General information for g8629.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Protein transport protein Sec61 subunit beta.
Parent gene
- The parent gene g8629 is located on chr_2: 31924498..31928604 (+ 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 | g8629 | g8629.t1 | TSS | g8629.t1 | 31924353 | 31924353 |
| chr_2 | g8629 | g8629.t1 | isoform | g8629.t1 | 31924498 | 31924927 |
| chr_2 | g8629 | g8629.t1 | exon | g8629.t1.exon1 | 31924498 | 31924500 |
| chr_2 | g8629 | g8629.t1 | cds | g8629.t1.CDS1 | 31924498 | 31924500 |
| chr_2 | g8629 | g8629.t1 | exon | g8629.t1.exon2 | 31924571 | 31924779 |
| chr_2 | g8629 | g8629.t1 | cds | g8629.t1.CDS2 | 31924571 | 31924779 |
| chr_2 | g8629 | g8629.t1 | exon | g8629.t1.exon3 | 31924840 | 31924927 |
| chr_2 | g8629 | g8629.t1 | cds | g8629.t1.CDS3 | 31924840 | 31924927 |
| chr_2 | g8629 | g8629.t1 | TTS | g8629.t1 | 31925188 | 31925188 |
Sequences
>g8629.t1 Gene=g8629 Length=300
ATGCCTGCACCAGCTTCTTCAACTTCAGTAGGATCAAAATCCGCGGCTCCAAGAGGCGCT
GGAAGTGCTCCAAGCTCAGGTGGAAACCTTAAACAAAGAAAGACAACTTCCTCATCATCA
TCGACTGCTCCAAGAAGTAATAGAGCTGCGGCTGGTTCTTCAGCTGGTGGTATGTGGAGA
TTTTATACAGACGATAGCCCAGGAATCAAAGTTGGACCAGTTCCAGTTCTTGTAATGTCG
TTGCTTTTCATCGCTTCAGTCTTCATGTTACACATTTGGGGAAAGTTTACTAAAGCTTAA
>g8629.t1 Gene=g8629 Length=99
MPAPASSTSVGSKSAAPRGAGSAPSSGGNLKQRKTTSSSSSTAPRSNRAAAGSSAGGMWR
FYTDDSPGIKVGPVPVLVMSLLFIASVFMLHIWGKFTKA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g8629.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 54 | - |
| 5 | g8629.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 15 | - |
| 6 | g8629.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 25 | 49 | - |
| 2 | g8629.t1 | PANTHER | PTHR13509 | SEC61 SUBUNIT BETA | 5 | 97 | 7.3E-29 |
| 10 | g8629.t1 | PIRSF | PIRSF006398 | Sec61_beta | 6 | 99 | 7.6E-31 |
| 1 | g8629.t1 | Pfam | PF03911 | Sec61beta family | 54 | 94 | 6.4E-20 |
| 8 | g8629.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 73 | - |
| 9 | g8629.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 74 | 93 | - |
| 7 | g8629.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 94 | 99 | - |
| 3 | g8629.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 71 | 93 | - |
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:0006886 | intracellular protein transport | BP |
| GO:0005784 | Sec61 translocon complex | CC |
KEGG
Orthology
- This transcript has been annotated with K09481 (protein transport protein SEC61 subunit beta)
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.
