General information for g12828.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Protein SSXT.
Parent gene
- The parent gene g12828 is located on chr_1: 26451910..26454473 (+ 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 | g12828 | g12828.t1 | TSS | g12828.t1 | 26451765 | 26451765 |
| chr_1 | g12828 | g12828.t1 | isoform | g12828.t1 | 26451910 | 26454473 |
| chr_1 | g12828 | g12828.t1 | exon | g12828.t1.exon1 | 26451910 | 26451989 |
| chr_1 | g12828 | g12828.t1 | cds | g12828.t1.CDS1 | 26451910 | 26451989 |
| chr_1 | g12828 | g12828.t1 | exon | g12828.t1.exon2 | 26452065 | 26452263 |
| chr_1 | g12828 | g12828.t1 | cds | g12828.t1.CDS2 | 26452065 | 26452263 |
| chr_1 | g12828 | g12828.t1 | exon | g12828.t1.exon3 | 26452323 | 26452830 |
| chr_1 | g12828 | g12828.t1 | cds | g12828.t1.CDS3 | 26452323 | 26452830 |
| chr_1 | g12828 | g12828.t1 | exon | g12828.t1.exon4 | 26452890 | 26453012 |
| chr_1 | g12828 | g12828.t1 | cds | g12828.t1.CDS4 | 26452890 | 26453012 |
| chr_1 | g12828 | g12828.t1 | exon | g12828.t1.exon5 | 26453623 | 26453851 |
| chr_1 | g12828 | g12828.t1 | cds | g12828.t1.CDS5 | 26453623 | 26453851 |
| chr_1 | g12828 | g12828.t1 | exon | g12828.t1.exon6 | 26453914 | 26454278 |
| chr_1 | g12828 | g12828.t1 | cds | g12828.t1.CDS6 | 26453914 | 26454278 |
| chr_1 | g12828 | g12828.t1 | exon | g12828.t1.exon7 | 26454340 | 26454473 |
| chr_1 | g12828 | g12828.t1 | cds | g12828.t1.CDS7 | 26454340 | 26454473 |
| chr_1 | g12828 | g12828.t1 | TTS | g12828.t1 | 26454826 | 26454826 |
Sequences
>g12828.t1 Gene=g12828 Length=1638
ATGTCTGTTGCCTATTCATCAAGTCAAAATCCGGCAACAAATCAGCAGCCGAGACCAAAT
GTTCCTCCACAACCGCAAAGACCAACTGGACCACCACCGAATCCTGCTCAAATACAGAAA
ATGCTCGATGAAAATTGCAGTCTTATTCAAACTATTCAAGATTATCAGAATATGGGAAAA
GCTAATGAATGCATTTCTCATCAACAAGCATTACATAGAAATCTTCTTTATCTTGCATCA
TTAGCAGATTCAACACAAAATATGTCACAATTATTGCCTCCACCTCATATTTTAGCACAA
GGTGGACCAATTCCTCCTCCAATGATGAATGAACCGTCTCAGCCGAATTACAATGCTCCC
ATGCAACAACCTGGTATGCAAATGGGAAATCAACCGATTCCATCGCCTCAACAAATGCCA
ATGCAAATGCCTCCACAACAAAATACAACTGTTAATCCACAAATGCCGCCAACTTCTCAA
GCAGCTGTTCCGAATCCGAATCAACCTTATAGAGTTCAAACACCAAGTTCACAACAACCT
CCAGTTTCAGCACAAAATCAACCACCCGTTACATCTCAAGCACAAATTAATTCTCCACAG
CCAACAACACAAACACAACAGCAACCTGCTCAAAATCCTCGTGCTGCAAACACACCTCAA
ACAAACCCAATAACGAACCCAGCGAGCTCACCTGCACCTGCACAACCGAATACAGTTCCA
GTTCCTCAACAGCCAAATGCTCCACCACAGCAGCCATATCAACAAAGAGCTCCTTATCCG
CCTTATGGATATCCACCGAATCAGCCAGCTTATCAACCGAATTACATGTATGGCCCGCCA
AATCAGCCCTATCAACAACATCCTTATCACGGTCCACCACCCCCACCACAAGGACAATAT
CAATATCAAGCCTATCCGCAACAAGGTGGCCCACCACCGCCTGGTCAATATCCGCCAACT
AATGGCCCTCCAATTAATTATTATGGCCCTGGGCCGTATCAAGGTCAAATGCCTCCAAAT
CAGCCTGGTCAATATCCGCCACCACCGGGTCAATATCATCAACAGCCATATTATGGACAA
GCACCGCCAATAGGTGCTCAACAACAACAACCTCCAATTGGAGCACAACAGGCACAAAGT
