General information for g15364.t1
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.t1 | TSS | g15364.t1 | 5117770 | 5117770 |
| chr_4 | g15364 | g15364.t1 | isoform | g15364.t1 | 5118091 | 5123110 |
| chr_4 | g15364 | g15364.t1 | exon | g15364.t1.exon1 | 5118091 | 5118130 |
| chr_4 | g15364 | g15364.t1 | cds | g15364.t1.CDS1 | 5118091 | 5118130 |
| chr_4 | g15364 | g15364.t1 | exon | g15364.t1.exon2 | 5118555 | 5118599 |
| chr_4 | g15364 | g15364.t1 | cds | g15364.t1.CDS2 | 5118555 | 5118599 |
| chr_4 | g15364 | g15364.t1 | exon | g15364.t1.exon3 | 5118885 | 5119006 |
| chr_4 | g15364 | g15364.t1 | cds | g15364.t1.CDS3 | 5118885 | 5119006 |
| chr_4 | g15364 | g15364.t1 | exon | g15364.t1.exon4 | 5119099 | 5119242 |
| chr_4 | g15364 | g15364.t1 | cds | g15364.t1.CDS4 | 5119099 | 5119242 |
| chr_4 | g15364 | g15364.t1 | exon | g15364.t1.exon5 | 5119433 | 5119495 |
| chr_4 | g15364 | g15364.t1 | cds | g15364.t1.CDS5 | 5119433 | 5119495 |
| chr_4 | g15364 | g15364.t1 | exon | g15364.t1.exon6 | 5119991 | 5120072 |
| chr_4 | g15364 | g15364.t1 | cds | g15364.t1.CDS6 | 5119991 | 5120072 |
| chr_4 | g15364 | g15364.t1 | exon | g15364.t1.exon7 | 5120907 | 5121511 |
| chr_4 | g15364 | g15364.t1 | cds | g15364.t1.CDS7 | 5120907 | 5121511 |
| chr_4 | g15364 | g15364.t1 | exon | g15364.t1.exon8 | 5122200 | 5122926 |
| chr_4 | g15364 | g15364.t1 | cds | g15364.t1.CDS8 | 5122200 | 5122926 |
| chr_4 | g15364 | g15364.t1 | exon | g15364.t1.exon9 | 5123052 | 5123110 |
| chr_4 | g15364 | g15364.t1 | cds | g15364.t1.CDS9 | 5123052 | 5123110 |
| chr_4 | g15364 | g15364.t1 | TTS | g15364.t1 | 5123112 | 5123112 |
Sequences
>g15364.t1 Gene=g15364 Length=1887
ATGTCTCTACCAAATTACAAACAAATTCTTCCAAATCCACATCTTATGACAGCTGGCCAT
CCTGTTACATTCAATATTTTGAAAGAACGTTTAAGACCGTCAGGATCAGGACAAATGATG
GGACGAGATCAATCACCTTTTATACATTCAGCTCATAGCAATCCATCATTTACACCACAA
AAGGCTGGCAAAAGCAGTTCAGCTAGTATTGATTCTCGTTATCCAAAACCACCAAAGGCA
CCAGAAAAGCCAGTGATGCCTTACATGAGATATTCAAAGAAACAATGGGAAGTTGTAAAA
AATTCTAATCCAGAATTGAAATTATGGGAAATTGGAAAGAAAATTGGAATGTTATGGCGT
GATTTATCAGAAGCCGAAAAACAAGTGTATATTGATGAATATGAAGCTGAAAAGAGTGAA
TATGAAAAGGCATTAAAAGCCTATCACACCTCACCTGCATATCTCGCTTATATGTCCACA
AAGAGCAAGAAAAACGATCCAAATGATATACACGACATGCCAAGATCAAGTTCAAAATCA
CAACAAGATCGTCGGGTTGACATTCAACCAGCAGAAGATGAAGAAGATCAGGACGATGGA
TTTTCATTCAAACAAGTCGCTTACAATCGCTACACTAGAAATCATCGACTGATTAATGAA
ATTTTCTCAGACGCAATTGTTCCAGATGTTCGTTCAGTTGTCACAACACAACGTATGCAT
GTTTTAAAACGTCAAGTTCAATCTTTAGCAATGCATCAAATGAAATTACAAGCTGAATTG
CAACAAATTGAAGAAAAATTTGAGGCAAAAAAGATGAAATTTATGGAAAGTTCTGAATTA
TTCCAAGAAGAGCTTAAAAAACATTGCAAGCCAGCAGTTGATGAGGATACATTTCAAAAA
ATGGTAGAGCGACAATATGAAGCTTTGAAGCGTGAAAGACTGAGAATAATTGAAGATCAA
AATAAACCACAAGCTCAGCAACAGCCACAACAGCCGACAACAGTACAGAAACCAGCTGAA
GAAGTTTCAGTTCAGGCAAATGCAGCACAACCAGCAGGTAATGCAGAACTGCCACCAGCT
GAAACACAATCAACATCTGAGCCAATGGATATTGAACCACCAATAAAATCATCAGTTGAA
GCTGAAGAACCAAAATCAATTTTGGAGCATGAAAATGCAGTTCCACCGACAACTGCACCA
GTAGCAGCAACAGTTCCCAATCATGTCACTGAAATGGCTCCAATAAAAGAACATGAAGCA
CCAGTTGAAGCACAAGCTAATGTTGCACCATCAGTATCTCAAGAACAACCACAACAAGCT
GCACCAACATCAGAAACTGCTCCTCATATTCCACCAGTTTCGATTCCAACATCAGCTCCT
CAAAATCCTCCAACTTCTGTTGCAGCTTCACCAACAGTTCCACCACCAATGCATGCACAA
GAACCACCAATTCCAGCTCCAAATGTTACAGTTAATCCAAGTATGGGAATGGGAATGCCA
