General information for g1133.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Mediator of RNA polymerase II transcription subunit 4.
Parent gene
- The parent gene g1133 is located on chr_3: 8355083..8355782 (+ 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 | g1133 | g1133.t1 | TSS | g1133.t1 | 8354369 | 8354369 |
| chr_3 | g1133 | g1133.t1 | isoform | g1133.t1 | 8354959 | 8355782 |
| chr_3 | g1133 | g1133.t1 | exon | g1133.t1.exon1 | 8354959 | 8355026 |
| chr_3 | g1133 | g1133.t1 | cds | g1133.t1.CDS1 | 8354959 | 8355026 |
| chr_3 | g1133 | g1133.t1 | exon | g1133.t1.exon2 | 8355083 | 8355782 |
| chr_3 | g1133 | g1133.t1 | cds | g1133.t1.CDS2 | 8355083 | 8355782 |
| chr_3 | g1133 | g1133.t1 | TTS | g1133.t1 | 8355820 | 8355820 |
Sequences
>g1133.t1 Gene=g1133 Length=768
ATGGCTCATAATTTAAGCACGAGAGATCGATTGTTGTCTGTAATTGATGATATTGAAATA
ATTTCAAAAGAAATCATAGAGAATTTAATGGCACCGAAGCATCAGAAAACTCATGATTAT
TTACAATTAGTAGATTTATTAGTTCTAAAAGATAACGAACTAAAACAACTATTGAAATTA
GCTGCTGAACAGGAAAAGATTTACGAGAAAATCAATGCATTGAAAGAGCAAGTTGGAAAA
TACGATAATGAGATAAATCAATTGCAAAAACATCTAAAAGAAGCCGAACAAATACTTTCA
ACTGCAATTTTCCAAGCAAAACAAAAGCTTGCAAGCATTGCCAAGGCAAATGAAAATCCA
GTACAAAGTGAAGAATTGATTAAATATGCATACAGAATAAGTGCTTCTCACGCTATCTCA
GCACCAAACACATGGCAGCAGGGTGATTTACGCCGTCCATATCCCACAGATTTTGAAACT
CGTCAAGGCTTTTTAGGCAAAACTGACCTCAATATGAACGGTCATGGTCACAATTTGCAG
TCACAAACGAGTATAAATGATATCAATAGAAGTAATAATTCAACAGTCGATTCACAAGCA
ATTCCAGCATCAGCAACAAATCAATTCTCATGGTTTCCATCAGGTGAACTTCATATGATG
TCAGGCCATCAATCGATTTCACTGGAAACAAATCGTTCACATAAAGATGCATCTCAAGAC
GATGCCTCATCGGATAGTTCAAGTTCAAGCTCAAGTGATTCTCAGTAA
>g1133.t1 Gene=g1133 Length=255
MAHNLSTRDRLLSVIDDIEIISKEIIENLMAPKHQKTHDYLQLVDLLVLKDNELKQLLKL
AAEQEKIYEKINALKEQVGKYDNEINQLQKHLKEAEQILSTAIFQAKQKLASIAKANENP
VQSEELIKYAYRISASHAISAPNTWQQGDLRRPYPTDFETRQGFLGKTDLNMNGHGHNLQ
SQTSINDINRSNNSTVDSQAIPASATNQFSWFPSGELHMMSGHQSISLETNRSHKDASQD
DASSDSSSSSSSDSQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g1133.t1 | Coils | Coil | Coil | 57 | 98 | - |
| 3 | g1133.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 227 | 255 | - |
| 2 | g1133.t1 | PANTHER | PTHR13208 | MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 4 | 3 | 241 | 8.9E-41 |
| 1 | g1133.t1 | Pfam | PF10018 | Vitamin-D-receptor interacting Mediator subunit 4 | 42 | 184 | 4.7E-31 |
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 K15146 (mediator of RNA polymerase II transcription subunit 4)
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.
