General information for g5740.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein Wnt-6.
Parent gene
- The parent gene g5740 is located on chr_2: 11488118..11495210 (+ 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 | g5740 | g5740.t1 | TSS | g5740.t1 | 11487900 | 11487900 |
| chr_2 | g5740 | g5740.t1 | isoform | g5740.t1 | 11488118 | 11495210 |
| chr_2 | g5740 | g5740.t1 | exon | g5740.t1.exon1 | 11488118 | 11488179 |
| chr_2 | g5740 | g5740.t1 | cds | g5740.t1.CDS1 | 11488118 | 11488179 |
| chr_2 | g5740 | g5740.t1 | exon | g5740.t1.exon2 | 11493566 | 11493798 |
| chr_2 | g5740 | g5740.t1 | cds | g5740.t1.CDS2 | 11493566 | 11493798 |
| chr_2 | g5740 | g5740.t1 | exon | g5740.t1.exon3 | 11493864 | 11494321 |
| chr_2 | g5740 | g5740.t1 | cds | g5740.t1.CDS3 | 11493864 | 11494321 |
| chr_2 | g5740 | g5740.t1 | exon | g5740.t1.exon4 | 11494508 | 11494540 |
| chr_2 | g5740 | g5740.t1 | cds | g5740.t1.CDS4 | 11494508 | 11494540 |
| chr_2 | g5740 | g5740.t1 | exon | g5740.t1.exon5 | 11494721 | 11494961 |
| chr_2 | g5740 | g5740.t1 | cds | g5740.t1.CDS5 | 11494721 | 11494961 |
| chr_2 | g5740 | g5740.t1 | exon | g5740.t1.exon6 | 11495023 | 11495210 |
| chr_2 | g5740 | g5740.t1 | cds | g5740.t1.CDS6 | 11495023 | 11495210 |
| chr_2 | g5740 | g5740.t1 | TTS | g5740.t1 | 11495975 | 11495975 |
Sequences
>g5740.t1 Gene=g5740 Length=1215
ATGCGTGTAATAGTTTGTGCCATATACCTCATGATCGGTATCATGCCCATGACAAGTGGA
TGGGCTGAGGGAAGTAATATTCTATTAGATCCGATTCAAGTTTGTAAGAAACAACAAAAA
TTACCCAACAAAATTCTCGAGATATGCAAGCAAGATAGTCGAAATAAAACATCATTACTA
AAGAAAATTTCTAATGGGATAACTTTAGGTTTTCGTGAATGTGAAAATCAATTTCGTCAT
CGAAAGTGGAACTGCACAACACAACGTCGTAGTATGAAAAAGATTTTGCTAAAAGATACA
CGAGAAACGGCATTTGTTAATGCCATCACAGCTGCAGGCATTTCATATACAATCGCAAAG
GCCTGTTCGATGGGTGAATTAGTTGAATGCTCATGCGATAAGAATCTCGTGCGGCATAAT
GTTTTATTAAATAATCAGATGACAAACATTGATGGGATGAGCCATACAGCCACAACAATT
AATATTAACAATAATAATAATAATAATTTTAATAATAAGAATCGTAATAAGAAGCCAAGA
AGGAATAACAACAATAATAATAAACGAAATGCCAATAAGAGGAAAGCACCCGATGGTTTA
CCTGGTATGGGTGAAAATTGGGAATGGAGTGGTTGTGATGATAACGTGAATTTCGGTAAT
CGCAAGTCAAAGGATTTTCTCGATGCACGCTATCGACGTCGTAGTGATATTAAAACATTA
GTCAGAATTCATAATAACGATGCTGGACGAATGGCTGTTAAGAAAAGTATGCGTCTTGAT
TGTAAATGTCATGGTCTCAGTGGAAGTTGTACAATGAAGACGTGCTGGATGAAATTGCCA
TCATTCGCAGAAGTTGCTAGTCGACTTCGTGACCGTTTTGATGCTTCATCAAAAGTGATT
GCAAGCAATGATGGCACAGGATTCATGACCGAAGGCTTAGCAATTAAGCCACCAACAAAG
CAAGATCTCGTCTACACTGAAGAATCGCCTGATTTTTGCAAGCCAAATCCTAAAATTGGG
TCATTAGGCGTTCACAATCGAGAATGCAACATTACATCGACTGGAGAAGACAGCTGTGAG
ATATTATGCTGTAATTATGGCTATCAAAGAACAACAATATTTGTCAAATCAAACTGTCAA
