General information for g11537.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Nuclear protein localization protein 4-like protein.
Parent gene
- The parent gene g11537 is located on chr_1: 16924417..16925334 (+ 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 | g11537 | g11537.t4 | TSS | g11537.t4 | 16922582 | 16922582 |
| chr_1 | g11537 | g11537.t4 | isoform | g11537.t4 | 16922678 | 16924396 |
| chr_1 | g11537 | g11537.t4 | exon | g11537.t4.exon1 | 16922678 | 16922692 |
| chr_1 | g11537 | g11537.t4 | cds | g11537.t4.CDS1 | 16922678 | 16922692 |
| chr_1 | g11537 | g11537.t4 | exon | g11537.t4.exon2 | 16923008 | 16923238 |
| chr_1 | g11537 | g11537.t4 | cds | g11537.t4.CDS2 | 16923008 | 16923238 |
| chr_1 | g11537 | g11537.t4 | exon | g11537.t4.exon3 | 16923300 | 16924164 |
| chr_1 | g11537 | g11537.t4 | cds | g11537.t4.CDS3 | 16923300 | 16924164 |
| chr_1 | g11537 | g11537.t4 | exon | g11537.t4.exon4 | 16924246 | 16924396 |
| chr_1 | g11537 | g11537.t4 | cds | g11537.t4.CDS4 | 16924246 | 16924394 |
| chr_1 | g11537 | g11537.t4 | TTS | g11537.t4 | NA | NA |
Sequences
>g11537.t4 Gene=g11537 Length=1262
ATGGCTGAGGAAATTATTATTCGCATTCAGACTCCAGATGGTATCAAAAGAATAACGATC
GCAAAAAATGCGACATTGAAAGAACTTTACGAAGTGGTATATAAGACTTTAAATCTGATT
GATTACGGATTTTCTTTGTTTTCGGATCGCAGTTGTTCCAAAGAAATCCGTTCTACTCGT
TCTTCAACGCTCTCATCATTTAATCATGGTGACATTTTGTATTACAAACACATGGCAAGC
ACATCTTCACAATCCGATCAGTCATCATCATCATCAAATATTACGCAAACTCCTTCAGCA
ACAAAGAAAAATCTTCTTGTAGAAGATGCCGTAGATGTTGAACTATCTAAACTAGATGGT
CGTATTGAACGTAAAAAGGATGAAAAATTGTGCAGACATGCTAGTGGAAATCGATGCGTT
CATTGCTCTTCACTCGAACCATATGATGAGAATTATTTGAAGGAACAGAAAATAAAACAT
CTCTCATTTCATTCATATTTAAGAAAAATGACTTCTGGCGTCGATCGTGGAAAATTTGTG
GCGTTTGATGATATTAACTGCAAAATTAAATCAGGTTGTCGTGAGCATCCTCCATGGCCT
AAAGGCATTTGTTCTAAATGTCAACCTTCAGCAATTACCTTAAATCGTCAAATTTATCGT
CATGTTGATAACGTCATGTTTGAAAATAATGAAATTGTCGATGAATTTATTAATTATTGG
CGCACTACAAGTCATCAGCGTCTTGGTTTTCTTTATGGATGCTATGAAAAAACTAACGAT
GTTCCGTTGGGTATTCGAGCAAGAGTCTGTGCTATCTATGAACCGCCTCAAGAAAGTACT
AAGACCAGCATAAAGTTACTTCATGATCCAAATGATGCAGAAGTTGAAGAGATGGCAGAA
CAACTTGGTCTCAAACGTATTGGCTGGATATTTACTGATTTGGAAGCGATAAATGACGGC
AAAGTTAAGCATCTTCGTGGAATCGATACCTTCTTTTTAACTGCGAAAGAATGTATACTT
GCAGGACATTTTCAAAATTTGCATCCGAATCCTTGCAGTCAATCATCTAATGGATTTTTT
GGATCTAAATTTGTTACAATTTGTGTAACTGGCGATAAAGAAAATCAAATTCATATGGAA
GGTTATCAAGTTTCGAATCAATGTATGGCTCTTGTTCGTGACAACTGCTTGCTCCCAACT
AAAGATGCACCAGAATTGGGCTATGTTCGTGAATCTACAGATAAACAATATGTACCAGAT
GT
>g11537.t4 Gene=g11537 Length=420
MAEEIIIRIQTPDGIKRITIAKNATLKELYEVVYKTLNLIDYGFSLFSDRSCSKEIRSTR
SSTLSSFNHGDILYYKHMASTSSQSDQSSSSSNITQTPSATKKNLLVEDAVDVELSKLDG
RIERKKDEKLCRHASGNRCVHCSSLEPYDENYLKEQKIKHLSFHSYLRKMTSGVDRGKFV
AFDDINCKIKSGCREHPPWPKGICSKCQPSAITLNRQIYRHVDNVMFENNEIVDEFINYW
RTTSHQRLGFLYGCYEKTNDVPLGIRARVCAIYEPPQESTKTSIKLLHDPNDAEVEEMAE
QLGLKRIGWIFTDLEAINDGKVKHLRGIDTFFLTAKECILAGHFQNLHPNPCSQSSNGFF
GSKFVTICVTGDKENQIHMEGYQVSNQCMALVRDNCLLPTKDAPELGYVRESTDKQYVPD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g11537.t4 | CDD | cd08061 | MPN_NPL4 | 213 | 420 | 0.0000000 |
| 5 | g11537.t4 | Gene3D | G3DSA:3.10.20.90 | - | 1 | 76 | 0.0000000 |
| 6 | g11537.t4 | Gene3D | G3DSA:3.40.140.10 | Cytidine Deaminase | 207 | 411 | 0.0000011 |
| 4 | g11537.t4 | PANTHER | PTHR12710 | NUCLEAR PROTEIN LOCALIZATION 4 | 6 | 415 | 0.0000000 |
| 8 | g11537.t4 | PIRSF | PIRSF010052 | Polyub_prc_Npl4 | 5 | 420 | 0.0000000 |
| 2 | g11537.t4 | Pfam | PF11543 | Nuclear pore localisation protein NPL4 | 1 | 78 | 0.0000000 |
| 1 | g11537.t4 | Pfam | PF05020 | NPL4 family, putative zinc binding region | 108 | 243 | 0.0000000 |
| 3 | g11537.t4 | Pfam | PF05021 | NPL4 family | 247 | 420 | 0.0000000 |
| 7 | g11537.t4 | ProSiteProfiles | PS50249 | MPN domain profile. | 225 | 360 | 16.5650000 |
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:0006511 | ubiquitin-dependent protein catabolic process | BP |
KEGG
Orthology
- This transcript has been annotated with K14015 (nuclear protein localization protein 4)
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.
