General information for g398.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Nuclear pore complex protein Nup93-1.
Parent gene
- The parent gene g398 is located on chr_3: 3163892..3164947 (+ 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 | g398 | g398.t1 | TSS | g398.t1 | 3161215 | 3161215 |
| chr_3 | g398 | g398.t1 | isoform | g398.t1 | 3161294 | 3163892 |
| chr_3 | g398 | g398.t1 | exon | g398.t1.exon1 | 3161294 | 3161457 |
| chr_3 | g398 | g398.t1 | cds | g398.t1.CDS1 | 3161294 | 3161457 |
| chr_3 | g398 | g398.t1 | exon | g398.t1.exon2 | 3161520 | 3161700 |
| chr_3 | g398 | g398.t1 | cds | g398.t1.CDS2 | 3161520 | 3161700 |
| chr_3 | g398 | g398.t1 | exon | g398.t1.exon3 | 3161766 | 3163594 |
| chr_3 | g398 | g398.t1 | cds | g398.t1.CDS3 | 3161766 | 3163594 |
| chr_3 | g398 | g398.t1 | exon | g398.t1.exon4 | 3163649 | 3163892 |
| chr_3 | g398 | g398.t1 | cds | g398.t1.CDS4 | 3163649 | 3163892 |
| chr_3 | g398 | g398.t1 | TTS | g398.t1 | 3163969 | 3163969 |
Sequences
>g398.t1 Gene=g398 Length=2418
ATGGATTTTACTACACTTATGCAGCAAGCGCAGAAGCTTGTAAATGAAACACAAAATAAT
GATGATCTACCGCGAGTTGAGCGTTCAATGCCGCAAATTTTAAAAGCAATAAATGAACTT
CATAGTAGAGTGACTTCATCCAGTAGTGCTCAAGATGTGCAAGCATATATTCTATTAGGA
TCAAAAGGTATTGATGTACCAAAGATTTCAAAAAATCTTGAAACTTTGAGCGCTCGAAAA
ACATTTGAGACATTAGATCCAGTTTATGACACAGATATTCATAGTTTTCTCAAAAATGAA
AAAGAAAATGCTATTCTATCAATTATTCAAGATGTTAACAAGAGTTCTTTTGAAAATGCT
CAAGCACAAAAATGGGATCATATTCAAAATGAATGGAAGCTAGAAAAAGTTAAATTAATG
AATGCCCTTGTTGGTCCATCTCAAAATTGGATTGATTTTAGAAAAATGCCAGAACAAACA
ATTTTAAATGAAGCATCACAAGGAACAATGAAGTCTTCTCTCAACTCAATTCAAATGGCT
TATGCAAGGGAAGTTTCAGAGTATAATCGCTATGACAAAGCTTTACGGCCTTCATTAGTT
GAAAAATTCACAAGTGTTGCACAATCATTCAATGATAAGAAAATTGTCGATATGTGGGAA
ATAATAAAATTTATGTCCAACGTTCGTCCTATTCCAAAGAATCAAGATCCAGCTAAGCAA
AGATTTCAAGCAGAATTTGTCGATCAAGCAAAGAAGTATCTCGAGAAGCATTTCAAAGTT
TTTATGCAAACCGTTATTTCAGAACATTTAAAAGAAGCTCAAAGAGGAGGTGAAGCAAGT
AATTATAAGCTTATCGAAGCATTTGTCAATCTCAAATTTAGAAATCCAAATGAATTGATT
GGATTACAAGATCGTAGAGACAATTTTTGGCCATGGCCAATGGTGTACTACTCAATGAGA
TGTGGAGATAATAAATCGGCTTTAAAATGTCTCGAAACATTCGTATCTGATCAAAAAGAG
CTCATTACAGCATTTGAAGAAATATTGAAAAATCCAGATGGAAAGATAAGCGCAAAAATC
AAATCACAAATTAAAATGCAATATAAACAGCATAAAATTCGAATGAGTGATCCTTATAAA
CGAACTGTTTATGCTATTTTGGGTTCATGTAATGAACAGTCAGAACTCACATCATCGTTT
GAAGATTACTTGTGGATGCAACTTTATTTAATTTCTAATGTATCGACTGACAGTTCTGAC
AAATTGACATTGCCTGCATTACAACGAATGATTTTAGAACAATATGGCGAGAAATATTTC
AAAGCAGATGAGCAACCGCAACGGTATTTTGAAGTTTTGGCTCTAACAGGACAATTTGAA
