General information for g5916.t1
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.t1 | TSS | g5916.t1 | 12844046 | 12844046 |
| chr_2 | g5916 | g5916.t1 | isoform | g5916.t1 | 12844266 | 12847518 |
| chr_2 | g5916 | g5916.t1 | exon | g5916.t1.exon1 | 12844266 | 12844270 |
| chr_2 | g5916 | g5916.t1 | cds | g5916.t1.CDS1 | 12844266 | 12844270 |
| chr_2 | g5916 | g5916.t1 | exon | g5916.t1.exon2 | 12844330 | 12845838 |
| chr_2 | g5916 | g5916.t1 | cds | g5916.t1.CDS2 | 12844330 | 12845838 |
| chr_2 | g5916 | g5916.t1 | exon | g5916.t1.exon3 | 12845904 | 12847518 |
| chr_2 | g5916 | g5916.t1 | cds | g5916.t1.CDS3 | 12845904 | 12847518 |
| chr_2 | g5916 | g5916.t1 | TTS | g5916.t1 | 12847586 | 12847586 |
Sequences
>g5916.t1 Gene=g5916 Length=3129
ATGGGGTATTTCATTTTTTTCTTCGTTTCTTCTTTAACTTTATTATTCGCAACAACGACA
ACAAATGCATCCGTTTCAAAATCATCTCAAAATTCTGAGAATGTTGAAACAATGCGCATA
ACACTTGAGTCTATAAATGGCACTAATAATTTTCGAATGCATGGAAAAAAATCAAAAGAT
GATCGATGGGTTTGGGATGGTAAAGAAGGAAGATACATTTATTGCGTTCGTGAAGCAATA
AATCCATGCGAAAAACTCGAAATAAAGCAATGTTTTGGTCAAAATATTCCCTATCAAAGT
ACAAATCAAGATCTGACGCATTTCTTTAGTCAAGATGTGGCACTTGAAAGAATTACAAGT
TATCAAGCGCTTAAACATGTACCTAAATGCTGGGCAGTTATTCAACCACTTCTTTGTGCT
GTTTTATTCCCAAAATGTGAGAAAATTATTGACAAAGATATGATTTATTTACCCTCACTT
GAAATGTGTAAAATTACAATGGAGCCTTGTAAAATTCTCTACAATACCTCTTATTTTCCT
GATTTTCTTAAATGTAATGAATCAAATTTTCCAACAAAATGTCACAATGATGTTCGTGAG
ATGAAATTCAATTTAACTGGTCAATGTTTGCATCCTCTTGTGCCAACAATGGATCCAACA
AACAGTTATAAAGATATTGAGGGATGTGGATTAGAATGTAAAGATCCACTCTACACTGAT
GATGAACATCGACAAATAAGAAAGCAAATTGGATGGTGTGCAAGTGTATCACTAGTACTT
CATCTTTTTGCAATTTTTACATTCACAGTTGATTGGCATAATGGTAATAAATATCCAGGA
TTAATTATCTTTTATGTCAATCTCTGCTACATGATATCATGCATTGGTTGGCTTGCTCAA
TTTATTCCTGGTGCTCGACAGGATATTGCATGTCGATTTGATAACACACTAAAACAAGGA
GAACCAAGTGGTGGTGAAAATTTATCATGCATCATTGTTTTCATTCTTGTTTATTACTTT
CTAATGGCTGCAATGTGTTGGTTTGTGATTTTCACTTATGCTTGGTATATGAGTTTCAAA
GCAATTGGAAAAATTCAAGAAAGAATTGACAAAAAAGCGTCCTACTTTCATGTCATATCA
TGGAGCATTCCTCTTGTATTAACAATAACAGTTTTAGCAATTTCTGAAGTTGATGCAAAT
AGCACAGTAGGAATTTGCTTTGTTGGATATGTCAATCATCCAATACGAGGTGGTTTTGTT
CTTGGACCAGTATTATGCAGCCTTTTAATAGGCGGATATTTTCTTGTGAGAGGAATTGTG
ATTTTAGTAAATTTGAAAATTTCAAGCAAGCAAATTATATCGACAAAAGCAAACAAGAAA
ATTCGACAATCGATCGTTAGAATGTGTGCATGCTCAACTCTCGTATTTGTCTTCATTATT
ATCACAATTTTGTGCCATATCTATGAGTTTAAAAATTCAACAAAATGGGCAACAAGCTTA
AGAGACTCAATAATTTGTAAAATTACATCAATTTACTCAGATGATTCATCATCATGTAAA
ATTGTGGATAGACCTTCAATATCAATTCTTCAACTTCATCTTCTCGCTCTGTTTGCATCT
GGAATGGTCATGGCATCATTTGTCTTTACTCCATCATCACTTGAAATTTGGTCTCGCTAC
TTTCGTCGTAAGTTTGGCAAAAAAGTAGAAGAACCATTAAAACTTCAAAAACATAAAGTA
ATTGCTCAAGCATTTGCTAAAAGAAAAGATTTTCAGAATCGAGGTAGATTATCGATAAGC
TTTCATAATTCACACACTGATCCAGTTGGATTGAAAATTGGAATGAGTGATATGAATTCA
ACAGTTGGTTCTCATGATTTTAGTACAACATGGGCAAATAATCTACCAAGAATTGTCAAT
AGACGATGTGCTTTAACAGGATGCCCATCATCATCTAGATCTTCACATGGTCATAGAAAA
AATTCAGTCGATTCTGAAATAAGCTTTAGCTATCGTCATGTATCAGTAGAATCAAGAAGA
AATTCAAATGACTCGCAAGTTTCTGTCAAAATTGCCGAGATGAAGACAAAGGTCGCAAGC
AGATCGCGTGGTTCAAAGTCGAAATCACGTTCATCTCGACATCAACGAAGAGACTTTACA
TCAAGAAGATATAGTAGAAAGGAAAGCAGTACATCAATGGAATCACAAATTCTTGCTATA
GCTCAGAAAGGAGCTCATTCGACATCAACAGCTGAAGCAAATGCTGGTATGCTTGTTCCT
GTATCGCATCGACGACGTTCTGGAATTGCCGATTTAAGTCGTGAACAAATCAATGAACTT
GTCGCCAAAAATCGATTTCTTTTGCCATATTTAACAACTTCAGAAGATGATAAATCTTCG
GTTGGTTCATTCATTCAACAAGATTCAAAAATTGATGCCATTCTCAAGCAAATAGGAATG
AGTGAACATCAAATTATAGAAAATAAGTTAAATAGTGATAATTTAGATGGAGATTCAGAA
GAGATTCAAGTAATGCGAAAATCAATGAATGAATATTCAGATGTGAGTGGCAAAGAAAAC
