General information for g15364.t3
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 E member 1.
Parent gene
- The parent gene g15364 is located on chr_4: 5122200..5123110 (+ 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_4 | g15364 | g15364.t3 | isoform | g15364.t3 | 5117736 | 5121511 |
| chr_4 | g15364 | g15364.t3 | exon | g15364.t3.exon1 | 5117736 | 5117959 |
| chr_4 | g15364 | g15364.t3 | TSS | g15364.t3 | 5117770 | 5117770 |
| chr_4 | g15364 | g15364.t3 | exon | g15364.t3.exon2 | 5118034 | 5118130 |
| chr_4 | g15364 | g15364.t3 | cds | g15364.t3.CDS1 | 5118091 | 5118130 |
| chr_4 | g15364 | g15364.t3 | exon | g15364.t3.exon3 | 5118885 | 5119006 |
| chr_4 | g15364 | g15364.t3 | cds | g15364.t3.CDS2 | 5118885 | 5119006 |
| chr_4 | g15364 | g15364.t3 | exon | g15364.t3.exon4 | 5119099 | 5119242 |
| chr_4 | g15364 | g15364.t3 | cds | g15364.t3.CDS3 | 5119099 | 5119242 |
| chr_4 | g15364 | g15364.t3 | exon | g15364.t3.exon5 | 5119433 | 5119495 |
| chr_4 | g15364 | g15364.t3 | cds | g15364.t3.CDS4 | 5119433 | 5119495 |
| chr_4 | g15364 | g15364.t3 | exon | g15364.t3.exon6 | 5119991 | 5120072 |
| chr_4 | g15364 | g15364.t3 | cds | g15364.t3.CDS5 | 5119991 | 5120072 |
| chr_4 | g15364 | g15364.t3 | exon | g15364.t3.exon7 | 5120907 | 5121511 |
| chr_4 | g15364 | g15364.t3 | cds | g15364.t3.CDS6 | 5120907 | 5121511 |
| chr_4 | g15364 | g15364.t3 | TTS | g15364.t3 | NA | NA |
Sequences
>g15364.t3 Gene=g15364 Length=1337
ATACGACGCTACTGAAAAGGGTATTCAATTACATCTAAAGTATTTTACAAGATTTAAACA
AATTTGTGTCAACAATAGTGAAAAATTAATAAAAACTACTTTAAAAAGATCAAATAAAGA
AAAATAAAAACTTTAACCATAAGGATAAAGTAAAATTTTACAAGTTTATAAACTTTAACA
TATAAAAAGTTTCAAATAAAGCAGAAATTTTAAAAATTGTAAAGCTAAATTTCATCAACT
GGAAGTTAAATAAATAAAATAAAAGTGAAAATTTGATCAAAATGTCTCTACCAAATTACA
AACAAATTCTTCCAAATCCACAACGTTTAAGACCGTCAGGATCAGGACAAATGATGGGAC
GAGATCAATCACCTTTTATACATTCAGCTCATAGCAATCCATCATTTACACCACAAAAGG
CTGGCAAAAGCAGTTCAGCTAGTATTGATTCTCGTTATCCAAAACCACCAAAGGCACCAG
AAAAGCCAGTGATGCCTTACATGAGATATTCAAAGAAACAATGGGAAGTTGTAAAAAATT
CTAATCCAGAATTGAAATTATGGGAAATTGGAAAGAAAATTGGAATGTTATGGCGTGATT
TATCAGAAGCCGAAAAACAAGTGTATATTGATGAATATGAAGCTGAAAAGAGTGAATATG
AAAAGGCATTAAAAGCCTATCACACCTCACCTGCATATCTCGCTTATATGTCCACAAAGA
GCAAGAAAAACGATCCAAATGATATACACGACATGCCAAGATCAAGTTCAAAATCACAAC
AAGATCGTCGGGTTGACATTCAACCAGCAGAAGATGAAGAAGATCAGGACGATGGATTTT
CATTCAAACAAGTCGCTTACAATCGCTACACTAGAAATCATCGACTGATTAATGAAATTT
TCTCAGACGCAATTGTTCCAGATGTTCGTTCAGTTGTCACAACACAACGTATGCATGTTT
