General information for g10829.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Nuclear pore complex protein Nup50.
Parent gene
- The parent gene g10829 is located on chr_1: 12165147..12165469 (+ 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 | g10829 | g10829.t1 | TSS | g10829.t1 | 12163779 | 12163779 |
| chr_1 | g10829 | g10829.t1 | isoform | g10829.t1 | 12163840 | 12165147 |
| chr_1 | g10829 | g10829.t1 | exon | g10829.t1.exon1 | 12163840 | 12165147 |
| chr_1 | g10829 | g10829.t1 | cds | g10829.t1.CDS1 | 12163840 | 12165147 |
| chr_1 | g10829 | g10829.t1 | TTS | g10829.t1 | 12165444 | 12165444 |
Sequences
>g10829.t1 Gene=g10829 Length=1308
ATGGCAGCAAAACGTATAGCAGGTAGAGAATTAAATCATGACAATTGGAATGAAGAAGAG
GAAGCTGAAGATGCTGGTGAATTTAAAAAAGCAAGTGAAGATATTTTAGCGAAAAGAGTA
CGAAAAGTCGCAAAAAGAAGAACTGCTGATAATGAAAGCGGCACTCAAGTTCTTAATCCG
TTTAGTGGATTCGGAGGCTTTGGATCAAACTCAAATACAGTTGCATCAACTCCAATAAGT
TCTTCAAGTCCATTTAGTTTTCTCGCAAAATTACCGGCTTCAGCATCATCTGCTTCTACT
GCTCCAATAATTTCATCAACAACAACCAAAACAAATGGCGAAGCAAAGGAAAATGGTGAC
TCAAAATACTCTGAATATAATGGAAAAGTAAAAGCATTAAATATTGCATTTACTGATTGG
ATTAAAAAGCATGTTGATGATAATGCACTTTGCGATTTGAGGCCAGTTTTTGCAGATTAT
GAAAAATATATGAAAGAATTTAATGAATTGAAACAAAAAATTTCAAGTTCATCAACATCA
TCAGAGAAGAAAGAAGAGTCATTTAAATCGGACACACCTGCAGGAGGTTTTACATTTGGA
AAACCCGCAACAACAACTGCCACAAGTCCAGTTGCTAGCATTTTCTCTTCTGTAAATACA
TCTTCAATCTTTTCATCATCAACTACAAAAGAAACATCGCCTGCTAAACCAACTGAGAGC
AAAGGATTTTCTTTTGGCCTAGCATCAAATTCACAACAGCCAACATCAGCACCAACATTC
TCATTTGGTTTAAAACCTACTTCATCACTACCCGGTTCTTCACTTTTTGGTATTTCTACG
ACTACATCAACTCCCTTTTCTTTTGCTAATGTTACTCAAACAAAAAGCACTGCTGATAAT
AATATTGATCAAGGAGAGAATACTGAAGCAGACGAAGAACCACCTAAAAATGAATTTGTT
CCTGTTGTTGAAGAGGATAGTTTACTATCAAAAAGATGTAAAGTATTTGTAAAAACTGGC
ACAGATTATACAGATAGAGGTGTTGGAACACTTTATTTAAAGAAGGTTGATGAAAAAGTA
CAATTAATTGTACGTGCAGATACAAATTTGGGCAACATTTTACTGAATATCATTTTACAA
GAAGGATTGCCTACATCTCGATTAGGAAAGAATAATGTTATGATCGTGTGTGTTCCAACG
CCTGAAAGTAAACCACCACCGACCCCTGTTCTAGTTCGTGTCAAGACTGGAGAAGAAGCT
GACGAATTATTATCAATTTTAGAAAAATATAAAAAGGGAGCAGAATAA
>g10829.t1 Gene=g10829 Length=435
MAAKRIAGRELNHDNWNEEEEAEDAGEFKKASEDILAKRVRKVAKRRTADNESGTQVLNP
FSGFGGFGSNSNTVASTPISSSSPFSFLAKLPASASSASTAPIISSTTTKTNGEAKENGD
SKYSEYNGKVKALNIAFTDWIKKHVDDNALCDLRPVFADYEKYMKEFNELKQKISSSSTS
SEKKEESFKSDTPAGGFTFGKPATTTATSPVASIFSSVNTSSIFSSSTTKETSPAKPTES
KGFSFGLASNSQQPTSAPTFSFGLKPTSSLPGSSLFGISTTTSTPFSFANVTQTKSTADN
NIDQGENTEADEEPPKNEFVPVVEEDSLLSKRCKVFVKTGTDYTDRGVGTLYLKKVDEKV
QLIVRADTNLGNILLNIILQEGLPTSRLGKNNVMIVCVPTPESKPPPTPVLVRVKTGEEA
DELLSILEKYKKGAE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g10829.t1 | CDD | cd13170 | RanBD_NUP50 | 321 | 431 | 1.12901E-38 |
| 13 | g10829.t1 | Gene3D | G3DSA:2.30.29.30 | - | 235 | 431 | 2.2E-30 |
| 9 | g10829.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 16 | - |
| 12 | g10829.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 28 | - |
| 11 | g10829.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 174 | 195 | - |
| 10 | g10829.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 294 | 316 | - |
| 3 | g10829.t1 | PANTHER | PTHR23138:SF147 | NUCLEAR PORE COMPLEX PROTEIN NUP50 | 3 | 107 | 2.3E-58 |
| 5 | g10829.t1 | PANTHER | PTHR23138 | RAN BINDING PROTEIN | 3 | 107 | 2.3E-58 |
| 4 | g10829.t1 | PANTHER | PTHR23138:SF147 | NUCLEAR PORE COMPLEX PROTEIN NUP50 | 108 | 430 | 2.3E-58 |
| 6 | g10829.t1 | PANTHER | PTHR23138 | RAN BINDING PROTEIN | 108 | 430 | 2.3E-58 |
| 2 | g10829.t1 | Pfam | PF08911 | NUP50 (Nucleoporin 50 kDa) | 3 | 69 | 3.6E-17 |
| 1 | g10829.t1 | Pfam | PF00638 | RanBP1 domain | 325 | 432 | 9.5E-8 |
| 8 | g10829.t1 | SMART | SM00160 | ranbd_3 | 312 | 430 | 0.0013 |
| 7 | g10829.t1 | SUPERFAMILY | SSF50729 | PH domain-like | 309 | 431 | 3.2E-20 |
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:0046907 | intracellular transport | BP |
| GO:0005643 | nuclear pore | CC |
KEGG
Orthology
- This transcript has been annotated with K14295 (nuclear pore complex protein Nup50)
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.
