General information for g11679.t18
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Splicing factor 3B subunit 6.
Parent gene
- The parent gene g11679 is located on chr_1: 17763149..17763651 (- 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 | g11679 | g11679.t18 | TTS | g11679.t18 | 17763087 | 17763087 |
| chr_1 | g11679 | g11679.t18 | isoform | g11679.t18 | 17763149 | 17763651 |
| chr_1 | g11679 | g11679.t18 | exon | g11679.t18.exon1 | 17763149 | 17763373 |
| chr_1 | g11679 | g11679.t18 | cds | g11679.t18.CDS1 | 17763149 | 17763373 |
| chr_1 | g11679 | g11679.t18 | exon | g11679.t18.exon2 | 17763419 | 17763560 |
| chr_1 | g11679 | g11679.t18 | cds | g11679.t18.CDS2 | 17763419 | 17763493 |
| chr_1 | g11679 | g11679.t18 | exon | g11679.t18.exon3 | 17763622 | 17763651 |
| chr_1 | g11679 | g11679.t18 | TSS | g11679.t18 | 17763786 | 17763786 |
Sequences
>g11679.t18 Gene=g11679 Length=397
ATGGCGTTGGCGATGCAAAAGCGGAATAATGTTCGACTTCCTCCAGAAGTTAATAGAATA
TTATATGTAAGAAACCTTCCCTATAAAATCACTAGTGATGAAATGTATGATATTTTTGGT
AAATATGGTGCAATCAGACAAATTAGAGTTGGAAATATTCCAGAAACAAAAGTTTGGTTT
TGTTATAGGAACGGCTTTTGTGGTATATGAAGATATTTGGGATGCAAAAAATGCATGTGA
TCATTTGTCTGGTTTTAATGTCTGCAATCGCTATCTCATTGTATTATATTATCAAGCATC
GAAAGCATTCAAAACTACTGACATAAATGCAAAACAAGATGAAATTGAAAAAATGAAGGC
AAAATACAACATAAATTCCGATGATTTACGAAAGTGA
>g11679.t18 Gene=g11679 Length=99
MKCMIFLVNMVQSDKLELEIFQKQKFGFVIGTAFVVYEDIWDAKNACDHLSGFNVCNRYL
IVLYYQASKAFKTTDINAKQDEIEKMKAKYNINSDDLRK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g11679.t18 | Gene3D | G3DSA:3.30.70.330 | - | 14 | 95 | 5.1E-6 |
| 1 | g11679.t18 | PANTHER | PTHR12785 | SPLICING FACTOR 3B | 31 | 89 | 9.7E-17 |
| 2 | g11679.t18 | PANTHER | PTHR12785:SF7 | SPLICING FACTOR 3B SUBUNIT 6 | 31 | 89 | 9.7E-17 |
| 6 | g11679.t18 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 13 | - |
| 7 | g11679.t18 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 8 | g11679.t18 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 8 | - |
| 9 | g11679.t18 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 9 | 13 | - |
| 5 | g11679.t18 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 14 | 99 | - |
| 3 | g11679.t18 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 23 | 69 | 3.66E-9 |
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:0003676 | nucleic acid binding | 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.
