General information for g5657.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5657 is located on chr_2: 10944574..10945004 (+ 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_2 | g5657 | g5657.t1 | TSS | g5657.t1 | 10943550 | 10943550 |
| chr_2 | g5657 | g5657.t1 | isoform | g5657.t1 | 10944355 | 10945004 |
| chr_2 | g5657 | g5657.t1 | exon | g5657.t1.exon1 | 10944355 | 10944366 |
| chr_2 | g5657 | g5657.t1 | cds | g5657.t1.CDS1 | 10944355 | 10944366 |
| chr_2 | g5657 | g5657.t1 | exon | g5657.t1.exon2 | 10944426 | 10944511 |
| chr_2 | g5657 | g5657.t1 | cds | g5657.t1.CDS2 | 10944426 | 10944511 |
| chr_2 | g5657 | g5657.t1 | exon | g5657.t1.exon3 | 10944575 | 10945004 |
| chr_2 | g5657 | g5657.t1 | cds | g5657.t1.CDS3 | 10944575 | 10945004 |
| chr_2 | g5657 | g5657.t1 | TTS | g5657.t1 | 10945273 | 10945273 |
Sequences
>g5657.t1 Gene=g5657 Length=528
ATGAACGTCAAAGTTAGCGAAATATTTACTTCAGCAGGTAAAGCCTTCAACACACTTGGT
GATCTCATACTTCAAGTACAGAGTCCAGACAAAGAAGGGAGTTCAAAATGGAATCAAGAA
GAGGTAGATACACTAAGAAATTCTTTAACAAAGTTCAATGAAGATTTAAATAAGCTTTCG
TCTCACATTAAAAATAAGCAAAAAACTCAAATTCGTCAAACATTGAAAAACAAACAGATC
CAACAAGCAGGTTTAAAAATTGAACAGCAACCACAAGTAAAGCATGTAACAGTTCAGCAA
CAACAACAACCAGTAGTGATTCAAGAACAAGTGATTTTTCATCAACCTTCGACTATCAAA
ATTGAGCAACAATTACCCGACAATCTAACAAGCATTTTACAAACTGAACCAGAAACATCA
CAATCACATATGACACTCAATCGACTTAATGCTCAAGAAGAAGAAATGTTGGATGATTCT
TTCCAAAGTGAAGTCAAAATAGAGACGAGTTACGCTGAAGTTTCTTGA
>g5657.t1 Gene=g5657 Length=175
MNVKVSEIFTSAGKAFNTLGDLILQVQSPDKEGSSKWNQEEVDTLRNSLTKFNEDLNKLS
SHIKNKQKTQIRQTLKNKQIQQAGLKIEQQPQVKHVTVQQQQQPVVIQEQVIFHQPSTIK
IEQQLPDNLTSILQTEPETSQSHMTLNRLNAQEEEMLDDSFQSEVKIETSYAEVS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value |
|---|---|---|---|---|---|---|
| g5657.t1 | PANTHER | PTHR21397:SF2 | CHROMATIN COMPLEXES SUBUNIT BAP18 | 3 | 155 | 0 |
| g5657.t1 | PANTHER | PTHR21397 | CHROMATIN COMPLEXES SUBUNIT BAP18-RELATED | 3 | 155 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5657/g5657.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5657.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0071339 | MLL1 complex | CC |
| GO:0016589 | NURF complex | CC |
KEGG
Orthology
- This transcript has been annotated with K23406 (chromatin complexes subunit BAP18)
Pathway
This gene does not belong to any 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.
