTGTCACAAGATGTAAAACAAATC
AAAGCAAAAAATGAAGCCCAAAGAAAAGCACTTGAAAGTTGGAGCAAGTCAAATGATGAT
TTTGTTAAAATTTCATTGCCACCAAAGCAGGAAGAGACAATTAAAGAATTTCTTAGCGAT
ATGATGCGTCAAATTCAAGGTTTAAAAGCTGATGTTCAAAAGATTAGTAATGTTATTGAT
TTCTAA
>g10576.t1 Gene=g10576 Length=701
MTEIDVFKFSQLKIFDGLKDNLPEESREIATVYEDLLFAWNFKENNLQVVNWRAAQNKEP
KIQKLILSAIPNFTISKVAISYGGSFAFVSGSKGIIMIEMPTRWGSDGIYQDGKAQITCK
TINIYEHSLQAEVMQARWHPNSPTDSHLLVLLSDNSLRIYDEGTLKHTWRVGPLPTGNNL
SYLKGLGDTAIDFDIAPAQVSNDLQSPNSTFALDINESNKSLTTHSFSNKRNQEQKKVAW
PIVILRGNGSVYVLTAGLNTEKPRLQGPLTMIPSQKDNYGDDSCSLIVIPTLPVTIVIAE
NSGVLHHALMLENQMNQDTFFDESTTLVPNDWNLYVIENIELELGLQENNNKSDLTTCPL
YLHRDPINEQRYFCYHDAGLHGITFGFVQQLQKYTDDQTNEDEINMNVPSRIEYILSTKA
FNNAKINAVVGFGILQLPSGVFAVLSSGQVISLSTVKTMLPLVTDLSAHQPSLDYFKTNV
QDQQLKVPFDQHIRALLKSDVSQPIFQLDKSKPPSSQETFQLLMNSIQIMRDKQFARHDK
VRQELIKRIKILSLMKNQQKDEIALLFESKEQIQENAYKLADMHEDIIDRQQLLQKRIQD
ISRLSSLRLPAISSNEKEFADTIKKFKSCIDKLSQDVKQIKAKNEAQRKALESWSKSNDD
FVKISLPPKQEETIKEFLSDMMRQIQGLKADVQKISNVIDF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g10576.t1 | Coils | Coil | Coil | 556 | 576 | - |
| 6 | g10576.t1 | Coils | Coil | Coil | 630 | 650 | - |
| 3 | g10576.t1 | PANTHER | PTHR13257 | NUCLEOPORIN NUP84-RELATED | 35 | 257 | 4.8E-95 |
| 2 | g10576.t1 | PANTHER | PTHR13257 | NUCLEOPORIN NUP84-RELATED | 264 | 699 | 4.8E-95 |
| 1 | g10576.t1 | Pfam | PF10168 | Nuclear pore component | 6 | 699 | 1.0E-185 |
| 4 | g10576.t1 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 37 | 173 | 1.36E-5 |
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:0000055 | ribosomal large subunit export from nucleus | BP |
| GO:0006913 | nucleocytoplasmic transport | BP |
| GO:0005515 | protein binding | MF |
| GO:0000056 | ribosomal small subunit export from nucleus | BP |
| GO:0017056 | structural constituent of nuclear pore | MF |
KEGG
Orthology
- This transcript has been annotated with K14318 (nuclear pore complex protein Nup88)
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.
