General information for g12545.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Frizzled-2.
Parent gene
- The parent gene g12545 is located on chr_1: 24352698..24353939 (+ 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_1 | g12545 | g12545.t3 | TSS | g12545.t3 | 24340221 | 24340221 |
| chr_1 | g12545 | g12545.t3 | isoform | g12545.t3 | 24341015 | 24352698 |
| chr_1 | g12545 | g12545.t3 | exon | g12545.t3.exon1 | 24341015 | 24341231 |
| chr_1 | g12545 | g12545.t3 | exon | g12545.t3.exon2 | 24350870 | 24351284 |
| chr_1 | g12545 | g12545.t3 | cds | g12545.t3.CDS1 | 24351122 | 24351284 |
| chr_1 | g12545 | g12545.t3 | exon | g12545.t3.exon3 | 24351353 | 24351961 |
| chr_1 | g12545 | g12545.t3 | cds | g12545.t3.CDS2 | 24351353 | 24351961 |
| chr_1 | g12545 | g12545.t3 | exon | g12545.t3.exon4 | 24352328 | 24352698 |
| chr_1 | g12545 | g12545.t3 | cds | g12545.t3.CDS3 | 24352328 | 24352698 |
| chr_1 | g12545 | g12545.t3 | TTS | g12545.t3 | NA | NA |
Sequences
>g12545.t3 Gene=g12545 Length=1612
AAGAAAGAAAAGAACTAGGAGAAGAATGAGTGTATGAAATGAGAAAAAAATCCACTTTTC
GTTTCTCGCTCTATATACATTTCACATCAAAGAACATGAAGTAATAAGTTGGAGTTATGT
GTATACACATAGATATATAAATTGGAGCTCTTATTTTACTCTTTTTCAATGAGATAAATA
CTAAAGAGATTTTCATAATTGCAATTTTCAAAGGCAAATTGCAAAAATATTTAAAGCTTT
AAATATACATCGCGCAATTCAGTATCATTACATATATACACACTACTAGGCAAGTGAGTG
GAATAATACACAGAAAAAAACATCGCAGCCGCTGCCGTGAGCTTCGATCAAAAAAAACTG
CGTGAACAAAACACACACGAGTGAAAGAGAAGAAGCAAAAACACAGACAGATAAAAAATT
ACTCAGCACAACAATGAGCCGGAATCGATCGCGACTGTTTAATTCTGTGATGCTGCTTGC
CGCATTTCTCATGCTGGCATCTGCAGATAAAGGATATTATGGTAATAGCGGAAGCATGAA
CGATGCTGGCGATATGGAAGTTCATATTTCAATGCAATCACAAAAGTCTGGTCATCCACG
TTGTGAAGAGATCAATATTCCCATGTGTAGAGGTATTGGTTATAATACGACAAAATTTCC
AAATCAACTCAACCATGAAACACAAGAAGAAGCTGGCCTTGAAGTTCATCAGTTCTGGCC
ACTTGTTGAAATAAAGTGTTCACCAGATTTAAAGTTTTTCTTATGCTCCATGTATACACC
AATTTGCATTGAAGATTATATGCAGCCACTGCCAGTTTGTCGTTCTGTTTGTGAACGTGC
ACGTGAAGGTTGTGAACCAATTATGGAGCAATACAATTTCAAGTGGCCAGAGACAATGAA
TTGCGATAGTTTGCCGGTGCATGGTGATAAAGATGTACTATGCATGGAGATACCAAGCTA
TCAGAATAATGACCAGTCATCGTCATCATCGAGTGACACGGGCAGTAATAATGTAAATAA
CAATAATAACAATAAAAAGAAGCATCAGGGCAGCTCATCAACGACACAGAAAAAGTGTCC
AAAAGGCGATAAAAAGTGTCAACAGGCATTGGAGCAACGTAATAAAGATTGTCAATGTAA
ATGTCGTTCGCCACTCGTTCCACTTGGAAAGGAAAGCATGTGGTACAATACGAGTACAGC
AAAAGTTGGCAGTGTAAGCAATTGTGGAATTCCATGCAAAGGCGCATTCTTTACACAAGA
TGAGAAAGACTTTGCAAGCTTCTGGATAACTTTATGGAGTGGTTTTTGTGCAGCGAGCAC
TTTTATGACACTTACAACTTTTTTAATTGATCCCGAGCGTTTCAAGTATCCGGAAAGGCC
AATTGTATTTCTATCAGCGTGCTACTTTATGGTGTCATTAGGATTCTTAACACGATACTT
TGTTGGCCATGAAAAAATTGCGTGCGATGGTCGCGCTATAAAATACTCATCAACGGGTCA
GAGCTCGTGCACAATTGTCTTTTTATTGATTTACTACTTTGGCATGGCATCTTCAATTTG
GTGGGTCATTTTGAGCTTCACTTGGTTCCTCTCGGCTGGTTTGAAATGGGGC
>g12545.t3 Gene=g12545 Length=381
MLLAAFLMLASADKGYYGNSGSMNDAGDMEVHISMQSQKSGHPRCEEINIPMCRGIGYNT
TKFPNQLNHETQEEAGLEVHQFWPLVEIKCSPDLKFFLCSMYTPICIEDYMQPLPVCRSV
CERAREGCEPIMEQYNFKWPETMNCDSLPVHGDKDVLCMEIPSYQNNDQSSSSSSDTGSN
NVNNNNNNKKKHQGSSSTTQKKCPKGDKKCQQALEQRNKDCQCKCRSPLVPLGKESMWYN