CCTCATGGTATGCAACATGGAGCTCCTTATGGCTACCCAATGCAAGGAGGCCATCCACCT
CGTCCTTATTATAGTCATATGCCATACCAACAAGGCTATCCAAATTATCCATATGGTCAT
CATATGCCACCTTATCAACAAAATTATCATCCATATGGTGAAGCACATCCTGCTTATCCA
CCACAAGGACCACCAATGCATCCAGGACAACAACCACCACCTCAAAGTGCTGCACCACCT
CATATGCCGAATGTTCCACCAACAACTGCTGCTCCACAACAACCAATTGCAGTACCAACT
GCAGGAAATGAAACAGAAGAAAAAAATGATATTGAGGAGAAAAAAGGAAATGATGAGAAG
GAAGAAGAAAAGAAAAAGGATGAATAG
>g15364.t1 Gene=g15364 Length=628
MSLPNYKQILPNPHLMTAGHPVTFNILKERLRPSGSGQMMGRDQSPFIHSAHSNPSFTPQ
KAGKSSSASIDSRYPKPPKAPEKPVMPYMRYSKKQWEVVKNSNPELKLWEIGKKIGMLWR
DLSEAEKQVYIDEYEAEKSEYEKALKAYHTSPAYLAYMSTKSKKNDPNDIHDMPRSSSKS
QQDRRVDIQPAEDEEDQDDGFSFKQVAYNRYTRNHRLINEIFSDAIVPDVRSVVTTQRMH
VLKRQVQSLAMHQMKLQAELQQIEEKFEAKKMKFMESSELFQEELKKHCKPAVDEDTFQK
MVERQYEALKRERLRIIEDQNKPQAQQQPQQPTTVQKPAEEVSVQANAAQPAGNAELPPA
ETQSTSEPMDIEPPIKSSVEAEEPKSILEHENAVPPTTAPVAATVPNHVTEMAPIKEHEA
PVEAQANVAPSVSQEQPQQAAPTSETAPHIPPVSIPTSAPQNPPTSVAASPTVPPPMHAQ
EPPIPAPNVTVNPSMGMGMPPHGMQHGAPYGYPMQGGHPPRPYYSHMPYQQGYPNYPYGH
HMPPYQQNYHPYGEAHPAYPPQGPPMHPGQQPPPQSAAPPHMPNVPPTTAAPQQPIAVPT
AGNETEEKNDIEEKKGNDEKEEEKKKDE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g15364.t1 | CDD | cd01390 | HMGB-UBF_HMG-box | 87 | 146 | 2.56202E-18 |
| 8 | g15364.t1 | Coils | Coil | Coil | 131 | 151 | - |
| 6 | g15364.t1 | Coils | Coil | Coil | 246 | 273 | - |
| 7 | g15364.t1 | Coils | Coil | Coil | 608 | 628 | - |
| 5 | g15364.t1 | Gene3D | G3DSA:1.10.30.10 | DNA Binding (I) | 77 | 181 | 2.2E-23 |
| 13 | g15364.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 53 | 72 | - |
| 18 | g15364.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 53 | 85 | - |
| 17 | g15364.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 173 | 199 | - |
| 21 | g15364.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 173 | 191 | - |
| 19 | g15364.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 320 | 350 | - |
| 20 | g15364.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 320 | 371 | - |
| 12 | g15364.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 357 | 371 | - |
| 22 | g15364.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 423 | 448 | - |
| 14 | g15364.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 427 | 445 | - |
| 16 | g15364.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 457 | 476 | - |
| 11 | g15364.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 565 | 628 | - |
| 15 | g15364.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 565 | 593 | - |
| 23 | g15364.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 605 | 628 | - |
| 2 | g15364.t1 | PANTHER | PTHR46232 | SMARCE1 REGULATOR OF CHROMATIN | 5 | 625 | 1.5E-138 |
| 3 | g15364.t1 | PANTHER | PTHR46232:SF1 | SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY E MEMBER 1 | 5 | 625 | 1.5E-138 |
| 1 | g15364.t1 | Pfam | PF00505 | HMG (high mobility group) box | 81 | 148 | 3.7E-17 |
| 24 | g15364.t1 | ProSiteProfiles | PS50118 | HMG boxes A and B DNA-binding domains profile. | 81 | 149 | 16.218 |
| 10 | g15364.t1 | SMART | SM00398 | hmgende2 | 80 | 150 | 3.9E-13 |
| 4 | g15364.t1 | SUPERFAMILY | SSF47095 | HMG-box | 69 | 152 | 3.27E-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.