CCTGCACCACCACAACAGCCACCTAATGCGGCACCAGCTACATCATCGTCTGGTCCAACA
TCAGGTACAAGTAGTGGACCAACTACTAGCCCACAACCGCAAGCAACTTCTCCAAATCCA
CAAACACCTCCAATTTCGACTGCTTCACAATCATATGCACCTCAACAACAAAATCAAGTG
CCACCACCGGTTTCATCAACTGCAGGTGTTCCAGTTCCAACATCGCAACAACCAAATCCA
AACAGTTATCAAGCCCCAGTTGTTAATGCTCAAGGTGCACCTCAAAATTTTCCTCCCGTT
CCTTATTCTGCTGCACCTAATCAATATGGACAAACTGGGCCATATCCTCCTCATGCACCT
TATGGATATGCACCACCTCAAAATCCACAAGGAGCTTACATGCCAGCACAACCCTATAAT
CCAAATTATCCACCAGGTCCAGGTTATCAAAGACCTCCAGGACAAAACAACAATTATTAT
TACGGACCACCGCAATAA
>g12828.t1 Gene=g12828 Length=545
MSVAYSSSQNPATNQQPRPNVPPQPQRPTGPPPNPAQIQKMLDENCSLIQTIQDYQNMGK
ANECISHQQALHRNLLYLASLADSTQNMSQLLPPPHILAQGGPIPPPMMNEPSQPNYNAP
MQQPGMQMGNQPIPSPQQMPMQMPPQQNTTVNPQMPPTSQAAVPNPNQPYRVQTPSSQQP
PVSAQNQPPVTSQAQINSPQPTTQTQQQPAQNPRAANTPQTNPITNPASSPAPAQPNTVP
VPQQPNAPPQQPYQQRAPYPPYGYPPNQPAYQPNYMYGPPNQPYQQHPYHGPPPPPQGQY
QYQAYPQQGGPPPPGQYPPTNGPPINYYGPGPYQGQMPPNQPGQYPPPPGQYHQQPYYGQ
APPIGAQQQQPPIGAQQAQSPAPPQQPPNAAPATSSSGPTSGTSSGPTTSPQPQATSPNP
QTPPISTASQSYAPQQQNQVPPPVSSTAGVPVPTSQQPNPNSYQAPVVNAQGAPQNFPPV
PYSAAPNQYGQTGPYPPHAPYGYAPPQNPQGAYMPAQPYNPNYPPGPGYQRPPGQNNNYY
YGPPQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g12828.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 37 | - |
| 16 | g12828.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 15 | - |
| 12 | g12828.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 16 | 35 | - |
| 7 | g12828.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 141 | 158 | - |
| 10 | g12828.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 141 | 545 | - |
| 13 | g12828.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 164 | 228 | - |
| 15 | g12828.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 229 | 268 | - |
| 6 | g12828.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 285 | 300 | - |
| 5 | g12828.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 307 | 326 | - |
| 9 | g12828.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 335 | 353 | - |
| 8 | g12828.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 361 | 376 | - |
| 4 | g12828.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 391 | 412 | - |
| 14 | g12828.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 421 | 471 | - |
| 2 | g12828.t1 | PANTHER | PTHR23107 | SYNOVIAL SARCOMA ASSOCIATED SS18 PROTEIN | 34 | 207 | 5.2E-16 |
| 3 | g12828.t1 | PANTHER | PTHR23107:SF21 | CALCIUM-RESPONSIVE TRANSACTIVATOR-RELATED | 34 | 207 | 5.2E-16 |
| 1 | g12828.t1 | Pfam | PF05030 | SSXT protein (N-terminal region) | 31 | 90 | 2.0E-29 |
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:0003713 | transcription coactivator activity | MF |
KEGG
Orthology
- This transcript has been annotated with K15623 (protein SSXT)
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.
