General information for g11646.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Proteasome subunit beta type-3.
Parent gene
- The parent gene g11646 is located on chr_1: 17611396..17612077 (- 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 | g11646 | g11646.t1 | TTS | g11646.t1 | 17611332 | 17611332 |
| chr_1 | g11646 | g11646.t1 | isoform | g11646.t1 | 17611396 | 17612077 |
| chr_1 | g11646 | g11646.t1 | exon | g11646.t1.exon1 | 17611396 | 17611920 |
| chr_1 | g11646 | g11646.t1 | cds | g11646.t1.CDS1 | 17611396 | 17611920 |
| chr_1 | g11646 | g11646.t1 | exon | g11646.t1.exon2 | 17611985 | 17612077 |
| chr_1 | g11646 | g11646.t1 | cds | g11646.t1.CDS2 | 17611985 | 17612077 |
| chr_1 | g11646 | g11646.t1 | TSS | g11646.t1 | 17612172 | 17612172 |
Sequences
>g11646.t1 Gene=g11646 Length=618
ATGTCTATTATGGCTTATAATGGTGGTTGCGTAGTCGCAATGAAAGGAAAAGAATGTGTA
GCGATCGCAACTGATCTTCGTTTTGGACTTCAGGCTCAAACGATTGATACCAACTTTGAA
AAAGTATTTCCAGTGAATAAACACATGTATTTGGGATTAGCTGGACTCCAGACAGATATA
ATAACCGTTTACAAGAGATTAATGTTCCGAAAAAATCTCTATGAAATTCGTGAAAATCGT
GTAATGCAACCAGAAAGATTTGCAGCAATGCTTTCAAGTTTTCTTTATGAGCATCGATTT
GGCCCATATTTCATTGAACCAGTAATTGCAGGATTAGATCCAAAAACTTTTAAACCTTTC
ATATGCAATATGGATCTTATCGGTTGTGCAAACATGCCTGATGATTTTGTTGTTGCTGGA
ACTTGCGAGGAACAACTTTTTGGCATGTGTGAGACATTGTGGCGTGAGAATATGGAACCG
GATGATTTATTTGAAACAATCTCACAAGCCATGTTAAATGCATTTGATCGTGACGCCATT
TCAGGATGGGGAGCTAAAGTCTATATTATTGAAAAAGATAAAGTTACAATAAGAAAGCTT
AAAACTCGTATGGATTAG
>g11646.t1 Gene=g11646 Length=205
MSIMAYNGGCVVAMKGKECVAIATDLRFGLQAQTIDTNFEKVFPVNKHMYLGLAGLQTDI
ITVYKRLMFRKNLYEIRENRVMQPERFAAMLSSFLYEHRFGPYFIEPVIAGLDPKTFKPF
ICNMDLIGCANMPDDFVVAGTCEEQLFGMCETLWRENMEPDDLFETISQAMLNAFDRDAI
SGWGAKVYIIEKDKVTIRKLKTRMD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g11646.t1 | CDD | cd03759 | proteasome_beta_type_3 | 6 | 201 | 6.03855E-128 |
| 6 | g11646.t1 | Gene3D | G3DSA:3.60.20.10 | Glutamine Phosphoribosylpyrophosphate | 1 | 205 | 1.9E-56 |
| 2 | g11646.t1 | PANTHER | PTHR11599 | PROTEASOME SUBUNIT ALPHA/BETA | 4 | 199 | 1.4E-84 |
| 3 | g11646.t1 | PANTHER | PTHR11599:SF62 | PROTEASOME SUBUNIT BETA TYPE-3 | 4 | 199 | 1.4E-84 |
| 1 | g11646.t1 | Pfam | PF00227 | Proteasome subunit | 7 | 190 | 2.1E-41 |
| 5 | g11646.t1 | ProSitePatterns | PS00854 | Proteasome beta-type subunits signature. | 12 | 59 | - |
| 7 | g11646.t1 | ProSiteProfiles | PS51476 | Proteasome beta-type subunit profile. | 8 | 190 | 46.078 |
| 4 | g11646.t1 | SUPERFAMILY | SSF56235 | N-terminal nucleophile aminohydrolases (Ntn hydrolases) | 3 | 205 | 1.71E-54 |
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:0051603 | proteolysis involved in cellular protein catabolic process | BP |
| GO:0043161 | proteasome-mediated ubiquitin-dependent protein catabolic process | BP |
| GO:0004298 | threonine-type endopeptidase activity | MF |
| GO:0019774 | proteasome core complex, beta-subunit complex | CC |
| GO:0005839 | proteasome core complex | CC |
KEGG
Orthology
- This transcript has been annotated with K02735 (20S proteasome subunit beta 3)
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.
