General information for g6275.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g6275 is located on chr_2: 15775233..15775880 (- 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_2 | g6275 | g6275.t1 | isoform | g6275.t1 | 15775233 | 15775880 |
| chr_2 | g6275 | g6275.t1 | exon | g6275.t1.exon1 | 15775233 | 15775794 |
| chr_2 | g6275 | g6275.t1 | cds | g6275.t1.CDS1 | 15775233 | 15775794 |
| chr_2 | g6275 | g6275.t1 | exon | g6275.t1.exon2 | 15775855 | 15775880 |
| chr_2 | g6275 | g6275.t1 | cds | g6275.t1.CDS2 | 15775855 | 15775880 |
| chr_2 | g6275 | g6275.t1 | TSS | g6275.t1 | 15776014 | 15776014 |
| chr_2 | g6275 | g6275.t1 | TTS | g6275.t1 | NA | NA |
Sequences
>g6275.t1 Gene=g6275 Length=588
ATGAGTGCCACAGAAAATAAAATTACTCAATGGAAGAGAGTTTATCAACTTGTATCAGGA
ACATTTTACAATGAGAATCAAGAAGTAGTAAAAAAGAAACTATTAGAGCTTCAAAATGAA
ATTCAAGATGGAATTAAAATTTTTAAAAAACCAAAAGCAGACGCGACTGAAGAGACTGAA
AAACTCCTCAATGAAAAGCAACAAACAAAAATACTACCATTTGCACAAAAACTCCAAAAA
TATCTAGACCTTGATGTTAAACAGTCATACAAAATTCTTTGCTATTATTTGGAAAATGAA
TATCGTGGATCAGCTTCCTCTTTGCAGAATTTTGTATCAAACGAATCTTTGATGATTAAA
TTACTCAATGATATTTGGTTTTATTATACACTCGAGAGGATGGTTTTGCTAAAAGTTGTG
AAATGTGTTTTAGAATATCATGAATCACCTGATCATCCATATAGAGAAGCCTTCAAAGCG
ATTGTTGATAAAATAGGCTTAGCAGTTCTTAGAAAATCATATATTGAACAGTTTGAGATG
ATCTTAAAAGATGTACAGCAGGGAAAATTTTTACCGATCATCTTCTAA
>g6275.t1 Gene=g6275 Length=195
MSATENKITQWKRVYQLVSGTFYNENQEVVKKKLLELQNEIQDGIKIFKKPKADATEETE
KLLNEKQQTKILPFAQKLQKYLDLDVKQSYKILCYYLENEYRGSASSLQNFVSNESLMIK
LLNDIWFYYTLERMVLLKVVKCVLEYHESPDHPYREAFKAIVDKIGLAVLRKSYIEQFEM
ILKDVQQGKFLPIIF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g6275.t1 | Coils | Coil | Coil | 52 | 72 | - |
| 2 | g6275.t1 | PANTHER | PTHR31431 | NUCLEOPORIN NUP188 HOMOLOG | 9 | 182 | 2.5E-29 |
| 1 | g6275.t1 | Pfam | PF10487 | Nucleoporin subcomplex protein binding to Pom34 | 30 | 189 | 9.7E-23 |
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:0017056 | structural constituent of nuclear pore | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