TGTCGATTTATATGGTGCTGCAATGTCATTTGCAGTGTTTGTACTGAAAAGCGTGAAATT
TATACGTGTCGCTAA
>g5740.t1 Gene=g5740 Length=404
MRVIVCAIYLMIGIMPMTSGWAEGSNILLDPIQVCKKQQKLPNKILEICKQDSRNKTSLL
KKISNGITLGFRECENQFRHRKWNCTTQRRSMKKILLKDTRETAFVNAITAAGISYTIAK
ACSMGELVECSCDKNLVRHNVLLNNQMTNIDGMSHTATTININNNNNNNFNNKNRNKKPR
RNNNNNNKRNANKRKAPDGLPGMGENWEWSGCDDNVNFGNRKSKDFLDARYRRRSDIKTL
VRIHNNDAGRMAVKKSMRLDCKCHGLSGSCTMKTCWMKLPSFAEVASRLRDRFDASSKVI
ASNDGTGFMTEGLAIKPPTKQDLVYTEESPDFCKPNPKIGSLGVHNRECNITSTGEDSCE
ILCCNYGYQRTTIFVKSNCQCRFIWCCNVICSVCTEKREIYTCR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g5740.t1 | CDD | cd19338 | Wnt_Wnt6 | 29 | 404 | 1.9235E-161 |
| 11 | g5740.t1 | Gene3D | G3DSA:3.30.2460.20 | - | 344 | 404 | 2.6E-10 |
| 20 | g5740.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 161 | 200 | - |
| 21 | g5740.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 174 | 188 | - |
| 2 | g5740.t1 | PANTHER | PTHR12027 | WNT RELATED | 3 | 404 | 3.3E-127 |
| 3 | g5740.t1 | PANTHER | PTHR12027:SF72 | PROTEIN WNT-6 | 3 | 404 | 3.3E-127 |
| 5 | g5740.t1 | PRINTS | PR01349 | Wnt protein signature | 101 | 115 | 1.7E-28 |
| 7 | g5740.t1 | PRINTS | PR01349 | Wnt protein signature | 120 | 133 | 1.7E-28 |
| 4 | g5740.t1 | PRINTS | PR01349 | Wnt protein signature | 207 | 219 | 1.7E-28 |
| 8 | g5740.t1 | PRINTS | PR01349 | Wnt protein signature | 262 | 276 | 1.7E-28 |
| 6 | g5740.t1 | PRINTS | PR01349 | Wnt protein signature | 322 | 333 | 1.7E-28 |
| 1 | g5740.t1 | Pfam | PF00110 | wnt family | 41 | 404 | 2.9E-104 |
| 13 | g5740.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 22 | - |
| 14 | g5740.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 15 | g5740.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 14 | - |
| 16 | g5740.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 22 | - |
| 12 | g5740.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 23 | 404 | - |
| 19 | g5740.t1 | ProSitePatterns | PS00246 | Wnt-1 family signature. | 261 | 270 | - |
| 18 | g5740.t1 | SMART | SM00097 | wnt1_3 | 37 | 404 | 1.1E-120 |
| 10 | g5740.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 22 | - |
| 9 | g5740.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 21 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5740/g5740.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5740.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 K00445 (wingless-type MMTV integration site family, member 6)
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.