TSTAKVGSVSNCGIPCKGAFFTQDEKDFASFWITLWSGFCAASTFMTLTTFLIDPERFKY
PERPIVFLSACYFMVSLGFLTRYFVGHEKIACDGRAIKYSSTGQSSCTIVFLLIYYFGMA
SSIWWVILSFTWFLSAGLKWG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 23 | g12545.t3 | CDD | cd07456 | CRD_FZ5_like | 44 | 163 | 2.98897E-81 |
| 11 | g12545.t3 | Gene3D | G3DSA:1.10.2000.10 | - | 37 | 163 | 3.3E-46 |
| 10 | g12545.t3 | Gene3D | G3DSA:1.20.1070.10 | - | 222 | 381 | 5.5E-59 |
| 29 | g12545.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 166 | 200 | - |
| 3 | g12545.t3 | PANTHER | PTHR11309:SF126 | FRIZZLED-2 | 35 | 381 | 2.6E-152 |
| 4 | g12545.t3 | PANTHER | PTHR11309 | FRIZZLED | 35 | 381 | 2.6E-152 |
| 7 | g12545.t3 | PRINTS | PR00489 | Frizzled protein signature | 272 | 294 | 2.1E-31 |
| 6 | g12545.t3 | PRINTS | PR00489 | Frizzled protein signature | 300 | 322 | 2.1E-31 |
| 5 | g12545.t3 | PRINTS | PR00489 | Frizzled protein signature | 349 | 373 | 2.1E-31 |
| 2 | g12545.t3 | Pfam | PF01392 | Fz domain | 45 | 150 | 3.3E-32 |
| 1 | g12545.t3 | Pfam | PF01534 | Frizzled/Smoothened family membrane region | 260 | 381 | 4.4E-51 |
| 16 | g12545.t3 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 12 | - |
| 17 | g12545.t3 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 1 | - |
| 18 | g12545.t3 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 2 | 7 | - |
| 22 | g12545.t3 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 8 | 12 | - |
| 15 | g12545.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 13 | 270 | - |
| 19 | g12545.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 271 | 293 | - |
| 13 | g12545.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 294 | 304 | - |
| 20 | g12545.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 305 | 325 | - |
| 14 | g12545.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 326 | 348 | - |
| 21 | g12545.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 349 | 374 | - |
| 12 | g12545.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 375 | 381 | - |
| 31 | g12545.t3 | ProSiteProfiles | PS50038 | Frizzled (fz) domain profile. | 40 | 161 | 29.358 |
| 30 | g12545.t3 | ProSiteProfiles | PS50261 | G-protein coupled receptors family 2 profile 2. | 269 | 381 | 16.681 |
| 27 | g12545.t3 | SMART | SM00063 | FRI_4 | 44 | 163 | 4.6E-69 |
| 28 | g12545.t3 | SMART | SM01330 | Frizzled_2 | 259 | 381 | 2.7E-15 |
| 8 | g12545.t3 | SUPERFAMILY | SSF63501 | Frizzled cysteine-rich domain | 44 | 163 | 4.45E-43 |
| 9 | g12545.t3 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 12 | - |
| 24 | g12545.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 271 | 293 | - |
| 25 | g12545.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 303 | 325 | - |
| 26 | g12545.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 346 | 368 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
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: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.
