General information for g10361.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as SWI/SNF complex subunit SMARCC2.
Parent gene
- The parent gene g10361 is located on chr_1: 9106070..9109573 (+ 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_1 | g10361 | g10361.t1 | TSS | g10361.t1 | 9105990 | 9105990 |
| chr_1 | g10361 | g10361.t1 | isoform | g10361.t1 | 9106070 | 9109573 |
| chr_1 | g10361 | g10361.t1 | exon | g10361.t1.exon1 | 9106070 | 9106183 |
| chr_1 | g10361 | g10361.t1 | cds | g10361.t1.CDS1 | 9106070 | 9106183 |
| chr_1 | g10361 | g10361.t1 | exon | g10361.t1.exon2 | 9106265 | 9106387 |
| chr_1 | g10361 | g10361.t1 | cds | g10361.t1.CDS2 | 9106265 | 9106387 |
| chr_1 | g10361 | g10361.t1 | exon | g10361.t1.exon3 | 9106447 | 9106560 |
| chr_1 | g10361 | g10361.t1 | cds | g10361.t1.CDS3 | 9106447 | 9106560 |
| chr_1 | g10361 | g10361.t1 | exon | g10361.t1.exon4 | 9106620 | 9108663 |
| chr_1 | g10361 | g10361.t1 | cds | g10361.t1.CDS4 | 9106620 | 9108663 |
| chr_1 | g10361 | g10361.t1 | exon | g10361.t1.exon5 | 9108807 | 9109573 |
| chr_1 | g10361 | g10361.t1 | cds | g10361.t1.CDS5 | 9108807 | 9109573 |
| chr_1 | g10361 | g10361.t1 | TTS | g10361.t1 | 9109996 | 9109996 |
Sequences
>g10361.t1 Gene=g10361 Length=3162
ATGAATTTAGGACCGAAAAAAGATGGAAGTCCAAATGTAGAGTTTTTTACATCACCTGAA
TCACTTCAGGGATTCGAGACTGTTCGATTATGGCTACAAAAACATCATAAAAAATATATT
CAGGCTGATCCACCAACAAAAGAGAGCCTTGCACAGCTCATTATTCAATTAATACAGTAT
CAAGAAACAAAACTTGGTAAAAATTCTCAAGATACATCGATGACAACAAGACTTCCGATG
AGATTTTTTCATGATTTCAAACCTGGTGGAGCACTTTGTGTCATTTTATCAACAATGTAT
CGCTTCAAGAGTGATCAACGTTGGAGAAAATTTGATTTCACTGTTAGCAAAACATCATCC
AAAAAAGATCCAAATCTTCAATTGCTTGTTGAAATTGAATCAAGTTTGATTGACGCTGAA
GTTTTTAGACTTCCAACAATTTACATTAGACCAGAAGTTGATCGACAACTTGCAGCAAGA
ATACGTGAAATTATTACAAATCATCAAGCTGAAATAACAGAAGATGAAGAAGAAGCGACA
CATATTGTGTATCCAGAAGTTGATCCTCTGCCTGAAGAATATGCGAGACCGCTATTTAAA
CGTGACAAATATGTCATGCTGCATTGGTATTATTTTCCAGAATCATACGATTCTTGGGTT
CCAAATAATTTCGATTTACCTGACAATGTTCCCGATTGTCCTGCATCACCTGCCGATCAT
TGGCGTGTTTCTGCTCAGTGGGTTCGTGATCTTGATCAATATAATGAATGGATGTCAGAA
GAAGATTATGAAGTTGATGAACAAGGACGTAAGAAAGTTCATAAATTAAGAATTTCTGTT
GAAGATCTTATGTCAGCTGATGGTGATAAGTCAAAGAAACAAATGGCATCAAAAGGTAAA
CGTAAGCGCTCACCATCACCAAAAAATCAAAAAAGAAAGTCAGGAAGATCACCAGCTGTT
TTTCAACAGAAAAAATCACGTGCTGATGATGATGAGTCTGAAGATTTGACAAAAGATATG
GACGATCCTTCAGCTGAACCAAATGTTCAAGAAGTTAAACCATCAATTAGCGCAGCAACA
TCTGGTCCAGCGACACCAACAACAAAGCGTGATCCTGATATGGCACCACTTAAAAGTTCA
GTTGTTCAAGATTTAGATGAAGATATGGAACGAGGTGAAGATTCACAGACTGGAAAAGCA
AGTGAAAATAGCAACACACAAGATTTTGCTAATAAAGATGATGTTGAGGATAACAATGTT
ACAGAACAAACTCATCACATTATAATACCATCATATTCTGCATGGTTTGATTATAATTCA
ATTCATGTTGTTGAAAAACGTGCTCTACCAGAATTCTTTAATGGTAAAAATAAGTCAAAG
AGTCCAGAAATTTATCTAGCTTATCGTAACTTTATGATTGACACTTATCGCTTGAATCCA
ACTGAATATTTGACAAGCACTGCATGTCGTCGTAATTTGGCAGGTGATGTATGTGCTATT
