General information for g5559.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Frizzled-4.
Parent gene
- The parent gene g5559 is located on chr_2: 10251181..10253298 (+ 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 | g5559 | g5559.t1 | TSS | g5559.t1 | 10251019 | 10251019 |
| chr_2 | g5559 | g5559.t1 | isoform | g5559.t1 | 10251181 | 10253298 |
| chr_2 | g5559 | g5559.t1 | exon | g5559.t1.exon1 | 10251181 | 10251404 |
| chr_2 | g5559 | g5559.t1 | cds | g5559.t1.CDS1 | 10251181 | 10251404 |
| chr_2 | g5559 | g5559.t1 | exon | g5559.t1.exon2 | 10251512 | 10251609 |
| chr_2 | g5559 | g5559.t1 | cds | g5559.t1.CDS2 | 10251512 | 10251609 |
| chr_2 | g5559 | g5559.t1 | exon | g5559.t1.exon3 | 10251672 | 10251782 |
| chr_2 | g5559 | g5559.t1 | cds | g5559.t1.CDS3 | 10251672 | 10251782 |
| chr_2 | g5559 | g5559.t1 | exon | g5559.t1.exon4 | 10251849 | 10252317 |
| chr_2 | g5559 | g5559.t1 | cds | g5559.t1.CDS4 | 10251849 | 10252317 |
| chr_2 | g5559 | g5559.t1 | exon | g5559.t1.exon5 | 10252383 | 10252576 |
| chr_2 | g5559 | g5559.t1 | cds | g5559.t1.CDS5 | 10252383 | 10252576 |
| chr_2 | g5559 | g5559.t1 | exon | g5559.t1.exon6 | 10252638 | 10252718 |
| chr_2 | g5559 | g5559.t1 | cds | g5559.t1.CDS6 | 10252638 | 10252718 |
| chr_2 | g5559 | g5559.t1 | exon | g5559.t1.exon7 | 10252781 | 10253298 |
| chr_2 | g5559 | g5559.t1 | cds | g5559.t1.CDS7 | 10252781 | 10253298 |
| chr_2 | g5559 | g5559.t1 | TTS | g5559.t1 | NA | NA |
Sequences
>g5559.t1 Gene=g5559 Length=1695
ATGAAAAATAAAATTTTTCTGATTTTAATTTATTGCTTGAGTTATAAATTTGCATCAGCA
AGAACTGAAACACAAATGAGAGTTTGTGAACCGATAAAAATTCAAATGTGTTCTCGAATG
GGTTATAATTTAACATCACTACCAAATTTAATTGGTCATGATTATCAAACTGATGTTGAT
TTGACATTACAAACATTCTCGCCTTTGATAAGCTACGGTTGCAGTGCACAACTCTCATTT
TTCCTCTGCGCAACTTATCTTCCTATGTGTTCCGAAAAAATTGGAGGTGTAATTGGTCCT
TGTCGATCTTTATGTGAAGCTGTTCGTGCGAGATGTCATCCGGTACTTACATCATTTGGT
TTTCAATGGCCTAATAGTCTTAATTGCAGTCGCTTTCCTAAAGATAATAATCATGAAAAT
ATGTGCATGGAAGGACCCGGTGAACCGACACTCGATCTTCCACCGACAAATATTAAACCA
AGTCAGTCTTCATGCAAATATTTATTTAAATCTCACTTATATGTGAGACTAAGCAGAAAC
AACAAATGTACTCCCTTGTGTGAAGCTGACATACTCTTTGAGAGTAATGAAAAGCAAATA
GCTTGGTTGTTTATAGGTAGCTGGAGTTTTGCTGCATTGCTTATAAGTAGCATTGCACTG
TTATGCTTGATTTTATCGGATGTTAGTTGGGATAGAAGTCTTTTACCACTTGTTTGTGTT
CATTGCCTTTCAAGTCTCTCATGGGGAATTCGAATATTAGCTGGACGAAATAACACAAGC
TGCGGTTATGATAATCAATTTCCTGGCATTTCTTTATTACTTAATGATGGTCATATTGCT
ACATCGCCTTGTTCATCCACTTTTCTATTGCGATACTATTTTGGCATGTGCGCTGCTTCA
TGGGTTGCAATTTTCTGTTATCGATGGAATTTTTTAATAAAGCAGCATATGGCAGAGGTC
TTAAATGGACAACCATCGGGTATCATTAAAGGCTTTCGCAATGGAAGATTTTTACAATTT
TGTGCTTTTGGATTACCTTTAATACAAACTGTCTTTGTTTTATGGATGAAACTTGTCGAT
GCAGATGAATTATTGGGAACTTGCTATGTTGGAAATCAATCCGATAAAGCACTGTTATCG
TTAGTTGCAATTCCAATTCTAATCTATTGGACAATTGGAACGGGGTATTTGCTCACTGGA
TATCTAACAAAGAAATCACTGCCCAATTTTCATTTGACTGCTTATCTAAATTCATTGGGA
TCTTTCTTATTGATTTATAATATACTTACTGTGTTCATTCTGCTATCATTATTTTTCATC
TTTGGTAATCGAGAGAGTTGGTTGATGATAAATTTAGATGGTTTACAACAACAGCAACCC
ACAGCTCCTCTTTGGCTTTATATGCTACATCCCTTCTTGGAGTTATTGCTTGCTGTTTTG
ACAGCAGCATGGGCAATTGGACCCAGATTAAGAGCAGGATTTTGTCGAACAGAAGTGAAA
CAGCCGAGCTATAAGCAGCCGCCTACAGTTTCTTCATATCAACAAAACGCTTCATATCAA
TCGATTTGTGTGCCACCAAACTCAATGATTTCATTAACAACGCCAGCAAAAATTTACAAG
TACCCCAATCCACACTACTCGTCGTCATCATCGCGTGCATGTCGCTCATCATTTAGGAGG
GAAACTATTTTATAA
>g5559.t1 Gene=g5559 Length=564
MKNKIFLILIYCLSYKFASARTETQMRVCEPIKIQMCSRMGYNLTSLPNLIGHDYQTDVD
LTLQTFSPLISYGCSAQLSFFLCATYLPMCSEKIGGVIGPCRSLCEAVRARCHPVLTSFG
FQWPNSLNCSRFPKDNNHENMCMEGPGEPTLDLPPTNIKPSQSSCKYLFKSHLYVRLSRN
NKCTPLCEADILFESNEKQIAWLFIGSWSFAALLISSIALLCLILSDVSWDRSLLPLVCV
HCLSSLSWGIRILAGRNNTSCGYDNQFPGISLLLNDGHIATSPCSSTFLLRYYFGMCAAS
WVAIFCYRWNFLIKQHMAEVLNGQPSGIIKGFRNGRFLQFCAFGLPLIQTVFVLWMKLVD
ADELLGTCYVGNQSDKALLSLVAIPILIYWTIGTGYLLTGYLTKKSLPNFHLTAYLNSLG
SFLLIYNILTVFILLSLFFIFGNRESWLMINLDGLQQQQPTAPLWLYMLHPFLELLLAVL
TAAWAIGPRLRAGFCRTEVKQPSYKQPPTVSSYQQNASYQSICVPPNSMISLTTPAKIYK
YPNPHYSSSSSRACRSSFRRETIL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g5559.t1 | Gene3D | G3DSA:1.10.2000.10 | - | 23 | 147 | 3.4E-42 |
| 11 | g5559.t1 | Gene3D | G3DSA:1.20.1070.10 | - | 163 | 497 | 2.9E-45 |
