General information for g442.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Tumor suppressor candidate 3.
Parent gene
- The parent gene g442 is located on chr_3: 3372035..3373124 (+ 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 | g442 | g442.t1 | TSS | g442.t1 | 3371808 | 3371808 |
| chr_3 | g442 | g442.t1 | isoform | g442.t1 | 3371890 | 3372948 |
| chr_3 | g442 | g442.t1 | exon | g442.t1.exon1 | 3371890 | 3371973 |
| chr_3 | g442 | g442.t1 | cds | g442.t1.CDS1 | 3371890 | 3371973 |
| chr_3 | g442 | g442.t1 | exon | g442.t1.exon2 | 3372037 | 3372948 |
| chr_3 | g442 | g442.t1 | cds | g442.t1.CDS2 | 3372037 | 3372948 |
| chr_3 | g442 | g442.t1 | TTS | g442.t1 | 3373100 | 3373100 |
Sequences
>g442.t1 Gene=g442 Length=996
ATGAAAATAGTGAATAGTATTGTATTTGCAATAGTAGCATTTATTCTTATCACTGCTGAT
GTAGAAGGACAAAAGAAACAAGCTAACAGCGGTGGTATCTCATTAAATGAAAAGGTACAG
CAATTACTAGACTGGAATGCAAAAAAGTCTGTGCTACGCTTGAACGGTCATAAATTCAAA
GAATATGTGAAGAATGCACCTAGAAATTATTCTATAATTGTAATGTTTACTGCTTTACAA
CCGGCTCGACAATGTATTATTTGCAGACCAGCATCAGACGAATATACAATCTTAGCAAAT
TCTTATCGCTATTCATCAGCATATTCTAATAAGCTTTTCTTCGCTATGGTTGATTTTGAT
GAAGGCTCAGACGTATTTCAAATGCTTAGACTTAATACTGCTCCAGTTTTTATGCATTTC
CCTGCTAAAGGCAAAGCAAAAGGCAGTGACACTATGGACATTCAAAGAGTAGGCATTTCT
GCGGAAGCAATTGCAAAATGGGTACAAGAGCGCACAGATATACAAATTAGAATTTTTAGA
CCACCAAATTATTCTGGAACTGTAGCAGTTATTATGTTAGTTGCATTCGTTGGAGGCTTT
TTGTATTTAAAGAGAAATAACTTAGAATTTCTACAAAACAAGCAACTTTGGGCATTGCTG
GCAGTTTTGTTTACTTTTGCAATGGTCTCAGGTCAAATGTGGAATCACATTCGATCACCA
CCTTTCGTTCACAAGAGTCAAAATGGAGGTATCTCATATTTCCATGGATCATCTCAAGGT
CAACTTGTATTTGAGACTTATATTGTAATGGTTCTTAATGGCCTTGTTGTAATTGGAATG
ATTCTATTAACTGAATCTGGAAGTCAAAGTGATACAAGAAAAGGAAAATTGATGGCAATT
GTTGGTCTCGTTTTTGTAGCTGTTTTCTTCTCTCTACTTCTATCAGCATTCAGATCAAAA
GCACACGGTTATCCATATTCATTCCTTTTCAAGTAA
>g442.t1 Gene=g442 Length=331
MKIVNSIVFAIVAFILITADVEGQKKQANSGGISLNEKVQQLLDWNAKKSVLRLNGHKFK
EYVKNAPRNYSIIVMFTALQPARQCIICRPASDEYTILANSYRYSSAYSNKLFFAMVDFD
EGSDVFQMLRLNTAPVFMHFPAKGKAKGSDTMDIQRVGISAEAIAKWVQERTDIQIRIFR
PPNYSGTVAVIMLVAFVGGFLYLKRNNLEFLQNKQLWALLAVLFTFAMVSGQMWNHIRSP
PFVHKSQNGGISYFHGSSQGQLVFETYIVMVLNGLVVIGMILLTESGSQSDTRKGKLMAI
VGLVFVAVFFSLLLSAFRSKAHGYPYSFLFK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g442.t1 | Gene3D | G3DSA:3.40.30.10 | Glutaredoxin | 33 | 190 | 5.6E-42 |
| 2 | g442.t1 | PANTHER | PTHR12692 | DOLICHYL-DIPHOSPHOOLIGOSACCHARIDE–PROTEIN GLYCOSYLTRANSFERASE-RELATED | 11 | 330 | 6.3E-136 |
| 3 | g442.t1 | PANTHER | PTHR12692:SF1 | TUMOR SUPPRESSOR CANDIDATE 3 | 11 | 330 | 6.3E-136 |
| 1 | g442.t1 | Pfam | PF04756 | OST3 / OST6 family, transporter family | 40 | 326 | 8.6E-105 |
| 16 | g442.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 23 | - |
| 17 | g442.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 6 | - |
| 18 | g442.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 7 | 18 | - |
| 23 | g442.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 19 | 23 | - |
| 15 | g442.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 24 | 183 | - |
| 22 | g442.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 184 | 203 | - |
| 12 | g442.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 204 | 214 | - |
| 21 | g442.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 215 | 234 | - |
| 13 | g442.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 235 | 266 | - |
| 19 | g442.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 267 | 285 | - |
| 11 | g442.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 286 | 296 | - |
| 20 | g442.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 297 | 317 | - |
| 14 | g442.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 318 | 331 | - |
| 8 | g442.t1 | SUPERFAMILY | SSF52833 | Thioredoxin-like | 44 | 172 | 1.66E-9 |
| 9 | g442.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 23 | - |
| 7 | g442.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 184 | 203 | - |
| 4 | g442.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 216 | 234 | - |
| 5 | g442.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 262 | 284 | - |
| 6 | g442.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 297 | 319 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K12669 (oligosaccharyltransferase complex subunit gamma)
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.