ATGAGAGTTCATGCATTTTTGGAGCAATGGGGGTTGATAAATTATCAAATTGATGCTGAA
TCTCGTCCTACACCGATGGGACCACCACCGACATCACATTTCCATATTTTGAGCGATACT
CCATGCGGTTTACAGCCAATTAATCCACAAAAAATTCCACAACCACTTGCTGCATCAAAA
GCATTATTGGATTTGGATAAGAAAATGCCAGAAAAGAAAGATAGTGATCCCAATGCACCA
CAAACACCAGCAACAATTAAACAAGAGCCTGGTGAGTTGGCTCCTGGTACACAGTTTGGC
CTAAGATTAGATCAATATGCAAAGAAACCAGCAGCAATGAAGAACAAAACAGCAGCAAGT
ATGACACGTGAATGGACAGATCAAGAAACTTTGTTACTACTTGAGGGTTTAGAAATGTAC
AAAGATGATTGGAATAAAGTGTGCGAACATGTTGGATCACGAACACAAGATGAATGCATT
CTGCACTTTTTACGATTGCCCATTGAAGATCCATACCTTGAGGATGATAGCACATTTTTG
GGTCCATTAAGTTACCAACCAATTCCATTCAGTAAAGCAGGAAATCCAATTATGTCAACA
GTTGCTTTTCTAGCATCTGTCGTTGATCCACGAATTGCAGCGAGTGCAGCAAAAGCAGCA
ATGGAAGAATTTGCAGCAATCAAAGATGAAGTTCCAGCAGCCATGCTTGATGCACATTTA
AAGAATGTTGAAAAGACAAATTTCGGTGGTAAATTTGATCCATATGCTGGTCTATCAACA
AGTGGCATTGCAGGCACAGCACCAGAAAAAGAAAAGGATGAAAATGCTGAAGGTGAAAAA
GAAAAGTCGACAAGTGAAGATGTTGAAATGAAAGATGCCACAAAGAAAGATTCAGATAAA
GAAAAAGAAACAACTGAACCAGAAAAACCTGAGGCAGTTGATGATAAAGAAAAAGATACT
AAAAAATCTGATTCTGAAACGACAGATAAAGACAAAGATGGTGCGGCAGCTGTAAAGAGC
GAAGCGATTGATGGCGAGAAGAAGACTGATGAGAAGCAAGATAATGAGGAAAAAGAAGAA
GGTGTCGAATCGAGAAAGATTTTTAATGAAGGCAATTTGCAGTCAGCAGCAGCAGCCGCT
TTAGCCGCAGCAGCTGTAAAAGCGAAACATCTTGCCGCAGTTGAAGAAAGAAAAATTAAG
AGTTTGGTTGCATTACTTGTTGAGACACAAATGAAAAAACTTGAAATTAAACTGCGTCAT
TTTGAAGAACTGGAAACAACAATGGAACGTGAGCGTGAAGGACTTGAATATCAAAGACAG
CAACTGATACAGGAACGACAACAATTTCATTTAGAACAATTGAAAGCTGCTGAATTCAGA
GCACGTCAGCAAGCACATCAACGTTTCCAACAAGAACATGGCCCATGGCAGAATCCAAAT
CATCCAATTCCTTCAAACATGCCACCACAGCAGCATCCGATAGGTGTTGGTCAAAATACA
CCACAAATCGCACAAGCACAACAGCAACCACCACCTCCAACTGCACCCAATGATGCAACA
CCTCCGAATTCCGCTGTACCAACTTCACAGCATGCAATGCCACCACAGCAGCCACAAAAT
TCAAATCCAATTCCACCTGCTGCAACTGGTGTACCAACTTAA
>g10361.t1 Gene=g10361 Length=1053
MNLGPKKDGSPNVEFFTSPESLQGFETVRLWLQKHHKKYIQADPPTKESLAQLIIQLIQY
QETKLGKNSQDTSMTTRLPMRFFHDFKPGGALCVILSTMYRFKSDQRWRKFDFTVSKTSS
KKDPNLQLLVEIESSLIDAEVFRLPTIYIRPEVDRQLAARIREIITNHQAEITEDEEEAT
HIVYPEVDPLPEEYARPLFKRDKYVMLHWYYFPESYDSWVPNNFDLPDNVPDCPASPADH
WRVSAQWVRDLDQYNEWMSEEDYEVDEQGRKKVHKLRISVEDLMSADGDKSKKQMASKGK
RKRSPSPKNQKRKSGRSPAVFQQKKSRADDDESEDLTKDMDDPSAEPNVQEVKPSISAAT
SGPATPTTKRDPDMAPLKSSVVQDLDEDMERGEDSQTGKASENSNTQDFANKDDVEDNNV
TEQTHHIIIPSYSAWFDYNSIHVVEKRALPEFFNGKNKSKSPEIYLAYRNFMIDTYRLNP
TEYLTSTACRRNLAGDVCAIMRVHAFLEQWGLINYQIDAESRPTPMGPPPTSHFHILSDT
PCGLQPINPQKIPQPLAASKALLDLDKKMPEKKDSDPNAPQTPATIKQEPGELAPGTQFG
LRLDQYAKKPAAMKNKTAASMTREWTDQETLLLLEGLEMYKDDWNKVCEHVGSRTQDECI
LHFLRLPIEDPYLEDDSTFLGPLSYQPIPFSKAGNPIMSTVAFLASVVDPRIAASAAKAA
MEEFAAIKDEVPAAMLDAHLKNVEKTNFGGKFDPYAGLSTSGIAGTAPEKEKDENAEGEK
EKSTSEDVEMKDATKKDSDKEKETTEPEKPEAVDDKEKDTKKSDSETTDKDKDGAAAVKS
EAIDGEKKTDEKQDNEEKEEGVESRKIFNEGNLQSAAAAALAAAAVKAKHLAAVEERKIK
SLVALLVETQMKKLEIKLRHFEELETTMEREREGLEYQRQQLIQERQQFHLEQLKAAEFR
ARQQAHQRFQQEHGPWQNPNHPIPSNMPPQQHPIGVGQNTPQIAQAQQQPPPPTAPNDAT
