General information for g3550.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Mediator of RNA polymerase II transcription subunit 1.
Parent gene
- The parent gene g3550 is located on chr_3: 26393918..26395693 (- 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 | g3550 | g3550.t2 | isoform | g3550.t2 | 26393918 | 26395693 |
| chr_3 | g3550 | g3550.t2 | exon | g3550.t2.exon1 | 26393918 | 26395201 |
| chr_3 | g3550 | g3550.t2 | cds | g3550.t2.CDS1 | 26393918 | 26395201 |
| chr_3 | g3550 | g3550.t2 | exon | g3550.t2.exon2 | 26395262 | 26395499 |
| chr_3 | g3550 | g3550.t2 | cds | g3550.t2.CDS2 | 26395262 | 26395499 |
| chr_3 | g3550 | g3550.t2 | exon | g3550.t2.exon3 | 26395560 | 26395693 |
| chr_3 | g3550 | g3550.t2 | cds | g3550.t2.CDS3 | 26395560 | 26395693 |
| chr_3 | g3550 | g3550.t2 | TSS | g3550.t2 | 26395761 | 26395761 |
| chr_3 | g3550 | g3550.t2 | TTS | g3550.t2 | NA | NA |
Sequences
>g3550.t2 Gene=g3550 Length=1656
ATGTCTACAATCGCGGTCGAAAAGAACAAGCAATGGAGAATGGAATGTTTGATGGAAAAT
TTGCGTTCAAAGCAGTCATCAAAAAGCTTTCTTGAACTTGCAAAATCGAGCAGAATGAAT
TTATTGGAGAAAAAATACAATATTGATGCTATTGAAAAACAGACATTGCAAACAGCATTA
GATCAACTTCAAAACAATATCACAATTAAAAATAGAACACAATTAGTTGAGAGATTAGAG
ATGATAACAAGACGTCAATTGAGTCTAAAATTTACAGAAAACATTAATACAAACAGTATT
TTCATTTCTTCCGATATGTTTTATCTTGAGATTTTACTTGATTCACAAAGTGGCTTTGTA
AATGATGTTAAGGTTCATCATGAATGCCTAAATGAATCAGAATCAGAACCACATCTTATA
GAAGTACTAAGGAAAGGCGATTTCATAGACTTCACTCAACAACTTGAGGGTTTTCAATCA
ATATATCAACTTAATTGTGAATCAAAGATAAAATCTAAAGCATTGATAGCTTTACAAGCA
CTTGAGACGGATCTCACAAATATTTATAATCAAGAAAATGCCTCAAATATTTTTCATGAG
TCAGTTGTTTTGACTTCATCCATTGGACTCTTAACTAAGAGGAGAGGTGGTCATCCGCTT
AAATTAACATTTTTTGTGCGTGCTTGTGAGATGCTTAATCTTGAACAAAAACGTATGGAT
ACATTAAAAGAAGCACTCGAGAATGCAGCTATATGTAAAAAAAATATTGGTAATAGTGTT
ACAGTGAACCTTGAAGCTGCAACACCATCAAACAAACTACAAATTGTACCATTACTTATT
AAAAATGGTGGAAAACAAGATGGTAATTATTCATACCAATGTATCACAAATGCTAGTACG
ACACTGCTTCCTGCTACTTTTGTATTGCGTCTCAATAAACCATTTCCAATTGCAAGTAAA
ATTATAGACAAAATTAAACAAATTACAAATTTAAATGTGCTAGAAGAGATTGCTTCAAAA
CCAATAGTTAAGATGGAAAATTCTTTGGCATCTGTTGAATCTCATAAAGAACATTGCTCT
CTATTGAATCAGATAATCACTCTCGAATCTGAAGGTTCATATACAAATGCACAAAAAGGT
CTCTTTGTATCACTTGCAGATCAATCACATTGTTATTTTATATCAGATAATCCCGAAATG
ACAGGAGTCAATGTTAAAAGCATTCAATTTACAGAACCATCACATGTAACAAAAATTATT
AAACTTTTGCGAGAACAAGCACTTTTTAACTCTTTAATAGCTAGTTGTGTGCGACAAAAT
AGCAAGCAAGATCTTGAGTCATGTTATATGTTTGAGGTGAATGTTGTTTCTTTACAATAT
ATTCAAATTTTTATTGAACATCCACTAAAAGAAACTATGGTAACAGTTGAATTAGATTTA
TCTGATGTTCGTCAAATTGCCTCATGCAAAATAAATGGAAATGATTTACAAACTGATATC
AAACTAGAAAATTACATCACTCGTGTACTTCAAAAAACTTGTTCTATTCCTCAACTTACA
AGATGTCTTTTAAAGTATTGGGAAAGTGAATCACAGTTATCTCGTATGCAGAAAAGAACT
TTCGATAATGGATTGTTTGGAATTTTAGAGCCAAAA
>g3550.t2 Gene=g3550 Length=552
MSTIAVEKNKQWRMECLMENLRSKQSSKSFLELAKSSRMNLLEKKYNIDAIEKQTLQTAL
DQLQNNITIKNRTQLVERLEMITRRQLSLKFTENINTNSIFISSDMFYLEILLDSQSGFV
NDVKVHHECLNESESEPHLIEVLRKGDFIDFTQQLEGFQSIYQLNCESKIKSKALIALQA
LETDLTNIYNQENASNIFHESVVLTSSIGLLTKRRGGHPLKLTFFVRACEMLNLEQKRMD
TLKEALENAAICKKNIGNSVTVNLEAATPSNKLQIVPLLIKNGGKQDGNYSYQCITNAST
TLLPATFVLRLNKPFPIASKIIDKIKQITNLNVLEEIASKPIVKMENSLASVESHKEHCS
LLNQIITLESEGSYTNAQKGLFVSLADQSHCYFISDNPEMTGVNVKSIQFTEPSHVTKII
KLLREQALFNSLIASCVRQNSKQDLESCYMFEVNVVSLQYIQIFIEHPLKETMVTVELDL
SDVRQIASCKINGNDLQTDIKLENYITRVLQKTCSIPQLTRCLLKYWESESQLSRMQKRT
FDNGLFGILEPK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g3550.t2 | Coils | Coil | Coil | 53 | 73 | - |
| 2 | g3550.t2 | PANTHER | PTHR12881 | MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 1 | 6 | 538 | 4.6E-139 |
| 3 | g3550.t2 | PANTHER | PTHR12881:SF10 | MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 1 | 6 | 538 | 4.6E-139 |
| 1 | g3550.t2 | Pfam | PF10744 | Mediator of RNA polymerase II transcription subunit 1 | 58 | 438 | 4.5E-48 |
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:0006357 | regulation of transcription by RNA polymerase II | BP |
| GO:0016592 | mediator complex | CC |
| GO:0003712 | transcription coregulator activity | MF |
KEGG
Orthology
- This transcript has been annotated with K15144 (mediator of RNA polymerase II transcription subunit 1)
Pathway
- This transcript belongs to the following pathways
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.
