General information for g928.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1.
Parent gene
- The parent gene g928 is located on chr_3: 6897254..6898461 (+ 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 | g928 | g928.t2 | TSS | g928.t2 | 6897187 | 6897187 |
| chr_3 | g928 | g928.t2 | isoform | g928.t2 | 6897254 | 6898461 |
| chr_3 | g928 | g928.t2 | exon | g928.t2.exon1 | 6897254 | 6898461 |
| chr_3 | g928 | g928.t2 | cds | g928.t2.CDS1 | 6897484 | 6898461 |
| chr_3 | g928 | g928.t2 | TTS | g928.t2 | 6898573 | 6898573 |
Sequences
>g928.t2 Gene=g928 Length=1208
ATGGCAGTAAGAACTTATGGTGATAAGCCCATTAGCTTTCAAGTTGAAGAGGGAGGTGAA
TACTATTGCATTGGATCAGAAGTGAGTAATAAAAATGACTTTTTGAGCATTTTTTAGTCG
GCGTCTCTCAAAGAAAATTTTTTCATCAAATTTCTAATTTTTTTAATCACTTATAGGTCG
GAAATTATTTGAGATTATGTCGTGGATCACTTTACAAAAAATATCCAGGCATGCACCGCC
GATCTCTTACAAATGAAGAGAGGAAGAAACTTATTGAAAGTGGTATCAGTAATCATCTTT
TTGCTAGTTCAGTGAGTCTATTGAAAGCATCTGAGGTTCAAGATATTATTGATGGAAATG
ATGAAAAATACAAAGCTGTGTCAGTGCATTCATCAGAATCTCTCATTCCTCGTGAAAGTA
GCAAAGCTAAAAAGCAAACACCTTGGATGCCGACTATGCCAAATTCATCACACCTGGATG
CTGTTCCTCAGGCCACACCGATTAATCGTAATCGTGTATACAACAAGAAAGTTCGAACTT
TTCCAATGTGCTTCGATGATACTGATCCAACTGCAATTTCAGAAAATTCTTCTCAGTCAG
AGACACTTGTTCCAATAAGATTAGATATGGAGCTTGAAGGACAAAAATTACGCGATACAT
TCACATGGAATAAAAATGAAAGCATAATTTCACCAGAACAATTCGCAGAAGTTCTTTGTG
ATGATTTAGATCTTAATCCAGTTCCATTTGTCCCAGCGATCTCTGCAGCAATTCGTCAAC
AAATTGAAGCTTATCCAACAGAATCAATTATTGAAGATAATTGCGATCAACGTGTAATTA
TAAAATTAAATATACATGTTGGTAACACATCACTTGTTGATCAAATTGAATGGGATATGT
CTGAAAAAGATAACAATCCAGAAGAATTTGCAATTAAACTTTGCGCAGAACTCGGTCTTG
GAGGAGAATTTGTGACTGCAATTGCATATTCAATTCGTGGTCAACTTTCATGGCATCAAC
GCACTTATGGTTTCAGTGAATCTCAATTGTCAACTGTTGAAATTCCATTCCGTGCACCTT
CAGAAGCTGATACTTGGTCACCTTTTCTCGAGACACTTACTGATGCTGAAATGGAGAAGA
AGATTCGTGATCAAGACAGAAACACAAGACGAATGAGACGTCTTGCCAATACAACATCTG
GCTGGTAA
>g928.t2 Gene=g928 Length=325
MHRRSLTNEERKKLIESGISNHLFASSVSLLKASEVQDIIDGNDEKYKAVSVHSSESLIP
RESSKAKKQTPWMPTMPNSSHLDAVPQATPINRNRVYNKKVRTFPMCFDDTDPTAISENS
SQSETLVPIRLDMELEGQKLRDTFTWNKNESIISPEQFAEVLCDDLDLNPVPFVPAISAA
IRQQIEAYPTESIIEDNCDQRVIIKLNIHVGNTSLVDQIEWDMSEKDNNPEEFAIKLCAE
LGLGGEFVTAIAYSIRGQLSWHQRTYGFSESQLSTVEIPFRAPSEADTWSPFLETLTDAE
MEKKIRDQDRNTRRMRRLANTTSGW
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g928.t2 | PANTHER | PTHR10019 | SNF5 | 3 | 325 | 0 |
| 4 | g928.t2 | PANTHER | PTHR10019:SF5 | SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY B MEMBER 1 | 3 | 325 | 0 |
| 5 | g928.t2 | PIRSF | PIRSF038126 | SWI_SNF | 1 | 325 | 0 |
| 1 | g928.t2 | Pfam | PF04855 | SNF5 / SMARCB1 / INI1 | 120 | 188 | 0 |
| 2 | g928.t2 | Pfam | PF04855 | SNF5 / SMARCB1 / INI1 | 195 | 313 | 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:0000228 | nuclear chromosome | CC |
| GO:0006338 | chromatin remodeling | BP |
KEGG
Orthology
- This transcript has been annotated with K11648 (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1)
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.
