General information for g7546.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Translocon-associated protein subunit beta.
Parent gene
- The parent gene g7546 is located on chr_2: 24459122..24466735 (- 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 | g7546 | g7546.t3 | isoform | g7546.t3 | 24456607 | 24459128 |
| chr_2 | g7546 | g7546.t3 | exon | g7546.t3.exon1 | 24456607 | 24456869 |
| chr_2 | g7546 | g7546.t3 | exon | g7546.t3.exon2 | 24457580 | 24458024 |
| chr_2 | g7546 | g7546.t3 | cds | g7546.t3.CDS1 | 24457824 | 24458024 |
| chr_2 | g7546 | g7546.t3 | exon | g7546.t3.exon3 | 24458083 | 24458460 |
| chr_2 | g7546 | g7546.t3 | cds | g7546.t3.CDS2 | 24458083 | 24458460 |
| chr_2 | g7546 | g7546.t3 | exon | g7546.t3.exon4 | 24458603 | 24459128 |
| chr_2 | g7546 | g7546.t3 | TSS | g7546.t3 | NA | NA |
| chr_2 | g7546 | g7546.t3 | TTS | g7546.t3 | NA | NA |
Sequences
>g7546.t3 Gene=g7546 Length=1612
ATGACAAGTGAAAAAAAATTTTTGATATGTTTTATGAATGAATATAATCTGTGTGTCGTT
TTATTTACTATGAAATATTTAGATTAGTATTCTTTAGTCGTGATTCACCAAAACAGCTGA
TTGACTGGTTTTACTGATACAAAAATAAATCGCCAGCGATTTAAAAATGTATATTCTATA
CAATCTTTCCTCACAACTTACACTACTGTCTCGCAAAAAAAAAATTATATTAAAAATTTT
CTGAAAATGCTCAAATTTCTAATTTAAATTAAAAAAATGATTTTTTTTAACTAAAATTGT
ATAAAAATTTGTTTTATCTTATAAAATCTCGTTAAATTCTTATAAGAAAAATTCTTTTTT
CAACTGTTACGAAAATTTTAAATTTTCCCCTAATTTTTCAGTTTATATTGCCCTACAATG
ACATTTGTGGTGCTACGTTGGAACACGAAAACATAAAAAGTTAGAAAGTAATTTTCATAA
TAATTTAATTAATTCGCAAAGTACACTCTATTATAAAATAATTAAGATGAACAAGCTAGT
GAAATGTCTTGCATTATTCTTCTTTGCATCAATGGTGATGGCTACTGATTCAGGAGATTC
TCGAGCACGATTATTAGTTTCAAAACAAATCCTCAATAAATATCTTGTTGAACAACGCGA
TGTCATGGTAAAATATACTTTATTCAATATTGGAAATGGTGCCGCCACACACGTCAGCTT
AGAAGATCAAGGTTTTCCAGCTGAAGCTTTTGATTTAGTCAGCGGAAAGTTGGAAGTTCA
AATTGATAGAATTGCACCAGCTACAAATGTCACTCATGTAGTTGTTGTTCGACCAAGAGC
GCACGGATACTTTAACTTCACTGCAGCTGCTATTAGCTACCGTCCAGTTGAATCATCACC
AGCTCTTCAATACGCAATTAGTTCAGAGCCAGGCGAAGGTGGAATTATTAATTTGGCTCA
ATTCAACAAACAATTCTCATCACATCTCTTTGATTGGATTGCTTTCGTCATCATGTGTCT
CCCAACAGTAGCCATTCCATACAGTTTATTCTACAAATCAAAGACAAAGTACGAGCTCTT
GGCACAAAAGAAAAAGGCCAACTAAAAAAAGACTTAGAAATTTTAACATCTTCTGTTTTC
GTTAGACTCATTTTTTAAGAAAACCCAATTGTGTGAGTAAAAATCATCATCATCCTTTTG
TTATGAGATATTTTGTGTAAAACAAATTTTAAAAGAGTGTAAGAAGCTGAAATCCAATAA
AAAGTTCATAAATGAAATTTTTTCTAATTCATTTTATTTTTCATGATATAAGAATTTTCA
TGGTTTATCTTCTTCCTCTTTAGTGAAAGAAAAAATTTCATTCTTTTCTAATAGTTTCAT
TGTTCATTCTACATTTTTTTGCTTAAACCTAAAAAATTATTTCTCTTCTTCCATCATCTA
TGAAGAATGATCGATTATATTTTTTTGTTCTTTACAATGTTTTATTTGAAGAAAAAAAGT
TATTTTCCACTAAACCTAAAATAAAGTTTTTCTTTCTTGAATATTTTTCAATTTTTTACG
CGTGTTGGTTTGTTCACAATTTTTTGCAAATAAATTGGAAAGAAAATTATCT
>g7546.t3 Gene=g7546 Length=192
MNKLVKCLALFFFASMVMATDSGDSRARLLVSKQILNKYLVEQRDVMVKYTLFNIGNGAA
THVSLEDQGFPAEAFDLVSGKLEVQIDRIAPATNVTHVVVVRPRAHGYFNFTAAAISYRP
VESSPALQYAISSEPGEGGIINLAQFNKQFSSHLFDWIAFVIMCLPTVAIPYSLFYKSKT
KYELLAQKKKAN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g7546.t3 | PANTHER | PTHR12861:SF3 | TRANSLOCON-ASSOCIATED PROTEIN SUBUNIT BETA | 1 | 189 | 5.8E-50 |
| 3 | g7546.t3 | PANTHER | PTHR12861 | TRANSLOCON-ASSOCIATED PROTEIN, BETA SUBUNIT PRECURSOR TRAP-BETA SIGNAL SEQUENCE RECEPTOR BETA SUBUNIT | 1 | 189 | 5.8E-50 |
| 13 | g7546.t3 | PIRSF | PIRSF016400 | TRAP-beta | 1 | 191 | 4.7E-68 |
| 1 | g7546.t3 | Pfam | PF05753 | Translocon-associated protein beta (TRAPB) | 10 | 184 | 3.2E-63 |
| 8 | g7546.t3 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 9 | g7546.t3 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 10 | g7546.t3 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 14 | - |
| 12 | g7546.t3 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 19 | - |
| 7 | g7546.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 153 | - |
| 11 | g7546.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 154 | 175 | - |
| 6 | g7546.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 176 | 192 | - |
| 5 | g7546.t3 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 14 | g7546.t3 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 4 | g7546.t3 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 19 | - |
| 15 | g7546.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 154 | 176 | - |
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:0005783 | endoplasmic reticulum | CC |
| GO:0016021 | integral component of membrane | CC |
KEGG
Orthology
- This transcript has been annotated with K13250 (translocon-associated protein 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.
