General information for g5916.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein smoothened.
Parent gene
- The parent gene g5916 is located on chr_2: 12844266..12847860 (+ 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 | g5916 | g5916.t3 | TSS | g5916.t3 | 12844046 | 12844046 |
| chr_2 | g5916 | g5916.t3 | isoform | g5916.t3 | 12844266 | 12845277 |
| chr_2 | g5916 | g5916.t3 | exon | g5916.t3.exon1 | 12844266 | 12844270 |
| chr_2 | g5916 | g5916.t3 | cds | g5916.t3.CDS1 | 12844266 | 12844270 |
| chr_2 | g5916 | g5916.t3 | exon | g5916.t3.exon2 | 12844330 | 12845277 |
| chr_2 | g5916 | g5916.t3 | cds | g5916.t3.CDS2 | 12844330 | 12845275 |
| chr_2 | g5916 | g5916.t3 | TTS | g5916.t3 | NA | NA |
Sequences
>g5916.t3 Gene=g5916 Length=953
ATGGGGTATTTCATTTTTTTCTTCGTTTCTTCTTTAACTTTATTATTCGCAACAACGACA
ACAAATGCATCCGTTTCAAAATCATCTCAAAATTCTGAGAATGTTGAAACAATGCGCATA
ACACTTGAGTCTATAAATGGCACTAATAATTTTCGAATGCATGGAAAAAAATCAAAAGAT
GATCGATGGGTTTGGGATGGTAAAGAAGGAAGATACATTTATTGCGTTCGTGAAGCAATA
AATCCATGCGAAAAACTCGAAATAAAGCAATGTTTTGGTCAAAATATTCCCTATCAAAGT
ACAAATCAAGATCTGACGCATTTCTTTAGTCAAGATGTGGCACTTGAAAGAATTACAAGT
TATCAAGCGCTTAAACATGTACCTAAATGCTGGGCAGTTATTCAACCACTTCTTTGTGCT
GTTTTATTCCCAAAATGTGAGAAAATTATTGACAAAGATATGATTTATTTACCCTCACTT
GAAATGTGTAAAATTACAATGGAGCCTTGTAAAATTCTCTACAATACCTCTTATTTTCCT
GATTTTCTTAAATGTAATGAATCAAATTTTCCAACAAAATGTCACAATGATGTTCGTGAG
ATGAAATTCAATTTAACTGGTCAATGTTTGCATCCTCTTGTGCCAACAATGGATCCAACA
AACAGTTATAAAGATATTGAGGGATGTGGATTAGAATGTAAAGATCCACTCTACACTGAT
GATGAACATCGACAAATAAGAAAGCAAATTGGATGGTGTGCAAGTGTATCACTAGTACTT
CATCTTTTTGCAATTTTTACATTCACAGTTGATTGGCATAATGGTAATAAATATCCAGGA
TTAATTATCTTTTATGTCAATCTCTGCTACATGATATCATGCATTGGTTGGCTTGCTCAA
TTTATTCCTGGTGCTCGACAGGATATTGCATGTCGATTTGATAACACACTAAA
>g5916.t3 Gene=g5916 Length=317
MGYFIFFFVSSLTLLFATTTTNASVSKSSQNSENVETMRITLESINGTNNFRMHGKKSKD
DRWVWDGKEGRYIYCVREAINPCEKLEIKQCFGQNIPYQSTNQDLTHFFSQDVALERITS
YQALKHVPKCWAVIQPLLCAVLFPKCEKIIDKDMIYLPSLEMCKITMEPCKILYNTSYFP
DFLKCNESNFPTKCHNDVREMKFNLTGQCLHPLVPTMDPTNSYKDIEGCGLECKDPLYTD
DEHRQIRKQIGWCASVSLVLHLFAIFTFTVDWHNGNKYPGLIIFYVNLCYMISCIGWLAQ
FIPGARQDIACRFDNTL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g5916.t3 | Gene3D | G3DSA:1.10.2000.10 | - | 67 | 193 | 8.2E-40 |
| 8 | g5916.t3 | Gene3D | G3DSA:1.20.1070.10 | - | 206 | 317 | 8.1E-31 |
| 3 | g5916.t3 | PANTHER | PTHR11309:SF35 | SMOOTHENED HOMOLOG | 78 | 317 | 5.3E-97 |
| 4 | g5916.t3 | PANTHER | PTHR11309 | FRIZZLED | 78 | 317 | 5.3E-97 |
| 2 | g5916.t3 | Pfam | PF01392 | Fz domain | 83 | 192 | 9.9E-13 |
| 1 | g5916.t3 | Pfam | PF01534 | Frizzled/Smoothened family membrane region | 237 | 315 | 4.5E-20 |
| 13 | g5916.t3 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 23 | - |
| 14 | g5916.t3 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 15 | g5916.t3 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 15 | - |
| 18 | g5916.t3 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 23 | - |
| 12 | g5916.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 24 | 248 | - |
| 17 | g5916.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 249 | 270 | - |
| 10 | g5916.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 271 | 281 | - |
| 16 | g5916.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 282 | 302 | - |
| 11 | g5916.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 303 | 317 | - |
| 24 | g5916.t3 | ProSiteProfiles | PS50038 | Frizzled (fz) domain profile. | 78 | 197 | 13.347 |
| 23 | g5916.t3 | SMART | SM00063 | FRI_4 | 82 | 199 | 1.7E-20 |
| 5 | g5916.t3 | SUPERFAMILY | SSF63501 | Frizzled cysteine-rich domain | 82 | 206 | 1.44E-18 |
| 7 | g5916.t3 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 23 | - |
| 19 | g5916.t3 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 23 | - |
| 6 | g5916.t3 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 25 | - |
| 20 | g5916.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 4 | 26 | - |
| 21 | g5916.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 251 | 270 | - |
| 22 | g5916.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 280 | 302 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5916/g5916.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5916.t3.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016020 | membrane | CC |
| GO:0005515 | protein binding | MF |
| GO:0007224 | smoothened signaling pathway | BP |
| GO:0007166 | cell surface receptor signaling pathway | BP |
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.
