General information for g6162.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Brahma-associated protein of 60 kDa.
Parent gene
- The parent gene g6162 is located on chr_2: 14660145..14661728 (- 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 | g6162 | g6162.t1 | isoform | g6162.t1 | 14660145 | 14661728 |
| chr_2 | g6162 | g6162.t1 | exon | g6162.t1.exon1 | 14660145 | 14661500 |
| chr_2 | g6162 | g6162.t1 | cds | g6162.t1.CDS1 | 14660145 | 14661500 |
| chr_2 | g6162 | g6162.t1 | TTS | g6162.t1 | 14661334 | 14661334 |
| chr_2 | g6162 | g6162.t1 | exon | g6162.t1.exon2 | 14661597 | 14661728 |
| chr_2 | g6162 | g6162.t1 | cds | g6162.t1.CDS2 | 14661597 | 14661728 |
| chr_2 | g6162 | g6162.t1 | TSS | g6162.t1 | 14661849 | 14661849 |
Sequences
>g6162.t1 Gene=g6162 Length=1488
ATGTCTCAACGATTTCCAACGCCAAATGTTACAGCGGGACAGCCAATTCCGCCTCAACAA
CAAAGATATATTGGTCCACCGAATTTTAATAATCAGCGTCCTCCTTCTTCACAAAGTTTT
CAAAGTTTCCCACCGAGGAACTTCACACCTCCACCTGGAATGCAACAAAGTGGTCCACCA
CAAAGACCACCGCCACCAAATGCAAATTTTCAACGACAAATGCCTACAACACCTTCTGGT
AAACGTCCTGATAGACCTATGAACTCAGGCCCAACAAAAGAAGGTGGTTATGGACCAGCA
AAGAAGAAAAAGAAATTAGCTGACAAGATTTTACCACAAAAAGTTCGTGATTTAGTTCCC
GAATCTCAAGCATACATGGATTTACTTGCTTTTGAAAGAAAACTTGATGCAACAATTATG
CGAAAACGATTAGACATACAAGAAGCATTAAAGCGACCAATGAAACAAAAGAGGAAGCTT
CGAATTTTCATTTCAAATACATTTTATCCAGCTAAAGAACCATCTGCTGAACCCGAAGGA
AGTGAAGGCTCAATTGCTTCATGGGAATTACGTGTAGAAGGTCGTTTACTTGAAGATAAC
AAAAATGATCCAAACAAGATTAAAAGAAAGTTTTCTAGTTTCTTTAAATCACTTGTTATT
GAATTGGATAAAGATCTTTATGGTCCAGATAATCATTTGGTTGAATGGCATCGTACACAT
ACAACACAAGAAACTGATGGTTTTCAAGTTAAACGTCCTGGTGACAAAAATGTTAGATGC
ACAATTCTTTTGCTCTTAGATTATCAACCATTACAATTTAAATTAGATCCACGTCTTGCA
CGTTTGCTTGGTGTTCACACACAGACACGTCCTGTTATTATATCAGCATTATGGCAATAC
ATTAAAACTCATAAATTGCAAGACGTTCACGAACGTGAATTTATCATTTGTGACAAATAT
TTAGAGCAAATTTTCGGTTGCCCAAAAATGAAATTTGCAGAAATTCCTCAACGATTGAAT
CCATTGCTTCATCCACCAGATCCGATTGTTATCAATCATGTAATTACAGTTGAAGGAGGA
TCAGAAAATAAGCAAACTGCATGCTATGATATTGATGTCGAAGTTGATGACACACTTAAA
AATCAAATGAATAGTTTCTTATTGAGCACTGCAAGTCAACTTGAAATTCAAGGATTAGAC
TCGAAAATTCATGAAACTGTTGATACCATAAATCAATTAAAGACAAATCGCGAATTTTTC
TTAAGTTTCGCTAAAGATCCACAAAATTTCATTCATAAATGGATTGTTTCTCAATCGCGT
GATTTGAAAACAATGACTGATGTTGTTGGTAATCCAGAAGAAGAGCGTCGTTCTGAATTC
TATTATCAACCTTGGGCACAAGAAGCTGTTTCGCGTTATTTCTTCACAAAAGTCAATCAA
AAGCGACTTGAATTGGAAAATGTCTTAACTTATAATAAAAATTTGTAA
>g6162.t1 Gene=g6162 Length=495
MSQRFPTPNVTAGQPIPPQQQRYIGPPNFNNQRPPSSQSFQSFPPRNFTPPPGMQQSGPP
QRPPPPNANFQRQMPTTPSGKRPDRPMNSGPTKEGGYGPAKKKKKLADKILPQKVRDLVP
ESQAYMDLLAFERKLDATIMRKRLDIQEALKRPMKQKRKLRIFISNTFYPAKEPSAEPEG
SEGSIASWELRVEGRLLEDNKNDPNKIKRKFSSFFKSLVIELDKDLYGPDNHLVEWHRTH
TTQETDGFQVKRPGDKNVRCTILLLLDYQPLQFKLDPRLARLLGVHTQTRPVIISALWQY
IKTHKLQDVHEREFIICDKYLEQIFGCPKMKFAEIPQRLNPLLHPPDPIVINHVITVEGG
SENKQTACYDIDVEVDDTLKNQMNSFLLSTASQLEIQGLDSKIHETVDTINQLKTNREFF
LSFAKDPQNFIHKWIVSQSRDLKTMTDVVGNPEEERRSEFYYQPWAQEAVSRYFFTKVNQ
KRLELENVLTYNKNL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g6162.t1 | CDD | cd17674 | SWIB_BAF60A | 272 | 348 | 5.52552E-52 |
| 9 | g6162.t1 | Gene3D | G3DSA:1.10.245.10 | MDM2 | 267 | 350 | 6.1E-27 |
| 6 | g6162.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 44 | - |
| 8 | g6162.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 108 | - |
| 7 | g6162.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 45 | 71 | - |
| 2 | g6162.t1 | PANTHER | PTHR13844:SF1 | SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY D MEMBER 1 | 51 | 489 | 8.5E-235 |
| 3 | g6162.t1 | PANTHER | PTHR13844 | SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY D | 51 | 489 | 8.5E-235 |
| 1 | g6162.t1 | Pfam | PF02201 | SWIB/MDM2 domain | 272 | 342 | 1.6E-23 |
| 5 | g6162.t1 | SMART | SM00151 | swib_2 | 269 | 348 | 1.9E-38 |
| 4 | g6162.t1 | SUPERFAMILY | SSF47592 | SWIB/MDM2 domain | 263 | 353 | 2.4E-28 |
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 K11650 (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D)
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.
