General information for g1180.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Mediator of RNA polymerase II transcription subunit 27.
Parent gene
- The parent gene g1180 is located on chr_3: 8507262..8508282 (+ 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 | g1180 | g1180.t1 | TSS | g1180.t1 | 8507199 | 8507199 |
| chr_3 | g1180 | g1180.t1 | isoform | g1180.t1 | 8507262 | 8508282 |
| chr_3 | g1180 | g1180.t1 | exon | g1180.t1.exon1 | 8507262 | 8507333 |
| chr_3 | g1180 | g1180.t1 | cds | g1180.t1.CDS1 | 8507262 | 8507333 |
| chr_3 | g1180 | g1180.t1 | exon | g1180.t1.exon2 | 8507391 | 8507564 |
| chr_3 | g1180 | g1180.t1 | cds | g1180.t1.CDS2 | 8507391 | 8507564 |
| chr_3 | g1180 | g1180.t1 | exon | g1180.t1.exon3 | 8507621 | 8507872 |
| chr_3 | g1180 | g1180.t1 | cds | g1180.t1.CDS3 | 8507621 | 8507872 |
| chr_3 | g1180 | g1180.t1 | exon | g1180.t1.exon4 | 8507929 | 8508282 |
| chr_3 | g1180 | g1180.t1 | cds | g1180.t1.CDS4 | 8507929 | 8508282 |
| chr_3 | g1180 | g1180.t1 | TTS | g1180.t1 | 8508348 | 8508348 |
Sequences
>g1180.t1 Gene=g1180 Length=852
ATGGAAAATCAAATAAATACAGCTTTAAATGCAATTAAAAATCTTCGTTCAAGTGTTTCT
AATATATTTGAGACAACAATATCGTCAGATATTTCTCAGTTGATTGAAATTCAAGACTCA
ATTGCTGCTGTGAGTGCAAATTTTAAAGATGTCGAAGGATCTATAAATAATTTAACAATA
CCAGCAGTTCCTTCATTGGGAAACACTGCTTTTCTCAACTATGAAACAGACTTAGAGAAA
CAAAATATGTATAGTGAACTTGTTAATGGATACAAATGGTATGAAAAGACTCATCAATAC
TCATCTATGGCAAGCACAATGTTACAACACAATTCTCTTAAAAGATCATATTACTCAACA
TCGAATAAAAGACGAAGATTATTGACAGGAGCACACACTGTGCCTCCAAAGTTGGTCGAT
CAGATTATCAGTACATTCAATTTGAATAATATGCAACTTAAAATTTATCGACCTTTTGCT
ACAAATGCATTTCTACATATTAATCTAAGCAGAGTATTGAAAGCAGCAATAATTCTTCGA
GGTCTCATGATTGAATGGATTACAGTTAAAGGATTTAATGAGTCACTTGATAACGTAGAT
GACCATTGGACTGAATCGAGATATGCTGTCTTCCGAAAAGTTCAAAAAGCTGCTCATTCA
GCTATGCTTCATTTCTACTCACCGACATTTGCCGAATTGGCAATAAGAAGTTTTATAACA
TGGTTCGGAAGCTACTCGACTCTGTTCAGTGAACCTTGCAAAAAATGTGGAAAACATTTA
TTAAACGGATTACCACCAACATTTCGAGATGTTCGCTCGTTAGATCCGATTCATGAAGAG
TGTAGAAATTAA
>g1180.t1 Gene=g1180 Length=283
MENQINTALNAIKNLRSSVSNIFETTISSDISQLIEIQDSIAAVSANFKDVEGSINNLTI
PAVPSLGNTAFLNYETDLEKQNMYSELVNGYKWYEKTHQYSSMASTMLQHNSLKRSYYST
SNKRRRLLTGAHTVPPKLVDQIISTFNLNNMQLKIYRPFATNAFLHINLSRVLKAAIILR
GLMIEWITVKGFNESLDNVDDHWTESRYAVFRKVQKAAHSAMLHFYSPTFAELAIRSFIT
WFGSYSTLFSEPCKKCGKHLLNGLPPTFRDVRSLDPIHEECRN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g1180.t1 | PANTHER | PTHR13130:SF4 | MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 27 | 4 | 147 | 0 |
| 5 | g1180.t1 | PANTHER | PTHR13130 | 34 KDA TRANSCRIPTIONAL CO-ACTIVATOR-RELATED | 4 | 147 | 0 |
| 2 | g1180.t1 | PANTHER | PTHR13130:SF4 | MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 27 | 159 | 282 | 0 |
| 4 | g1180.t1 | PANTHER | PTHR13130 | 34 KDA TRANSCRIPTIONAL CO-ACTIVATOR-RELATED | 159 | 282 | 0 |
| 1 | g1180.t1 | Pfam | PF11571 | Mediator complex subunit 27 | 201 | 282 | 0 |
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:0016592 | mediator complex | CC |
KEGG
Orthology
- This transcript has been annotated with K15170 (mediator of RNA polymerase II transcription subunit 27)
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.