ATGTCGAGAGCAATTAAAGCAAGTAATAGAAGTATAAATAGTAAGAAAGCATTAAAAGCA
TCATGTAGTTCAAGAACAAGAAAAGGAAGAAAATCATCTCGATCGATAACAAGAAATGCC
AATCCACTGTCTATTACAAATGGTTCAGGAAAAATGAAACTAGAGAAAAAAATGGAAAAA
GAAAGAAAATCCAAAGATATTTTAAGGAAATCTCAAGAGGAAACATTTATGGCAATCGAA
ATGATGCCGATAAATGACACTTTACAAGGCTCTTGCTCAGGTAGAAGTGACATAGGTATA
CAAACCGAAATGGGAGAAGTGCACACAATCTCATCAATGGAGTTTGCAGAAAATTTAATG
AAACAAGATCGTGAAAATAATCAGCATGATGAAGACATCATTGATGATGATGAAGATGAC
CCAACAGAGAATTTCAAATTACTTCCTAAAAAGACTTCCATTAACCACACAACGAAAAAA
CGTGACACAAATGAAATCTCATTGACAGAATCAGAAAAACTTAAATTACTCTTATTGCCT
TCGAAATAG
>g5916.t1 Gene=g5916 Length=1042
MGYFIFFFVSSLTLLFATTTTNASVSKSSQNSENVETMRITLESINGTNNFRMHGKKSKD
DRWVWDGKEGRYIYCVREAINPCEKLEIKQCFGQNIPYQSTNQDLTHFFSQDVALERITS
YQALKHVPKCWAVIQPLLCAVLFPKCEKIIDKDMIYLPSLEMCKITMEPCKILYNTSYFP
DFLKCNESNFPTKCHNDVREMKFNLTGQCLHPLVPTMDPTNSYKDIEGCGLECKDPLYTD
DEHRQIRKQIGWCASVSLVLHLFAIFTFTVDWHNGNKYPGLIIFYVNLCYMISCIGWLAQ
FIPGARQDIACRFDNTLKQGEPSGGENLSCIIVFILVYYFLMAAMCWFVIFTYAWYMSFK
AIGKIQERIDKKASYFHVISWSIPLVLTITVLAISEVDANSTVGICFVGYVNHPIRGGFV
LGPVLCSLLIGGYFLVRGIVILVNLKISSKQIISTKANKKIRQSIVRMCACSTLVFVFII
ITILCHIYEFKNSTKWATSLRDSIICKITSIYSDDSSSCKIVDRPSISILQLHLLALFAS
GMVMASFVFTPSSLEIWSRYFRRKFGKKVEEPLKLQKHKVIAQAFAKRKDFQNRGRLSIS
FHNSHTDPVGLKIGMSDMNSTVGSHDFSTTWANNLPRIVNRRCALTGCPSSSRSSHGHRK
NSVDSEISFSYRHVSVESRRNSNDSQVSVKIAEMKTKVASRSRGSKSKSRSSRHQRRDFT
SRRYSRKESSTSMESQILAIAQKGAHSTSTAEANAGMLVPVSHRRRSGIADLSREQINEL
VAKNRFLLPYLTTSEDDKSSVGSFIQQDSKIDAILKQIGMSEHQIIENKLNSDNLDGDSE
EIQVMRKSMNEYSDVSGKENMSRAIKASNRSINSKKALKASCSSRTRKGRKSSRSITRNA
NPLSITNGSGKMKLEKKMEKERKSKDILRKSQEETFMAIEMMPINDTLQGSCSGRSDIGI
QTEMGEVHTISSMEFAENLMKQDRENNQHDEDIIDDDEDDPTENFKLLPKKTSINHTTKK
RDTNEISLTESEKLKLLLLPSK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 36 | g5916.t1 | CDD | cd15030 | 7tmF_SMO_homolog | 236 | 562 | 0.0 |
| 16 | g5916.t1 | Coils | Coil | Coil | 911 | 931 | - |
| 15 | g5916.t1 | Gene3D | G3DSA:1.10.2000.10 | - | 67 | 193 | 6.4E-39 |
| 14 | g5916.t1 | Gene3D | G3DSA:1.20.1070.10 | - | 206 | 566 | 1.8E-101 |
| 49 | g5916.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 676 | 690 | - |
| 51 | g5916.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 676 | 734 | - |
| 48 | g5916.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 701 | 720 | - |
| 50 | g5916.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 870 | 926 | - |
| 52 | g5916.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 912 | 926 | - |
| 53 | g5916.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 992 | 1025 | - |
| 3 | g5916.t1 | PANTHER | PTHR11309:SF35 | SMOOTHENED HOMOLOG | 78 | 752 | 1.6E-252 |
| 4 | g5916.t1 | PANTHER | PTHR11309 | FRIZZLED | 78 | 752 | 1.6E-252 |
| 9 | g5916.t1 | PRINTS | PR00489 | Frizzled protein signature | 249 | 271 | 1.3E-31 |
| 10 | g5916.t1 | PRINTS | PR00489 | Frizzled protein signature | 278 | 300 | 1.3E-31 |
| 8 | g5916.t1 | PRINTS | PR00489 | Frizzled protein signature | 332 | 356 | 1.3E-31 |
| 7 | g5916.t1 | PRINTS | PR00489 | Frizzled protein signature | 376 | 399 | 1.3E-31 |
| 6 | g5916.t1 | PRINTS | PR00489 | Frizzled protein signature | 421 | 443 | 1.3E-31 |
| 5 | g5916.t1 | PRINTS | PR00489 | Frizzled protein signature | 464 | 485 | 1.3E-31 |
| 2 | g5916.t1 | Pfam | PF01392 | Fz domain | 83 | 192 | 7.9E-12 |
| 1 | g5916.t1 | Pfam | PF01534 | Frizzled/Smoothened family membrane region | 237 | 563 | 4.4E-91 |
| 25 | g5916.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 23 | - |