PPNSAVPTSQHAMPPQQPQNSNPIPPAATGVPT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g10361.t1 | Coils | Coil | Coil | 158 | 178 | - |
| 14 | g10361.t1 | Coils | Coil | Coil | 911 | 945 | - |
| 12 | g10361.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 433 | 520 | 5.2E-43 |
| 11 | g10361.t1 | Gene3D | G3DSA:1.10.10.60 | - | 619 | 671 | 6.0E-28 |
| 20 | g10361.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 283 | 414 | - |
| 25 | g10361.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 295 | 310 | - |
| 16 | g10361.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 350 | 367 | - |
| 22 | g10361.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 570 | 594 | - |
| 23 | g10361.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 760 | 867 | - |
| 19 | g10361.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 767 | 866 | - |
| 21 | g10361.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 986 | 1053 | - |
| 26 | g10361.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 991 | 1005 | - |
| 17 | g10361.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1006 | 1020 | - |
| 24 | g10361.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1021 | 1037 | - |
| 18 | g10361.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1038 | 1053 | - |
| 6 | g10361.t1 | PANTHER | PTHR12802 | SWI/SNF COMPLEX-RELATED | 225 | 1049 | 1.5E-294 |
| 7 | g10361.t1 | PANTHER | PTHR12802:SF105 | SWI/SNF COMPLEX SUBUNIT SMARCC2 | 225 | 1049 | 1.5E-294 |
| 3 | g10361.t1 | Pfam | PF16496 | SWIRM-associated domain at the N-terminal | 5 | 423 | 3.8E-168 |
| 2 | g10361.t1 | Pfam | PF04433 | SWIRM domain | 430 | 515 | 2.1E-31 |
| 4 | g10361.t1 | Pfam | PF00249 | Myb-like DNA-binding domain | 623 | 666 | 5.4E-11 |
| 1 | g10361.t1 | Pfam | PF16498 | SWIRM-associated domain at the C-terminal | 708 | 771 | 2.3E-28 |
| 5 | g10361.t1 | Pfam | PF16495 | SWIRM-associated region 1 | 879 | 958 | 4.3E-28 |
| 27 | g10361.t1 | ProSiteProfiles | PS50934 | SWIRM domain profile. | 427 | 524 | 31.014 |
| 28 | g10361.t1 | ProSiteProfiles | PS51293 | SANT domain profile. | 620 | 671 | 23.724 |
| 15 | g10361.t1 | SMART | SM00717 | sant | 621 | 669 | 9.2E-10 |
| 8 | g10361.t1 | SUPERFAMILY | SSF52113 | BRCT domain | 141 | 271 | 2.94E-11 |
| 10 | g10361.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 423 | 529 | 1.16E-35 |
| 9 | g10361.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 621 | 673 | 2.77E-11 |
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:0071564 | npBAF complex | CC |
| GO:0005515 | protein binding | MF |
| GO:0016514 | SWI/SNF complex | CC |
| GO:0071565 | nBAF complex | CC |
KEGG
Orthology
- This transcript has been annotated with K11649 (SWI/SNF related-matrix-associated actin-dependent regulator of chromatin subfamily C)
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.
