General information for g5742.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein Wnt-1.
Parent gene
- The parent gene g5742 is located on chr_2: 11522426..11523810 (- 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 | g5742 | g5742.t1 | TTS | g5742.t1 | 11506435 | 11506435 |
| chr_2 | g5742 | g5742.t1 | isoform | g5742.t1 | 11506471 | 11523416 |
| chr_2 | g5742 | g5742.t1 | exon | g5742.t1.exon1 | 11506471 | 11506554 |
| chr_2 | g5742 | g5742.t1 | cds | g5742.t1.CDS1 | 11506471 | 11506554 |
| chr_2 | g5742 | g5742.t1 | exon | g5742.t1.exon2 | 11507752 | 11508007 |
| chr_2 | g5742 | g5742.t1 | cds | g5742.t1.CDS2 | 11507752 | 11508007 |
| chr_2 | g5742 | g5742.t1 | exon | g5742.t1.exon3 | 11508071 | 11508354 |
| chr_2 | g5742 | g5742.t1 | cds | g5742.t1.CDS3 | 11508071 | 11508354 |
| chr_2 | g5742 | g5742.t1 | exon | g5742.t1.exon4 | 11509353 | 11509481 |
| chr_2 | g5742 | g5742.t1 | cds | g5742.t1.CDS4 | 11509353 | 11509481 |
| chr_2 | g5742 | g5742.t1 | exon | g5742.t1.exon5 | 11509700 | 11509869 |
| chr_2 | g5742 | g5742.t1 | cds | g5742.t1.CDS5 | 11509700 | 11509869 |
| chr_2 | g5742 | g5742.t1 | exon | g5742.t1.exon6 | 11517629 | 11517894 |
| chr_2 | g5742 | g5742.t1 | cds | g5742.t1.CDS6 | 11517629 | 11517894 |
| chr_2 | g5742 | g5742.t1 | exon | g5742.t1.exon7 | 11523307 | 11523416 |
| chr_2 | g5742 | g5742.t1 | cds | g5742.t1.CDS7 | 11523307 | 11523416 |
| chr_2 | g5742 | g5742.t1 | TSS | g5742.t1 | 11523809 | 11523809 |
Sequences
>g5742.t1 Gene=g5742 Length=1299
ATGGATATGCTAAAGTTATTTTATCTTCTCATCATGGCATTATGTGCCTATGTCAATGCC
GACGCCGAAAAGCAATCAAAACAAAATCGTGGACGTGGATCGATATGGTGGGGAATAGCA
AAAGCTGGTGAACCAAACAACATTTCTCCAGTGACACCAACACATGTCTATATGGACCCA
GCAATACATGCTACACTTAGAAGAAAGCAACGACGATTAGCACGAGAAAATCCAGGAATT
TTAGCAGCAATTGCAAAAGGTGCAAACATGGCAATTGCCGAATGCCAACATCAATTCAGA
AATCGCAGATGGAACTGCTCAACTCGAAATTTCCTACAACGTGGAAAAAATCTTTTCGGT
AAAATTGTCGATCGCGGTTGTAGAGAGACTGCATTTATTTATGCTATAACTAGTGCTGCA
GTTACACATTCAATTGCTCGTGCTTGCAGTGAGGGATCAATTGAATCATGTACATGCGAT
TGGTCACATCAAAATGAACCACCACAAGCTAGTAAATCTGAATCAGTTTCTGATGTTAGA
ATGTGGGAATGGGGAGGATGCTCAGACAATATTGTATTCGGCTACAAACTCGCTAGGGAA
TTTGTCGACACCGGTGAACGAGGACGATCATTGCGTGAGAAAATGAACTTGCACAATAAT
GAAGCAGGCCGTGTGCACGTGCAGTCAGAAATGCGTGAAGAATGCAAGTGCCATGGAATG
TCGGGATCATGTTCAGTAAAAACCTGTTGGATGCGATTGCCAAACTTCCGTGTCATTGGT
GATGCTCTTAAGGATCGTTTTGATGCAGCCATTCGTGTACAGGTCAATAATAATCTTAAA
AATAACAATGAAAATCAAATTATGAGAAATAATAGAAGAAACAATAAAAATTTGGCAAAT
ACAAACAGTGAAACAAACTCAGTTCATGGACGTGGTCAAAATCAAAGAAAACAAAATCGT
TATCGATTCTCATTAAAACCATACAATCCCGATCACAAGCCACCAATGATGAAAGACCTC
GTGTTTTTTGAACAATCCCCCGGATTTTGTGAGAAAAATCTGCGTTTGGGAATTTTGGGC
ACACACGGACGTCAATGCAATGATACATCGATAGGTGTCGATGGTTGCGATTTGATGTGT
TGTGGACGTGGTTATAGAACACAAGAAGTGACTGTTGTTGAACGATGTGCCTGCACATTC
CATTGGTGCTGCGAGATAAAGAAAGATTTAAAAAGCAAAATAATTTTGAAAGTGGCTGAT