| 26 | g5916.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 27 | g5916.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 15 | - |
| 35 | g5916.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 23 | - |
| 24 | g5916.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 24 | 248 | - |
| 33 | g5916.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 249 | 270 | - |
| 20 | g5916.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 271 | 281 | - |
| 32 | g5916.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 282 | 302 | - |
| 23 | g5916.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 303 | 330 | - |
| 31 | g5916.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 331 | 355 | - |
| 17 | g5916.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 356 | 374 | - |
| 28 | g5916.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 375 | 394 | - |
| 21 | g5916.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 395 | 419 | - |
| 30 | g5916.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 420 | 445 | - |
| 18 | g5916.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 446 | 464 | - |
| 29 | g5916.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 465 | 490 | - |
| 22 | g5916.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 491 | 533 | - |
| 34 | g5916.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 534 | 557 | - |
| 19 | g5916.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 558 | 1042 | - |
| 55 | g5916.t1 | ProSiteProfiles | PS50038 | Frizzled (fz) domain profile. | 78 | 197 | 13.347 |
| 54 | g5916.t1 | ProSiteProfiles | PS50261 | G-protein coupled receptors family 2 profile 2. | 244 | 513 | 26.139 |
| 46 | g5916.t1 | SMART | SM00063 | FRI_4 | 82 | 199 | 1.7E-20 |
| 47 | g5916.t1 | SMART | SM01330 | Frizzled_2 | 236 | 567 | 1.3E-132 |
| 11 | g5916.t1 | SUPERFAMILY | SSF63501 | Frizzled cysteine-rich domain | 82 | 206 | 1.14E-17 |
| 13 | g5916.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 23 | - |
| 37 | g5916.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 23 | - |
| 12 | g5916.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 25 | - |
| 38 | g5916.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 4 | 26 | - |
| 41 | g5916.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 251 | 270 | - |
| 42 | g5916.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 280 | 302 | - |
| 44 | g5916.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 333 | 355 | - |
| 45 | g5916.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 375 | 397 | - |
| 40 | g5916.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 418 | 440 | - |
| 39 | g5916.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 465 | 487 | - |
| 43 | g5916.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 529 | 551 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5916/g5916.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5916.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016020 | membrane | CC |
| GO:0005515 | protein binding | MF |
| GO:0016021 | integral component of membrane | CC |
| GO:0004888 | transmembrane signaling receptor activity | MF |
| GO:0007224 | smoothened signaling pathway | BP |
| GO:0007166 | cell surface receptor signaling pathway | BP |
KEGG
Orthology
- This transcript has been annotated with K06226 (smoothened)
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.