TAAAACGTCAAGTTCAATCTTTAGCAATGCATCAAATGAAATTACAAGCTGAATTGCAAC
AAATTGAAGAAAAATTTGAGGCAAAAAAGATGAAATTTATGGAAAGTTCTGAATTATTCC
AAGAAGAGCTTAAAAAACATTGCAAGCCAGCAGTTGATGAGGATACATTTCAAAAAATGG
TAGAGCGACAATATGAAGCTTTGAAGCGTGAAAGACTGAGAATAATTGAAGATCAAAATA
AACCACAAGCTCAGCAACAGCCACAACAGCCGACAACAGTACAGAAACCAGCTGAAGAAG
TTTCAGTTCAGGCAAATGCAGCACAACCAGCAGGTAATGCAGAACTGCCACCAGCTGAAA
CACAATCAACATCTGAG
>g15364.t3 Gene=g15364 Length=352
MSLPNYKQILPNPQRLRPSGSGQMMGRDQSPFIHSAHSNPSFTPQKAGKSSSASIDSRYP
KPPKAPEKPVMPYMRYSKKQWEVVKNSNPELKLWEIGKKIGMLWRDLSEAEKQVYIDEYE
AEKSEYEKALKAYHTSPAYLAYMSTKSKKNDPNDIHDMPRSSSKSQQDRRVDIQPAEDEE
DQDDGFSFKQVAYNRYTRNHRLINEIFSDAIVPDVRSVVTTQRMHVLKRQVQSLAMHQMK
LQAELQQIEEKFEAKKMKFMESSELFQEELKKHCKPAVDEDTFQKMVERQYEALKRERLR
IIEDQNKPQAQQQPQQPTTVQKPAEEVSVQANAAQPAGNAELPPAETQSTSE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g15364.t3 | CDD | cd01390 | HMGB-UBF_HMG-box | 72 | 131 | 2.03648E-16 |
| 7 | g15364.t3 | Coils | Coil | Coil | 116 | 136 | - |
| 6 | g15364.t3 | Coils | Coil | Coil | 231 | 258 | - |
| 5 | g15364.t3 | Gene3D | G3DSA:1.10.30.10 | DNA Binding (I) | 62 | 167 | 1.1E-23 |
| 11 | g15364.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 71 | - |
| 15 | g15364.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 57 | - |
| 13 | g15364.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 158 | 176 | - |
| 14 | g15364.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 158 | 184 | - |
| 12 | g15364.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 299 | 352 | - |
| 10 | g15364.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 305 | 335 | - |
| 2 | g15364.t3 | PANTHER | PTHR46232 | SMARCE1 REGULATOR OF CHROMATIN | 13 | 338 | 4.8E-135 |
| 3 | g15364.t3 | PANTHER | PTHR46232:SF1 | SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY E MEMBER 1 | 13 | 338 | 4.8E-135 |
| 1 | g15364.t3 | Pfam | PF00505 | HMG (high mobility group) box | 66 | 133 | 1.6E-17 |
| 16 | g15364.t3 | ProSiteProfiles | PS50118 | HMG boxes A and B DNA-binding domains profile. | 66 | 134 | 16.218 |
| 9 | g15364.t3 | SMART | SM00398 | hmgende2 | 65 | 135 | 3.9E-13 |
| 4 | g15364.t3 | SUPERFAMILY | SSF47095 | HMG-box | 54 | 137 | 1.27E-21 |
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:0043044 | NA | NA |
| GO:0016514 | SWI/SNF complex | CC |
KEGG
Orthology
- This transcript has been annotated with K11651 (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E, 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.
