General information for g12170.t1
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.t1 | isoform | g12170.t1 | 21445314 | 21450055 |
| chr_1 | g12170 | g12170.t1 | exon | g12170.t1.exon1 | 21445314 | 21445467 |
| chr_1 | g12170 | g12170.t1 | cds | g12170.t1.CDS1 | 21445314 | 21445467 |
| chr_1 | g12170 | g12170.t1 | exon | g12170.t1.exon2 | 21445550 | 21445763 |
| chr_1 | g12170 | g12170.t1 | cds | g12170.t1.CDS2 | 21445550 | 21445763 |
| chr_1 | g12170 | g12170.t1 | exon | g12170.t1.exon3 | 21446371 | 21447682 |
| chr_1 | g12170 | g12170.t1 | cds | g12170.t1.CDS3 | 21446371 | 21447682 |
| chr_1 | g12170 | g12170.t1 | exon | g12170.t1.exon4 | 21448259 | 21448512 |
| chr_1 | g12170 | g12170.t1 | cds | g12170.t1.CDS4 | 21448259 | 21448512 |
| chr_1 | g12170 | g12170.t1 | exon | g12170.t1.exon5 | 21449368 | 21449494 |
| chr_1 | g12170 | g12170.t1 | cds | g12170.t1.CDS5 | 21449368 | 21449494 |
| chr_1 | g12170 | g12170.t1 | exon | g12170.t1.exon6 | 21449558 | 21449823 |
| chr_1 | g12170 | g12170.t1 | cds | g12170.t1.CDS6 | 21449558 | 21449823 |
| chr_1 | g12170 | g12170.t1 | exon | g12170.t1.exon7 | 21450049 | 21450055 |
| chr_1 | g12170 | g12170.t1 | cds | g12170.t1.CDS7 | 21450049 | 21450055 |
| chr_1 | g12170 | g12170.t1 | TSS | g12170.t1 | 21450082 | 21450082 |
| chr_1 | g12170 | g12170.t1 | TTS | g12170.t1 | NA | NA |
Sequences
>g12170.t1 Gene=g12170 Length=2334
ATGGAAGATATCGAGTCACAAATTAAAGACATTCAAGAGAAGAAACGACAGGCTCAAGCT
CAAGAGGAGAGGCAGAAAGGAATTGGATTATTAGAAAGTGGATATTTTGATTCAGAAATC
TATGAGGGAGGACAAAAAGGAAAATATGAGGGCTATGTAACATCAATTGCGACAAATGAA
GAAGATGAGGACGATGATGATGAACCAATCAGACCAGATAAAAAGTCTTCAGCATTTAAT
GCTCCAATTTCATTTATTAAAGAAATCACAAGAAATGAACCAGAATATGATCCATTCGAG
GATCGAAGACAAAAGACTGTTGGTGAAAAAGAAGATGAATATCGTCAGAGACGTAGAAAA
TTAGTCATTTCTCCAGAACGTGTTGATCCTTTTGCTGATGGTGGCAAAACTCCTGATGTC
AAATCAAGAACATACACTGAAATTATGCGTGAGCAACAGCTCCGCGGTGAAGAAGCAGAA
TTGCGTAAAAAGATTCAAGAAAAGGCAAAAGATGGGACATTAAAAGTGGCATCAAATGGC
GATTCTAATCGTTCAGAGTCAAAGAAACGAGGGAGATGGGACCAGACAGTTGATGAACAA
TTTGTTCCTGCTAAGAAATCAGCTTCAGGTGCTACACCGACATGGGAAGCAGATAAAACA
CCAGCAGATCATCGTTGGGATGAGACACCTGGAAGAGCAATTGGAAGTGAAACGCCCGGA
GCAACTCCTGCAGCAAGAAATGTTTGGGATGCTACACCTGCAGCACAACATGCAACAACA
CCAGGCCGCGAAACACCCGCTCAAGAGAAATCAGTTCGTAGAAATCGTTGGGATGAAACG
CCAAAAACAGAAAGAGAAACTCCTGGTCATAATTCGGGTTGGATGGAAACGCCTCGTGCT
GATCGTGGTGCTCCTGATATGATTGATTCAACGCCAGGTGCTTCAAAGAGAAGATCAAGA
TGGGACGAAACTCCATCAGGCGCAACACCTTCAAATGCTGCAATGACACCGAGCATGACA
CCTCATGCAACTCCTAGTCATGCAACACCGATACTTACTCCAAGCGGAACTACTCCGATC
GGAACTAAAGCTATGGCAATGGCAACACCAACTCCTGGTCATTTGGCTTCAATGACACCT
GAACAATTGCAAGCATATCGTTGGGAAAAAGAAATTGACGAAAGAAATAGACCATTTACT
GATGAAGAATTGGACTCATTATTCCCACCTGGTTATAAAATTCTTCCCGCTCCTGCTGGC
TATATTCCTATTAGAACTCCAGCCAGAAAATTAACTGCAACACCTACACCGATAGCAGGA
ACTCCGACAGGATTTTTCATTCAACAAGAAGACAAAACAGCTGCAAAATTTAATGATAAT
CAACCAAAAGGAAATTTACCGTTTATGAAACCAGAAGATGCTCAATATTTTGATAAATTG
CTTGTTGATGTCGATGAAGAAGCTCTAAGTCCAGAAGAACAGCGTGAAAGAAAAATTATG
AAATTGCTATTGAAAATTAAAAATGGAACTCCACCAATGAGAAAAGCTGCATTGCGTCAA
