General information for g3552.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Corepressor interacting with RBPJ 1.
Parent gene
- The parent gene g3552 is located on chr_3: 26398000..26398956 (- 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_3 | g3552 | g3552.t1 | TTS | g3552.t1 | 26397143 | 26397143 |
| chr_3 | g3552 | g3552.t1 | isoform | g3552.t1 | 26397216 | 26398434 |
| chr_3 | g3552 | g3552.t1 | exon | g3552.t1.exon1 | 26397216 | 26397929 |
| chr_3 | g3552 | g3552.t1 | cds | g3552.t1.CDS1 | 26397216 | 26397929 |
| chr_3 | g3552 | g3552.t1 | exon | g3552.t1.exon2 | 26398000 | 26398293 |
| chr_3 | g3552 | g3552.t1 | cds | g3552.t1.CDS2 | 26398000 | 26398293 |
| chr_3 | g3552 | g3552.t1 | exon | g3552.t1.exon3 | 26398363 | 26398434 |
| chr_3 | g3552 | g3552.t1 | cds | g3552.t1.CDS3 | 26398363 | 26398434 |
| chr_3 | g3552 | g3552.t1 | TSS | g3552.t1 | 26398523 | 26398523 |
Sequences
>g3552.t1 Gene=g3552 Length=1080
ATGGGTAAAGGTTTCAATAATTATATGAGCAAGAAGTTCTTTCATCCAGCATCTCGAGAT
AATCTGAAACGAGTATGGATGGCAGAACAACAAGAGGAAGCATACAAGAAAAAGCAAGAA
GAATTGCGAGCACAGTATGAAAAAGAACAGAATTTACATGAAAACAAGTTGATGCTAAGC
AAAGAATCCAAGGACAAATTGGCACTTAACTTTATGTATGAACCACCACCTGGAATTAAA
AAAGAGAGAGAAAAGGAAGAAAATGAACCTGAATACAAATTTGAATGGCAGAGAAAATAC
AATGCTCCCCGCGAAAGCTATTGCAAAGGAAATGAAGAAATAAGGGATCAACCATTTGGA
ATCCAAGTTCGCAACGTAAGATGTATTAAATGTCACAAATACGGTCATATAAATACAGAT
AAAGAATGTTCTATGTTCAGTATGTCGATGAGTGAAGCGAGAAAGTTTCATTCAGATCAA
GAACAGCAGCAATTATTAGCCAAAGGCGGAATTGAGTTAGAAGAACAATTGAAAGAAGGA
ATGAAAGAAGATGGACTCGCATTGAAAAGAAATGCGTTGAGTTTAGAGCAGCAACAAAAG
CACAAAATTAAACAACAACTTATTCCAGATGAAGATGAGAAAAATGATGTACCAGAAGCT
GAATTTATTAAAGGATTGAGCAAGAAACAGAAGAAAGAATTGCTTAAGAAACTCAATTTA
ATAGAAAAGAAGCATAAGAAAAAGTCTGATGATTCGTCATCTGATGAAAGTTTAAAAAAG
AGAAAAAAGTCCTCAAAGAAAAAGAAGCGACATTATTCTAGTTCATCATCATCTAGCGAT
GAGAAGCACTATAAAAAATCAAGCAAGAAAAATAACGAAAGGAATAATAATCCTATATAT
GTACCTATTCCAGTAGCAGTTCCAATACCTGTTTATGACAAATATAATCGAGAAAGGAAA
AGATCAAGGGAACGCACTAATAGAGAGAGTTATCGTGAACGAAGCAGAGAGCATAAAAGA
AAGGATCGAAGTCGTTCAAGAGAATACAGAAGAAGAAGTCGTTCACGTGAACGACGATAA
>g3552.t1 Gene=g3552 Length=359
MGKGFNNYMSKKFFHPASRDNLKRVWMAEQQEEAYKKKQEELRAQYEKEQNLHENKLMLS
KESKDKLALNFMYEPPPGIKKEREKEENEPEYKFEWQRKYNAPRESYCKGNEEIRDQPFG
IQVRNVRCIKCHKYGHINTDKECSMFSMSMSEARKFHSDQEQQQLLAKGGIELEEQLKEG
MKEDGLALKRNALSLEQQQKHKIKQQLIPDEDEKNDVPEAEFIKGLSKKQKKELLKKLNL
IEKKHKKKSDDSSSDESLKKRKKSSKKKKRHYSSSSSSSDEKHYKKSSKKNNERNNNPIY
VPIPVAVPIPVYDKYNRERKRSRERTNRESYRERSREHKRKDRSRSREYRRRSRSRERR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g3552.t1 | Coils | Coil | Coil | 28 | 56 | - |
| 11 | g3552.t1 | Coils | Coil | Coil | 231 | 251 | - |
| 7 | g3552.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 73 | 92 | - |
| 5 | g3552.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 77 | 92 | - |
| 4 | g3552.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 239 | 260 | - |
| 10 | g3552.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 239 | 359 | - |
| 9 | g3552.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 273 | 292 | - |
| 6 | g3552.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 313 | 337 | - |
| 8 | g3552.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 338 | 359 | - |
| 2 | g3552.t1 | PANTHER | PTHR13151 | CBF1 INTERACTING COREPRESSOR CIR | 6 | 355 | 4.4E-68 |
| 1 | g3552.t1 | Pfam | PF10197 | N-terminal domain of CBF1 interacting co-repressor CIR | 14 | 49 | 5.2E-14 |
| 3 | g3552.t1 | SMART | SM01083 | Cir_N_3 | 13 | 49 | 4.8E-14 |
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:0003714 | transcription corepressor activity | MF |
KEGG
Orthology
- This transcript has been annotated with K06066 (CBF1 interacting corepressor)
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.
