General information for g12170.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Splicing factor 3B subunit 1.
Parent gene
- The parent gene g12170 is located on chr_1: 21450055..21451031 (- 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 | g12170 | g12170.t2 | isoform | g12170.t2 | 21447036 | 21448512 |
| chr_1 | g12170 | g12170.t2 | exon | g12170.t2.exon1 | 21447036 | 21447682 |
| chr_1 | g12170 | g12170.t2 | cds | g12170.t2.CDS1 | 21447038 | 21447682 |
| chr_1 | g12170 | g12170.t2 | exon | g12170.t2.exon2 | 21448259 | 21448512 |
| chr_1 | g12170 | g12170.t2 | cds | g12170.t2.CDS2 | 21448259 | 21448468 |
| chr_1 | g12170 | g12170.t2 | TSS | g12170.t2 | NA | NA |
| chr_1 | g12170 | g12170.t2 | TTS | g12170.t2 | NA | NA |
Sequences
>g12170.t2 Gene=g12170 Length=901
GTGGCAAAACTCCTGATGTCAAATCAAGAACATACACTGAAATTATGCGTGAGCAACAGC
TCCGCGGTGAAGAAGCAGAATTGCGTAAAAAGATTCAAGAAAAGGCAAAAGATGGGACAT
TAAAAGTGGCATCAAATGGCGATTCTAATCGTTCAGAGTCAAAGAAACGAGGGAGATGGG
ACCAGACAGTTGATGAACAATTTGTTCCTGCTAAGAAATCAGCTTCAGGTGCTACACCGA
CATGGGAAGCAGATAAAACACCAGCAGATCATCGTTGGGATGAGACACCTGGAAGAGCAA
TTGGAAGTGAAACGCCCGGAGCAACTCCTGCAGCAAGAAATGTTTGGGATGCTACACCTG
CAGCACAACATGCAACAACACCAGGCCGCGAAACACCCGCTCAAGAGAAATCAGTTCGTA
GAAATCGTTGGGATGAAACGCCAAAAACAGAAAGAGAAACTCCTGGTCATAATTCGGGTT
GGATGGAAACGCCTCGTGCTGATCGTGGTGCTCCTGATATGATTGATTCAACGCCAGGTG
CTTCAAAGAGAAGATCAAGATGGGACGAAACTCCATCAGGCGCAACACCTTCAAATGCTG
CAATGACACCGAGCATGACACCTCATGCAACTCCTAGTCATGCAACACCGATACTTACTC
CAAGCGGAACTACTCCGATCGGAACTAAAGCTATGGCAATGGCAACACCAACTCCTGGTC
ATTTGGCTTCAATGACACCTGAACAATTGCAAGCATATCGTTGGGAAAAAGAAATTGACG
AAAGAAATAGACCATTTACTGATGAAGAATTGGACTCATTATTCCCACCTGGTTATAAAA
TTCTTCCCGCTCCTGCTGGCTATATTCCTATTAGAACTCCAGCCAGAAAATTAACTGCAA
C
>g12170.t2 Gene=g12170 Length=285
MREQQLRGEEAELRKKIQEKAKDGTLKVASNGDSNRSESKKRGRWDQTVDEQFVPAKKSA
SGATPTWEADKTPADHRWDETPGRAIGSETPGATPAARNVWDATPAAQHATTPGRETPAQ
EKSVRRNRWDETPKTERETPGHNSGWMETPRADRGAPDMIDSTPGASKRRSRWDETPSGA
TPSNAAMTPSMTPHATPSHATPILTPSGTTPIGTKAMAMATPTPGHLASMTPEQLQAYRW
EKEIDERNRPFTDEELDSLFPPGYKILPAPAGYIPIRTPARKLTA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g12170.t2 | Coils | Coil | Coil | 3 | 23 | - |
| 4 | g12170.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 199 | - |
| 8 | g12170.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 23 | - |
| 5 | g12170.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 34 | 48 | - |
| 7 | g12170.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 119 | 138 | - |
| 6 | g12170.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 176 | 199 | - |
| 2 | g12170.t2 | PANTHER | PTHR12097 | SPLICING FACTOR 3B, SUBUNIT 1-RELATED | 111 | 283 | 1.6E-24 |
| 3 | g12170.t2 | PANTHER | PTHR12097:SF1 | BNAA06G23400D PROTEIN | 111 | 283 | 1.6E-24 |
| 1 | g12170.t2 | Pfam | PF08920 | Splicing factor 3B subunit 1 | 164 | 285 | 7.6E-41 |
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:0003729 | mRNA binding | MF |
| GO:0000245 | spliceosomal complex assembly | BP |
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.
