General information for g442.t3
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.t3 | TSS | g442.t3 | 3371808 | 3371808 |
| chr_3 | g442 | g442.t3 | isoform | g442.t3 | 3371890 | 3372948 |
| chr_3 | g442 | g442.t3 | exon | g442.t3.exon1 | 3371890 | 3371973 |
| chr_3 | g442 | g442.t3 | cds | g442.t3.CDS1 | 3371890 | 3371973 |
| chr_3 | g442 | g442.t3 | exon | g442.t3.exon2 | 3372037 | 3372571 |
| chr_3 | g442 | g442.t3 | cds | g442.t3.CDS2 | 3372037 | 3372571 |
| chr_3 | g442 | g442.t3 | exon | g442.t3.exon3 | 3372644 | 3372948 |
| chr_3 | g442 | g442.t3 | cds | g442.t3.CDS3 | 3372644 | 3372948 |
| chr_3 | g442 | g442.t3 | TTS | g442.t3 | 3373100 | 3373100 |
Sequences
>g442.t3 Gene=g442 Length=924
ATGAAAATAGTGAATAGTATTGTATTTGCAATAGTAGCATTTATTCTTATCACTGCTGAT
GTAGAAGGACAAAAGAAACAAGCTAACAGCGGTGGTATCTCATTAAATGAAAAGGTACAG
CAATTACTAGACTGGAATGCAAAAAAGTCTGTGCTACGCTTGAACGGTCATAAATTCAAA
GAATATGTGAAGAATGCACCTAGAAATTATTCTATAATTGTAATGTTTACTGCTTTACAA
CCGGCTCGACAATGTATTATTTGCAGACCAGCATCAGACGAATATACAATCTTAGCAAAT
TCTTATCGCTATTCATCAGCATATTCTAATAAGCTTTTCTTCGCTATGGTTGATTTTGAT
GAAGGCTCAGACGTATTTCAAATGCTTAGACTTAATACTGCTCCAGTTTTTATGCATTTC
CCTGCTAAAGGCAAAGCAAAAGGCAGTGACACTATGGACATTCAAAGAGTAGGCATTTCT
GCGGAAGCAATTGCAAAATGGGTACAAGAGCGCACAGATATACAAATTAGAATTTTTAGA
CCACCAAATTATTCTGGAACTGTAGCAGTTATTATGTTAGTTGCATTCGTTGGAGGCTTT
TTGTATTTAAAGAGAAATAGTCAAATGTGGAATCACATTCGATCACCACCTTTCGTTCAC
AAGAGTCAAAATGGAGGTATCTCATATTTCCATGGATCATCTCAAGGTCAACTTGTATTT
GAGACTTATATTGTAATGGTTCTTAATGGCCTTGTTGTAATTGGAATGATTCTATTAACT
GAATCTGGAAGTCAAAGTGATACAAGAAAAGGAAAATTGATGGCAATTGTTGGTCTCGTT
TTTGTAGCTGTTTTCTTCTCTCTACTTCTATCAGCATTCAGATCAAAAGCACACGGTTAT
CCATATTCATTCCTTTTCAAGTAA
>g442.t3 Gene=g442 Length=307
MKIVNSIVFAIVAFILITADVEGQKKQANSGGISLNEKVQQLLDWNAKKSVLRLNGHKFK
EYVKNAPRNYSIIVMFTALQPARQCIICRPASDEYTILANSYRYSSAYSNKLFFAMVDFD
EGSDVFQMLRLNTAPVFMHFPAKGKAKGSDTMDIQRVGISAEAIAKWVQERTDIQIRIFR
PPNYSGTVAVIMLVAFVGGFLYLKRNSQMWNHIRSPPFVHKSQNGGISYFHGSSQGQLVF
ETYIVMVLNGLVVIGMILLTESGSQSDTRKGKLMAIVGLVFVAVFFSLLLSAFRSKAHGY
PYSFLFK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g442.t3 | Gene3D | G3DSA:3.40.30.10 | Glutaredoxin | 33 | 190 | 4.7E-42 |
| 4 | g442.t3 | PANTHER | PTHR12692 | DOLICHYL-DIPHOSPHOOLIGOSACCHARIDE–PROTEIN GLYCOSYLTRANSFERASE-RELATED | 11 | 207 | 2.8E-119 |
| 6 | g442.t3 | PANTHER | PTHR12692:SF1 | TUMOR SUPPRESSOR CANDIDATE 3 | 11 | 207 | 2.8E-119 |
| 3 | g442.t3 | PANTHER | PTHR12692 | DOLICHYL-DIPHOSPHOOLIGOSACCHARIDE–PROTEIN GLYCOSYLTRANSFERASE-RELATED | 207 | 306 | 2.8E-119 |
| 5 | g442.t3 | PANTHER | PTHR12692:SF1 | TUMOR SUPPRESSOR CANDIDATE 3 | 207 | 306 | 2.8E-119 |
| 1 | g442.t3 | Pfam | PF04756 | OST3 / OST6 family, transporter family | 40 | 207 | 2.0E-56 |
| 2 | g442.t3 | Pfam | PF04756 | OST3 / OST6 family, transporter family | 208 | 302 | 1.0E-29 |
| 17 | g442.t3 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 23 | - |
| 18 | g442.t3 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 6 | - |
| 19 | g442.t3 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 7 | 18 | - |
| 23 | g442.t3 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 19 | 23 | - |
| 15 | g442.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 24 | 183 | - |
| 22 | g442.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 184 | 203 | - |
| 13 | g442.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 204 | 237 | - |
| 21 | g442.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 238 | 259 | - |
| 16 | g442.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 260 | 270 | - |
| 20 | g442.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 271 | 293 | - |
| 14 | g442.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 294 | 307 | - |
| 10 | g442.t3 | SUPERFAMILY | SSF52833 | Thioredoxin-like | 44 | 172 | 1.39E-9 |
| 11 | g442.t3 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 23 | - |
| 8 | g442.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 181 | 203 | - |
| 9 | g442.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 238 | 260 | - |
| 7 | g442.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 273 | 295 | - |
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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