GCAGCAATTGAATTTCTTTCTCGTTTTGATCGTTATAGAACTCATGCTGTTCATTTTGCT
CTTGCTTTAAATGAACTTCATTTGATTGTAGGACCTAGAAATATTCAAGAGCCGTTAATT
TCTGTCGATATTGAAGATCCAAAACCATTACGTCGTTTAAATCTTGCGAGACTTGTAATG
CTCTATGTAGAAAAATTTGAAATTAGTGATCCAGCTGAAGCACTTCAATATTACTATTTC
TTGCGACACTTGACTGATCCTGATGGCAAAAATCTTTTCCTTTCATGTGTCACTGATTTG
GTTGTTGAAAATCTCAATTATGAGCTGGTTTTCGGAAAAATGCAACCCAGTGGGATCAGA
TCACGTGGTCTCATTGATGAATTTGACAACACAATCAACGTTTCTGCAGCTTGCAATTCG
ATTGCTGATGAATTTGTTAAGAAAGGCTTATTTGAAGATGCCATTAAGATGTATGACATA
GCTGATAATCATGAGCAAACGATTCGATATATTATTACACTCTTATCGCAAGTTGTTCAT
CAACAAACAAAACCAGGTTCTGTAAAAGAAAGACTTCAACAAATAACGATGGAAGTTAAT
GAACGATATCGCTCAAAAGAAATATCATGCGATCCGCAAGTACTAAAAACATTCAATATT
TTGCGAAATTTAATGGACTTCTTTCAATGCTATCATGATAACAAGCATGAAGATGCATTA
GAAATTTTGGCTCAAACAAAACTTGTGCCATTGAGTATGAACGATTTAGATGTTTGTGTA
CAAAATTTTAAAAAAACTGGAGGAGAAGTTTGCAAAATTTTGCCAGATTTATTGCTTTCA
ACAATGGAAATCATTTATAAAAAATATACGATGCTGAAGAAAGACGTTAATAAATTCAAT
GAAAGTGTAAGTGATGACAAATTAAAATTCCTGCGTGAACAAGCTAAAGCAATCACAGTT
ATGGCTGCAACTGTTCCATATCGAATGCCAGGTGACACTAATGCTCGTCTTATTCAAACT
GAAATTTTGATGCATTAA
>g398.t1 Gene=g398 Length=805
MDFTTLMQQAQKLVNETQNNDDLPRVERSMPQILKAINELHSRVTSSSSAQDVQAYILLG
SKGIDVPKISKNLETLSARKTFETLDPVYDTDIHSFLKNEKENAILSIIQDVNKSSFENA
QAQKWDHIQNEWKLEKVKLMNALVGPSQNWIDFRKMPEQTILNEASQGTMKSSLNSIQMA
YAREVSEYNRYDKALRPSLVEKFTSVAQSFNDKKIVDMWEIIKFMSNVRPIPKNQDPAKQ
RFQAEFVDQAKKYLEKHFKVFMQTVISEHLKEAQRGGEASNYKLIEAFVNLKFRNPNELI
GLQDRRDNFWPWPMVYYSMRCGDNKSALKCLETFVSDQKELITAFEEILKNPDGKISAKI
KSQIKMQYKQHKIRMSDPYKRTVYAILGSCNEQSELTSSFEDYLWMQLYLISNVSTDSSD
KLTLPALQRMILEQYGEKYFKADEQPQRYFEVLALTGQFEAAIEFLSRFDRYRTHAVHFA
LALNELHLIVGPRNIQEPLISVDIEDPKPLRRLNLARLVMLYVEKFEISDPAEALQYYYF
LRHLTDPDGKNLFLSCVTDLVVENLNYELVFGKMQPSGIRSRGLIDEFDNTINVSAACNS
IADEFVKKGLFEDAIKMYDIADNHEQTIRYIITLLSQVVHQQTKPGSVKERLQQITMEVN
ERYRSKEISCDPQVLKTFNILRNLMDFFQCYHDNKHEDALEILAQTKLVPLSMNDLDVCV
QNFKKTGGEVCKILPDLLLSTMEIIYKKYTMLKKDVNKFNESVSDDKLKFLREQAKAITV
MAATVPYRMPGDTNARLIQTEILMH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g398.t1 | PANTHER | PTHR11225 | NUCLEAR PORE COMPLEX PROTEIN NUP93 NUCLEOPORIN NUP93 DEAD EYE PROTEIN | 2 | 805 | 0 |
| 3 | g398.t1 | PANTHER | PTHR11225:SF4 | NUCLEAR PORE COMPLEX PROTEIN NUP93 | 2 | 805 | 0 |
| 1 | g398.t1 | Pfam | PF04097 | Nup93/Nic96 | 211 | 790 | 0 |
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 K14309 (nuclear pore complex protein Nup93)
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.