AATGTCGTACTTAAAGTTTGCGCCACAATTAGTTATTAA
>g5742.t1 Gene=g5742 Length=432
MDMLKLFYLLIMALCAYVNADAEKQSKQNRGRGSIWWGIAKAGEPNNISPVTPTHVYMDP
AIHATLRRKQRRLARENPGILAAIAKGANMAIAECQHQFRNRRWNCSTRNFLQRGKNLFG
KIVDRGCRETAFIYAITSAAVTHSIARACSEGSIESCTCDWSHQNEPPQASKSESVSDVR
MWEWGGCSDNIVFGYKLAREFVDTGERGRSLREKMNLHNNEAGRVHVQSEMREECKCHGM
SGSCSVKTCWMRLPNFRVIGDALKDRFDAAIRVQVNNNLKNNNENQIMRNNRRNNKNLAN
TNSETNSVHGRGQNQRKQNRYRFSLKPYNPDHKPPMMKDLVFFEQSPGFCEKNLRLGILG
THGRQCNDTSIGVDGCDLMCCGRGYRTQEVTVVERCACTFHWCCEIKKDLKSKIILKVAD
NVVLKVCATISY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g5742.t1 | CDD | cd19333 | Wnt_Wnt1 | 66 | 407 | 0.0 |
| 11 | g5742.t1 | Coils | Coil | Coil | 432 | 432 | - |
| 10 | g5742.t1 | Gene3D | G3DSA:3.30.2460.20 | - | 361 | 417 | 8.5E-10 |
| 21 | g5742.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 287 | 316 | - |
| 2 | g5742.t1 | PANTHER | PTHR12027 | WNT RELATED | 14 | 407 | 4.8E-155 |
| 3 | g5742.t1 | PANTHER | PTHR12027:SF91 | PROTO-ONCOGENE WNT-1 | 14 | 407 | 4.8E-155 |
| 5 | g5742.t1 | PRINTS | PR01349 | Wnt protein signature | 128 | 142 | 2.8E-29 |
| 8 | g5742.t1 | PRINTS | PR01349 | Wnt protein signature | 147 | 160 | 2.8E-29 |
| 6 | g5742.t1 | PRINTS | PR01349 | Wnt protein signature | 182 | 194 | 2.8E-29 |
| 7 | g5742.t1 | PRINTS | PR01349 | Wnt protein signature | 236 | 250 | 2.8E-29 |
| 4 | g5742.t1 | PRINTS | PR01349 | Wnt protein signature | 339 | 350 | 2.8E-29 |
| 1 | g5742.t1 | Pfam | PF00110 | wnt family | 63 | 407 | 4.2E-127 |
| 13 | g5742.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 20 | - |
| 14 | g5742.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 5 | - |
| 15 | g5742.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 6 | 16 | - |
| 16 | g5742.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 17 | 20 | - |
| 12 | g5742.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 21 | 432 | - |
| 20 | g5742.t1 | ProSitePatterns | PS00246 | Wnt-1 family signature. | 235 | 244 | - |
| 19 | g5742.t1 | SMART | SM00097 | wnt1_3 | 62 | 421 | 5.9E-174 |
| 9 | g5742.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 20 | - |
| 18 | g5742.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 20 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5742/g5742.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5742.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0007275 | multicellular organism development | BP |
| GO:0016055 | Wnt signaling pathway | BP |
| GO:0005576 | extracellular region | CC |
| GO:0005102 | signaling receptor binding | MF |
KEGG
Orthology
- This transcript has been annotated with K03209 (wingless-type MMTV integration site family, member 1)
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. There were no conditions that were differentially expressed