General information for g228.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Mediator of RNA polymerase II transcription subunit 17.
Parent gene
- The parent gene g228 is located on chr_3: 1877661..1883015 (- 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 | g228 | g228.t1 | TTS | g228.t1 | 1877022 | 1877022 |
| chr_3 | g228 | g228.t1 | isoform | g228.t1 | 1877094 | 1879049 |
| chr_3 | g228 | g228.t1 | exon | g228.t1.exon1 | 1877094 | 1877177 |
| chr_3 | g228 | g228.t1 | cds | g228.t1.CDS1 | 1877094 | 1877177 |
| chr_3 | g228 | g228.t1 | exon | g228.t1.exon2 | 1877236 | 1878904 |
| chr_3 | g228 | g228.t1 | cds | g228.t1.CDS2 | 1877236 | 1878904 |
| chr_3 | g228 | g228.t1 | exon | g228.t1.exon3 | 1878961 | 1879049 |
| chr_3 | g228 | g228.t1 | cds | g228.t1.CDS3 | 1878961 | 1879049 |
| chr_3 | g228 | g228.t1 | TSS | g228.t1 | 1879138 | 1879138 |
Sequences
>g228.t1 Gene=g228 Length=1842
ATGGCTCAATCTGTTTCTGTATCAGTTGAAGCGCCAATAGAAAATCAAATTTTATCTATA
GATTATGATGGAACTGAAGTTTATGCGACACCTTTAACTCAATCAGAATATCTTACACGC
AATGCAGCTCGCATTAATTTTTCTAAAACAATTGATTCTACAGAAGAGAATAAAGAAGAA
GAACAAACAATTCAACCTACATCAAATCCATTTGAAAATATTCTAAACAAATTGAAAGAA
GCTTATACAGAAGTTACAGTGCTTCATGATGTATTGAGTATAGCAAAGGAAAAACATTAT
TTAGTTCTTGATCCAGTTCCAATTCATGAACCTATTGAAGTTAAACCAATGGCTGTTGTC
TATGCGAGAAAAAAAGCACTTGGAATGGCGGGTAATATTTTGATATCAGGTGCAGAGAGA
TTAAAAAGACTTGATAATGGTCCAGACTTTCAAATTGAATTGTTGAGATTAAGACAAAAT
TGGCGCTTAAAGAAAGTAAGTGATAATATTATTGGTGATTTGAGTTTTCGAACAGCTGGA
TCAAAGTTTATGCATCCTGGTAATTTTGAAGTGTCAAAAGCCGATGAATCTGAAATGAAA
GGACCAAATCCATCAACATTATCAGTTACAATACCGTCAGATTTACAAGGAGTTGCTTAT
ATAAAAGTTGTCACACAAAAAGATCAAGAAGATTTGTGCTCTGCAAACGTGAGTACAATC
GATCAAAAATGTAAACTGCAAGTTGGTGAAATCTCTTCATGGCAAAAGAAATTTGAATTT
GCACAAAATGTTTTATTCTGTAAAGAACTTTTTAATCAACTTGCACGTGAAGCAGTTCAG
CTTCAAGCTACGATTCCGCATGTTGTAATTGGAAATCAAATTAGAGCTACATTACTTCCA
GGCATTCAACTTATCATTAGTTTATGTCATTCAAATTCTTACCAAGAATTTCAAGAGGAG
AATAAGAAAAAAGTTGATGATTTACACGACCATGTACTTGAGCATTCTTTGCATCAACTT
CTTCGTGAGATACATTATAAAAATGTGCATTTTCCAATTCCACATTCAGGTCATGCAGTT
GGTATTGCTAAAAAAAGATTATTGGCTGGTCCACACTCTTATGATCGTCATGAATTGTGG
GAAATTACAAAGAGTCAAAATCAGACATTACTTGAACAAATAATTGCACAAGCTCAACAT
GTATTTATGAGAAAAAGAACTCAATATGTACTCGATACTCTTGCGAGAGATGTTAAAGAT
CCACAAATCACATCACACTGGAATGCTCTTAATTCACCAACATTATCATGGGTGAAAATC
AATATTACAACACACGGATATGATACAATTACAAGAACATCATTAGTGATTCATGTAAAA
GAAAGATCGTTAAAAGCAATTTGTAGAGATGGTCGAGTTATGCATATGTCTTATGAACCT
CAAGAACTTCGTGATTTAATTCTACAGCAAATTTGTCAGCATCAAATAAGTGGATTACAA
AGTTTGAGTCGTTGTATGGCATGGCAATTGCTATCAAATTCAAATCATTTAGGAATTGGC
GATGTAGAACCACTTGGAAATGCAAATTCAATTTTAATTTCTTCTCCACTTGGTGATCGT
GTGATTGCAGTTCAAGTGAGATGTGATCCACAAATTGTTGTGAAAGTTTATGTTTCACAC
AGTCCAAAAGAATTTTTCACAAGTGGTCCATTGGTACAAGGAAAACATTGGGAAAATCTC
GGTAGTGAATTTAAAGAGGTAAATTTCGAAAAGATGGAAGGAAGAAATTTTCTCAATAAA
ATGGAATTCTTGATGGCTGCTCTCACTAAAATTAAGGAATAA
>g228.t1 Gene=g228 Length=613
MAQSVSVSVEAPIENQILSIDYDGTEVYATPLTQSEYLTRNAARINFSKTIDSTEENKEE
EQTIQPTSNPFENILNKLKEAYTEVTVLHDVLSIAKEKHYLVLDPVPIHEPIEVKPMAVV
YARKKALGMAGNILISGAERLKRLDNGPDFQIELLRLRQNWRLKKVSDNIIGDLSFRTAG
SKFMHPGNFEVSKADESEMKGPNPSTLSVTIPSDLQGVAYIKVVTQKDQEDLCSANVSTI
DQKCKLQVGEISSWQKKFEFAQNVLFCKELFNQLAREAVQLQATIPHVVIGNQIRATLLP
GIQLIISLCHSNSYQEFQEENKKKVDDLHDHVLEHSLHQLLREIHYKNVHFPIPHSGHAV
GIAKKRLLAGPHSYDRHELWEITKSQNQTLLEQIIAQAQHVFMRKRTQYVLDTLARDVKD
PQITSHWNALNSPTLSWVKINITTHGYDTITRTSLVIHVKERSLKAICRDGRVMHMSYEP
QELRDLILQQICQHQISGLQSLSRCMAWQLLSNSNHLGIGDVEPLGNANSILISSPLGDR
VIAVQVRCDPQIVVKVYVSHSPKEFFTSGPLVQGKHWENLGSEFKEVNFEKMEGRNFLNK
MEFLMAALTKIKE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g228.t1 | PANTHER | PTHR13114 | MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 17 | 1 | 609 | 0.0e+00 |
| 1 | g228.t1 | Pfam | PF10156 | Subunit 17 of Mediator complex | 225 | 414 | 1.5e-06 |
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 K15133 (mediator of RNA polymerase II transcription subunit 17)
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.