ATTACTGATAAAGCAAGAGAATTCGGAGCTGGACCATTGTTTAATCAAATTTTACCATTG
CTTATGTCACCAACACTTGAAGATCAAGAACGTCATTTACTTGTTAAAGTTATTGATCGA
ATTCTTTATAAATTGGATGATTTGGTACGTCCATATGTGCACAAAATTCTTGTCGTTATT
GAACCACTATTGATTGATGAAGATTACTATGCACGTGTTGAAGGTCGTGAAATTATATCG
AATTTAGCAAAAGCAGCTGGTCTTGCAACAATGATCAGTACTATGCGTCCTGATATCGAT
AACATTGATGAATATGTAAGAAATACAACAGCAAGAGCTTTCGCAGTTGTCGCTTCATCA
CTTGGAATTCCATCACTTTTGCCATTCTTGAAAGCTGTCTGTAAAAGAAATCCACCACAC
TGCATCCCTGATGGGTCGAACATCAATCATAAAAAAACTTTATTATGGCCATCTTTATAT
TGCTACGACTTCAAAGAAACCCTTGTTCCACCTAACCAAAGTATAATTGAAAATAGTGGA
TTCACTTCCGTATTTGGAAACATTTCCTGCGTTGTTTATTTGACGTCCACTAGTGGAAAT
ACGCCACCTTCGCTGCACCTATTTTTTGGTGAAAAAAAGTTTTTTGAAGGTCCATTCGGT
GGACGTCCACCATATGCATGCCATAGCTCGGCATGGAGAACGAATCTCGCGGAAAGCTTC
CGTTACACCGGTCTCATAGTCAGAACCAACAGATTGGTGCAAAAAGTTTGGTAA
>g12170.t1 Gene=g12170 Length=777
MEDIESQIKDIQEKKRQAQAQEERQKGIGLLESGYFDSEIYEGGQKGKYEGYVTSIATNE
EDEDDDDEPIRPDKKSSAFNAPISFIKEITRNEPEYDPFEDRRQKTVGEKEDEYRQRRRK
LVISPERVDPFADGGKTPDVKSRTYTEIMREQQLRGEEAELRKKIQEKAKDGTLKVASNG
DSNRSESKKRGRWDQTVDEQFVPAKKSASGATPTWEADKTPADHRWDETPGRAIGSETPG
ATPAARNVWDATPAAQHATTPGRETPAQEKSVRRNRWDETPKTERETPGHNSGWMETPRA
DRGAPDMIDSTPGASKRRSRWDETPSGATPSNAAMTPSMTPHATPSHATPILTPSGTTPI
GTKAMAMATPTPGHLASMTPEQLQAYRWEKEIDERNRPFTDEELDSLFPPGYKILPAPAG
YIPIRTPARKLTATPTPIAGTPTGFFIQQEDKTAAKFNDNQPKGNLPFMKPEDAQYFDKL
LVDVDEEALSPEEQRERKIMKLLLKIKNGTPPMRKAALRQITDKAREFGAGPLFNQILPL
LMSPTLEDQERHLLVKVIDRILYKLDDLVRPYVHKILVVIEPLLIDEDYYARVEGREIIS
NLAKAAGLATMISTMRPDIDNIDEYVRNTTARAFAVVASSLGIPSLLPFLKAVCKRNPPH
CIPDGSNINHKKTLLWPSLYCYDFKETLVPPNQSIIENSGFTSVFGNISCVVYLTSTSGN
TPPSLHLFFGEKKFFEGPFGGRPPYACHSSAWRTNLAESFRYTGLIVRTNRLVQKVW
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g12170.t1 | Coils | Coil | Coil | 1 | 28 | - |
| 15 | g12170.t1 | Coils | Coil | Coil | 151 | 171 | - |
| 8 | g12170.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 27 | - |
| 13 | g12170.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 22 | - |
| 10 | g12170.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 52 | 348 | - |
| 14 | g12170.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 90 | 136 | - |
| 9 | g12170.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 143 | 171 | - |
| 11 | g12170.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 182 | 196 | - |
| 12 | g12170.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 267 | 286 | - |
| 7 | g12170.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 324 | 348 | - |
| 3 | g12170.t1 | PANTHER | PTHR12097 | SPLICING FACTOR 3B, SUBUNIT 1-RELATED | 1 | 282 | 1.4E-174 |
| 5 | g12170.t1 | PANTHER | PTHR12097:SF1 | BNAA06G23400D PROTEIN | 1 | 282 | 1.4E-174 |
| 2 | g12170.t1 | PANTHER | PTHR12097 | SPLICING FACTOR 3B, SUBUNIT 1-RELATED | 258 | 655 | 1.4E-174 |
| 4 | g12170.t1 | PANTHER | PTHR12097:SF1 | BNAA06G23400D PROTEIN | 258 | 655 | 1.4E-174 |
| 1 | g12170.t1 | Pfam | PF08920 | Splicing factor 3B subunit 1 | 312 | 452 | 7.9E-48 |
| 6 | g12170.t1 | SUPERFAMILY | SSF48371 | ARM repeat | 483 | 657 | 7.68E-21 |
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.
