General information for g1135.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Mediator of RNA polymerase II transcription subunit 4.
Parent gene
- The parent gene g1135 is located on chr_3: 8366065..8366891 (+ 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 | g1135 | g1135.t1 | isoform | g1135.t1 | 8366065 | 8366891 |
| chr_3 | g1135 | g1135.t1 | exon | g1135.t1.exon1 | 8366065 | 8366132 |
| chr_3 | g1135 | g1135.t1 | cds | g1135.t1.CDS1 | 8366065 | 8366132 |
| chr_3 | g1135 | g1135.t1 | exon | g1135.t1.exon2 | 8366189 | 8366249 |
| chr_3 | g1135 | g1135.t1 | cds | g1135.t1.CDS2 | 8366189 | 8366249 |
| chr_3 | g1135 | g1135.t1 | exon | g1135.t1.exon3 | 8366303 | 8366489 |
| chr_3 | g1135 | g1135.t1 | cds | g1135.t1.CDS3 | 8366303 | 8366489 |
| chr_3 | g1135 | g1135.t1 | exon | g1135.t1.exon4 | 8366545 | 8366891 |
| chr_3 | g1135 | g1135.t1 | cds | g1135.t1.CDS4 | 8366545 | 8366891 |
| chr_3 | g1135 | g1135.t1 | TTS | g1135.t1 | 8366925 | 8366925 |
| chr_3 | g1135 | g1135.t1 | TSS | g1135.t1 | NA | NA |
Sequences
>g1135.t1 Gene=g1135 Length=663
ATGGCTCATAATTTAAGCACGAGAGATCGATTGTTGTCTGTAATTGATGATATTGAAATA
ATTTCAAAAGAAATCATAGAGAATTTAATGGCACCGAAGCATCAGAAAACTCATGATTAT
TTACAATTACTGTCTGAACAGGAAAAGATTTACGAGAAAATCAATGCATTGAAAGAGCAA
GTTGGAAAATACGATAATGAGATAAATCAATTGCAAAAACATCTAAAAGAAGCCGAACAA
ATACTTTCAACTGCAATTTTTCAAGCAAAAACAAAGCTTGCAAGCATTGCCAAGGCAAAT
GAAAATCCAGTACAAACACCAAACACATGGCAGCAGGGTGATTTACGCCGTCCATATCCC
ACAGATTTTGAAACTCGTCAAGGCTTTTTAGGCAAAACTGACCTCAATATGAACGGTCAT
GGTCACAATTTGCAGTCACAAACGAGTATAAATGATATCAATAGAAGTAATAATTCAACA
GTCGATTCACAAGCAATTCCAGCATCAGCAACAAATCAATTCTCATGGTTTCCATCAGGT
GAAATTCATATGATGTCAGGTCATCAATCGATTTCACTGGAAACAAATCGTTCACATAAA
GATGCATCTCAAGACGATGCCTCATCAGATAGTTCAAGTTCGAGCTCAAGTGATTCTCAG
TAA
>g1135.t1 Gene=g1135 Length=220
MAHNLSTRDRLLSVIDDIEIISKEIIENLMAPKHQKTHDYLQLLSEQEKIYEKINALKEQ
VGKYDNEINQLQKHLKEAEQILSTAIFQAKTKLASIAKANENPVQTPNTWQQGDLRRPYP
TDFETRQGFLGKTDLNMNGHGHNLQSQTSINDINRSNNSTVDSQAIPASATNQFSWFPSG
EIHMMSGHQSISLETNRSHKDASQDDASSDSSSSSSSDSQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g1135.t1 | Coils | Coil | Coil | 47 | 81 | - |
| 3 | g1135.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 191 | 220 | - |
| 2 | g1135.t1 | PANTHER | PTHR13208 | MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 4 | 6 | 207 | 9.4E-17 |
| 1 | g1135.t1 | Pfam | PF10018 | Vitamin-D-receptor interacting Mediator subunit 4 | 26 | 106 | 2.5E-8 |
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 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.
