General information for g3959.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Nuclear cap-binding protein subunit 1.
Parent gene
- The parent gene g3959 is located on chr_3: 29277905..29279135 (- 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 | g3959 | g3959.t2 | TTS | g3959.t2 | 29276352 | 29276352 |
| chr_3 | g3959 | g3959.t2 | isoform | g3959.t2 | 29276548 | 29277149 |
| chr_3 | g3959 | g3959.t2 | exon | g3959.t2.exon1 | 29276548 | 29276658 |
| chr_3 | g3959 | g3959.t2 | cds | g3959.t2.CDS1 | 29276548 | 29276658 |
| chr_3 | g3959 | g3959.t2 | exon | g3959.t2.exon2 | 29276728 | 29276916 |
| chr_3 | g3959 | g3959.t2 | cds | g3959.t2.CDS2 | 29276728 | 29276916 |
| chr_3 | g3959 | g3959.t2 | exon | g3959.t2.exon3 | 29276977 | 29277149 |
| chr_3 | g3959 | g3959.t2 | cds | g3959.t2.CDS3 | 29276977 | 29277132 |
| chr_3 | g3959 | g3959.t2 | TSS | g3959.t2 | NA | NA |
Sequences
>g3959.t2 Gene=g3959 Length=473
ATTTGACTATAAAGAAAATGAACAAACACGTTATGAAATTGAGTGCAGAATTAGCTGATG
CAAAAGAAAAGTTAGCTAAAGATGCTGATTCATCATCGAGTGACGATTCAGATAATGAAA
GCATGACACCTAAAAAGAAAAAAGATGAGACAGTGGAAAAACCAACAGAAGAAGCTGTAG
AAAAGATGGAAGAAAAACTTGAAGCAGCATATGGTGATCAAAAGAGAATCTTTTTAATCA
TATTTCAACGTTTCATCATGATTCTTTCGGAACATTTAGTTAAATGTGACACTGATGGTA
GAGATTTTAGTACTGATTGGTATCGTTGGACAATTGGACGATTACAGCAAGTTTTTCTTG
TCCATCACGAGCAGGTTCAAAAGTACTCGAGTACATTGGAAAGTCTTCTTTTTACGCAAG
TCGATTCTCATATATTGGACGTTTTTCTACAATTTGTTGCACTTACAAAATAA
>g3959.t2 Gene=g3959 Length=151
MNKHVMKLSAELADAKEKLAKDADSSSSDDSDNESMTPKKKKDETVEKPTEEAVEKMEEK
LEAAYGDQKRIFLIIFQRFIMILSEHLVKCDTDGRDFSTDWYRWTIGRLQQVFLVHHEQV
QKYSSTLESLLFTQVDSHILDVFLQFVALTK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g3959.t2 | Gene3D | G3DSA:1.25.40.180 | - | 43 | 149 | 2.3E-32 |
| 4 | g3959.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 16 | 54 | - |
| 2 | g3959.t2 | PANTHER | PTHR12412 | CAP BINDING PROTEIN | 1 | 150 | 2.5E-28 |
| 1 | g3959.t2 | Pfam | PF09090 | MIF4G like | 1 | 122 | 3.0E-27 |
| 3 | g3959.t2 | SUPERFAMILY | SSF48371 | ARM repeat | 1 | 149 | 2.07E-30 |
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:0016070 | RNA metabolic process | BP |
| GO:0000339 | RNA cap binding | MF |
| GO:0045292 | mRNA cis splicing, via spliceosome | BP |
| GO:0051028 | mRNA transport | BP |
| GO:0005846 | nuclear cap binding complex | CC |
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.
