General information for g13900.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Nuclear cap-binding protein subunit 2.
Parent gene
- The parent gene g13900 is located on chr_1: 33202121..33202639 (- 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 | g13900 | g13900.t1 | TTS | g13900.t1 | 33202011 | 33202011 |
| chr_1 | g13900 | g13900.t1 | isoform | g13900.t1 | 33202121 | 33202639 |
| chr_1 | g13900 | g13900.t1 | exon | g13900.t1.exon1 | 33202121 | 33202363 |
| chr_1 | g13900 | g13900.t1 | cds | g13900.t1.CDS1 | 33202121 | 33202363 |
| chr_1 | g13900 | g13900.t1 | exon | g13900.t1.exon2 | 33202424 | 33202639 |
| chr_1 | g13900 | g13900.t1 | cds | g13900.t1.CDS2 | 33202424 | 33202639 |
| chr_1 | g13900 | g13900.t1 | TSS | g13900.t1 | 33202700 | 33202700 |
Sequences
>g13900.t1 Gene=g13900 Length=459
ATGTCAAGCAATAGTGGAGTAAGTGTTGAATTAAGTAGTTATCGAGACCAACACTTTAAA
GGAACAAGATATGATCAAGAGAAGCTACTTAAGCAAACATCTACACTTTATGTCGGAAAT
TTAGCTTTTTATACAACCGAAGAACAAATTCATGAATTATTTTCACGTTGTGGCGATATT
AGAAGAATCATAATGGGATTAGATAAATTCAAGAAGACTCCATGTGGTTTTTGTTTTGTC
GAATACTACACTCGAGAAGATGCTGAGGCTGCAATGCGATATGTTAATGGAACTCGTTTA
GATGATCGAATTGTTAGAGTTGATTGGGATGCAGGTTTTGTCGAAGGCAGACAATATGGA
AGAGGGAAGAGTGGTGGTCAAGTAAGAGACGAATATAGAACTGATTATGATTCAGGACGA
GGAGGATATGGTAAAGCAGTGGTTGTCAATCAAAAATAA
>g13900.t1 Gene=g13900 Length=152
MSSNSGVSVELSSYRDQHFKGTRYDQEKLLKQTSTLYVGNLAFYTTEEQIHELFSRCGDI
RRIIMGLDKFKKTPCGFCFVEYYTREDAEAAMRYVNGTRLDDRIVRVDWDAGFVEGRQYG
RGKSGGQVRDEYRTDYDSGRGGYGKAVVVNQK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g13900.t1 | CDD | cd12240 | RRM_NCBP2 | 36 | 113 | 0.000 |
| 6 | g13900.t1 | Gene3D | G3DSA:3.30.70.330 | - | 3 | 120 | 0.000 |
| 2 | g13900.t1 | PANTHER | PTHR18847 | 20 KD NUCLEAR CAP BINDING PROTEIN | 4 | 149 | 0.000 |
| 3 | g13900.t1 | PANTHER | PTHR18847:SF4 | NUCLEAR CAP-BINDING PROTEIN SUBUNIT 2 | 4 | 149 | 0.000 |
| 1 | g13900.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 36 | 104 | 0.000 |
| 7 | g13900.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 34 | 112 | 16.722 |
| 5 | g13900.t1 | SMART | SM00360 | rrm1_1 | 35 | 108 | 0.000 |
| 4 | g13900.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 26 | 144 | 0.000 |
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:0000339 | RNA cap binding | MF |
| GO:0045292 | mRNA cis splicing, via spliceosome | BP |
| GO:0005846 | nuclear cap binding complex | CC |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12883 (nuclear cap-binding protein subunit 2)
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.