| 3 | g5559.t1 | PANTHER | PTHR11309:SF23 | FRIZZLED-4 | 10 | 518 | 3.7E-132 |
| 4 | g5559.t1 | PANTHER | PTHR11309 | FRIZZLED | 10 | 518 | 3.7E-132 |
| 6 | g5559.t1 | PRINTS | PR00489 | Frizzled protein signature | 204 | 226 | 9.9E-9 |
| 8 | g5559.t1 | PRINTS | PR00489 | Frizzled protein signature | 338 | 361 | 9.9E-9 |
| 7 | g5559.t1 | PRINTS | PR00489 | Frizzled protein signature | 383 | 405 | 9.9E-9 |
| 5 | g5559.t1 | PRINTS | PR00489 | Frizzled protein signature | 466 | 486 | 9.9E-9 |
| 2 | g5559.t1 | Pfam | PF01392 | Fz domain | 29 | 136 | 2.8E-31 |
| 1 | g5559.t1 | Pfam | PF01534 | Frizzled/Smoothened family membrane region | 192 | 486 | 1.6E-30 |
| 21 | g5559.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 20 | - |
| 22 | g5559.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 4 | - |
| 23 | g5559.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 5 | 15 | - |
| 31 | g5559.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 20 | - |
| 17 | g5559.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 21 | 199 | - |
| 27 | g5559.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 200 | 225 | - |
| 14 | g5559.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 226 | 233 | - |
| 30 | g5559.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 234 | 254 | - |
| 19 | g5559.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 255 | 289 | - |
| 24 | g5559.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 290 | 307 | - |
| 16 | g5559.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 308 | 336 | - |
| 29 | g5559.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 337 | 358 | - |
| 20 | g5559.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 359 | 377 | - |
| 26 | g5559.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 378 | 398 | - |
| 15 | g5559.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 399 | 418 | - |
| 28 | g5559.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 419 | 442 | - |
| 18 | g5559.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 443 | 461 | - |
| 25 | g5559.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 462 | 486 | - |
| 13 | g5559.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 487 | 564 | - |
| 42 | g5559.t1 | ProSiteProfiles | PS50038 | Frizzled (fz) domain profile. | 24 | 145 | 26.886 |
| 41 | g5559.t1 | ProSiteProfiles | PS50261 | G-protein coupled receptors family 2 profile 2. | 198 | 401 | 14.494 |
| 39 | g5559.t1 | SMART | SM00063 | FRI_4 | 28 | 147 | 9.8E-61 |
| 40 | g5559.t1 | SMART | SM01330 | Frizzled_2 | 191 | 491 | 1.6E-31 |
| 9 | g5559.t1 | SUPERFAMILY | SSF63501 | Frizzled cysteine-rich domain | 28 | 145 | 7.98E-41 |
| 10 | g5559.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 20 | - |
| 37 | g5559.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 204 | 226 | - |
| 38 | g5559.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 233 | 255 | - |
| 36 | g5559.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 290 | 312 | - |
| 35 | g5559.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 337 | 359 | - |
| 32 | g5559.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 379 | 401 | - |
| 34 | g5559.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 422 | 444 | - |
| 33 | g5559.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 464 | 486 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5559/g5559.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5559.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016020 | membrane | CC |
| GO:0005515 | protein binding | MF |
| GO:0042813 | Wnt-activated receptor activity | MF |
| GO:0016055 | Wnt signaling pathway | BP |
| GO:0016021 | integral component of membrane | CC |
| GO:0004888 | transmembrane signaling receptor activity | MF |
| GO:0007166 | cell surface receptor signaling pathway | BP |
KEGG
Orthology
- This transcript has been annotated with K02354 (frizzled 4)
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.
