General information for g3959.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t4 | TTS | g3959.t4 | 29276352 | 29276352 |
| chr_3 | g3959 | g3959.t4 | isoform | g3959.t4 | 29277149 | 29277905 |
| chr_3 | g3959 | g3959.t4 | exon | g3959.t4.exon1 | 29277149 | 29277905 |
| chr_3 | g3959 | g3959.t4 | cds | g3959.t4.CDS1 | 29277151 | 29277876 |
| chr_3 | g3959 | g3959.t4 | TSS | g3959.t4 | NA | NA |
Sequences
>g3959.t4 Gene=g3959 Length=757
TTTTAGCTCAGGCAACTGAAATTCTTTTTATGAGAATTGATTCAATGAATACATCATGTT
TTGATCGCTTTGTCAATTGGTTTTCATATCATTTGAGTAACTTCCAATTTCGTTGGTCAT
GGGATGATTGGGATAGTTGCTTATTCTTGGAACCAGAGCATCCGAGACCAAAGTTTATTC
AAGAAGTCTTACAAAAATGCTTAAGATTATCCTATTATCAACGCATAAAGGATATGATGC
CTGTAGCTTACGAAAAGTTGCTGCCACCAATGACTACACCAGAATATAAATATACTTCTG
AAGATGCTGCTTCTTTACCAGGAACAGCAACTGCTCACAAACTTGTCGTAGCTATTCGTC
AAAAATGTACACCAGAAGAAATCCTTAATGAACTCAAAGATTTGCCAAATCCACGCGATA
CTGAAAATGACATGGTAGAGTCAACATTTAATCCACTGAAAATTGATGTTTTCACTCAAA
CACTTTTGAATTTGGGTTCAAAGAGTTTTTCACATACATTTGCGGCAATTTCAAAGTTTC
ACTATGTCTTTAAACAGCTTGCTGATTCTGAAGAAGCTCAAATATGCATATTGCATAATG
TATTTGAATTGTGGCGTAATCATCAGCAAATGATAGTTGTTATTGTTGATAAATTACTAA
AAACTCAGATTGTTGAGTGTTCTTCTGTCGCTACTTGGGTTTTTTCAAAAGAAATGTCAT
CAGAATTTACTAAAATGTATTTATGGGAAATTTTACA
>g3959.t4 Gene=g3959 Length=242
MRIDSMNTSCFDRFVNWFSYHLSNFQFRWSWDDWDSCLFLEPEHPRPKFIQEVLQKCLRL
SYYQRIKDMMPVAYEKLLPPMTTPEYKYTSEDAASLPGTATAHKLVVAIRQKCTPEEILN
ELKDLPNPRDTENDMVESTFNPLKIDVFTQTLLNLGSKSFSHTFAAISKFHYVFKQLADS
EEAQICILHNVFELWRNHQQMIVVIVDKLLKTQIVECSSVATWVFSKEMSSEFTKMYLWE
IL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g3959.t4 | Gene3D | G3DSA:1.25.40.180 | - | 1 | 82 | 0 |
| 6 | g3959.t4 | Gene3D | G3DSA:1.25.40.180 | - | 90 | 242 | 0 |
| 3 | g3959.t4 | PANTHER | PTHR12412 | CAP BINDING PROTEIN | 1 | 242 | 0 |
| 2 | g3959.t4 | Pfam | PF09088 | MIF4G like | 4 | 71 | 0 |
| 1 | g3959.t4 | Pfam | PF09090 | MIF4G like | 86 | 242 | 0 |
| 5 | g3959.t4 | SUPERFAMILY | SSF48371 | ARM repeat | 2 | 80 | 0 |
| 4 | g3959.t4 | SUPERFAMILY | SSF48371 | ARM repeat | 83 | 242 | 0 |
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.
