General information for g5739.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein Wnt-10a.
Parent gene
- The parent gene g5739 is located on chr_2: 11467084..11476363 (- 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 | g5739 | g5739.t3 | TTS | g5739.t3 | 11466846 | 11466846 |
| chr_2 | g5739 | g5739.t3 | isoform | g5739.t3 | 11467084 | 11476363 |
| chr_2 | g5739 | g5739.t3 | exon | g5739.t3.exon1 | 11467084 | 11467610 |
| chr_2 | g5739 | g5739.t3 | cds | g5739.t3.CDS1 | 11467084 | 11467610 |
| chr_2 | g5739 | g5739.t3 | exon | g5739.t3.exon2 | 11467673 | 11467700 |
| chr_2 | g5739 | g5739.t3 | cds | g5739.t3.CDS2 | 11467673 | 11467700 |
| chr_2 | g5739 | g5739.t3 | exon | g5739.t3.exon3 | 11467760 | 11468181 |
| chr_2 | g5739 | g5739.t3 | cds | g5739.t3.CDS3 | 11467760 | 11468181 |
| chr_2 | g5739 | g5739.t3 | exon | g5739.t3.exon4 | 11470423 | 11470501 |
| chr_2 | g5739 | g5739.t3 | cds | g5739.t3.CDS4 | 11470423 | 11470501 |
| chr_2 | g5739 | g5739.t3 | exon | g5739.t3.exon5 | 11470561 | 11470708 |
| chr_2 | g5739 | g5739.t3 | cds | g5739.t3.CDS5 | 11470561 | 11470708 |
| chr_2 | g5739 | g5739.t3 | exon | g5739.t3.exon6 | 11474276 | 11474395 |
| chr_2 | g5739 | g5739.t3 | cds | g5739.t3.CDS6 | 11474276 | 11474395 |
| chr_2 | g5739 | g5739.t3 | exon | g5739.t3.exon7 | 11476284 | 11476363 |
| chr_2 | g5739 | g5739.t3 | cds | g5739.t3.CDS7 | 11476284 | 11476363 |
| chr_2 | g5739 | g5739.t3 | TSS | g5739.t3 | 11476549 | 11476549 |
Sequences
>g5739.t3 Gene=g5739 Length=1404
ATGGTCGAATCACAACGCTGGATTAAGGATTTGGGAGTTATTAAAATTATATACTTGCTT
GTAGTTTTTGTTATTCAGATCGTAAATTGTTTACCTGATGTTCGTGCATCATGCAAAACA
GTGCCGAATCTCACCAAATCTCAATTAGACTTGTGCTATAAAGCAAACGATGTGACATTG
GCTGCCATTGAGGGTTTAGACGTAAATTGTTTACCTGATGTTCGTGCATCATGCAAAACA
GTGCCGAATCTCACCAAATCTCAATTAGACTTGTGCTATAAAGCAAACGATGTGACATTG
GCTGCCATTGAGGGTTTAGAGTTGGCAATTTTTGAGTGTCAGCATCAATTCCGATGGAAT
CGATGGAATTGTTCATCTCTAAAAAGTAAAAGTCGAAATCCTCATTCATCAAATTTATTC
AAAAAAGGATACAGAGAAAGTGCCTTTGGGCATGCTATTACAGCAGCTGGTGTTGTTTTA
AGTGTGGCTCGAGCATGCAGTCAAGGACGTCTTCTCTCATGTGGTTGCGATCCAAATGCT
CATCGTAGAAGTCTTTCAAAATCATTACGTGATACACTTGAGGTTGAAAAATCACGATTT
TTGGACACAATCATTGACAATCCTTTCATTATCGACAAACGATTGGAGAGAAATTTCGGA
TTGGACACTAATGAAGTTGTTTCGAAAAAACGAATAAAACAGCAACTAGCAAATCGCTGG
AAATGGGCAGGATGTAGTCATAATATTGACTTTGGTGTTGAATTTTCAGAATTATTTTTG
GACTCGCGTGAAAAAGCCGGTGATTTGCAGTCACAAATTAATCTTCATAATAATAATGTT
GGACGATCTGTAGTTGAAAGAAATCTCGTAAGCAAATGTAAATGTCATGGACTCTCAGGT
TCCTGTCAATTAAAAACATGCTGGAAATCTTCGCCTGACTTTCGAACAGTAGGAAAAATT
TTGAAACAACAATTCCGACGTGCAGTGTTGGTGGATCAGTCCAATTTTGGAAATGGCATG
ATCATTTACAATGGAAACAATAAACGGCGAAAATCGAAATCAGCCAATTTTCGACCATCG
ATCGTACAAAATGAAATGCACAACAATGTGATGCTGCCAAAGCGTCGAAATAAGCGTAAT
AAGATGGAAAATTCGTTGTTTTACTTTCAAAAGTCACCAAATTTCTGTGAACGCGACACA
TTATCAGACATTGCAGGCACACATGGTCGTCGATGCAATCGAAATAGCACAGGAAGCGAC
TCATGTTCATCGCTTTGTTGTGGCCGCGGTTACAATCTTGTTAAAGAGGTGACAAATCAG
AGATGTAATTGTCGCTTTCATTGGTGTTGCTATGTTGAATGTCAAACATGTGAAGTGGTC
GAATGGATAAGCATATGCAATTAA
>g5739.t3 Gene=g5739 Length=467
MVESQRWIKDLGVIKIIYLLVVFVIQIVNCLPDVRASCKTVPNLTKSQLDLCYKANDVTL
AAIEGLDVNCLPDVRASCKTVPNLTKSQLDLCYKANDVTLAAIEGLELAIFECQHQFRWN
RWNCSSLKSKSRNPHSSNLFKKGYRESAFGHAITAAGVVLSVARACSQGRLLSCGCDPNA
HRRSLSKSLRDTLEVEKSRFLDTIIDNPFIIDKRLERNFGLDTNEVVSKKRIKQQLANRW
KWAGCSHNIDFGVEFSELFLDSREKAGDLQSQINLHNNNVGRSVVERNLVSKCKCHGLSG
SCQLKTCWKSSPDFRTVGKILKQQFRRAVLVDQSNFGNGMIIYNGNNKRRKSKSANFRPS
IVQNEMHNNVMLPKRRNKRNKMENSLFYFQKSPNFCERDTLSDIAGTHGRRCNRNSTGSD
SCSSLCCGRGYNLVKEVTNQRCNCRFHWCCYVECQTCEVVEWISICN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g5739.t3 | CDD | cd19342 | Wnt_Wnt10 | 78 | 467 | 3.12003E-175 |
| 11 | g5739.t3 | Gene3D | G3DSA:3.30.2460.20 | - | 407 | 467 | 2.8E-11 |
| 3 | g5739.t3 | PANTHER | PTHR12027:SF98 | PROTEIN WNT | 34 | 68 | 4.8E-145 |
| 5 | g5739.t3 | PANTHER | PTHR12027 | WNT RELATED | 34 | 68 | 4.8E-145 |
| 2 | g5739.t3 | PANTHER | PTHR12027:SF98 | PROTEIN WNT | 74 | 466 | 4.8E-145 |
| 4 | g5739.t3 | PANTHER | PTHR12027 | WNT RELATED | 74 | 466 | 4.8E-145 |
| 6 | g5739.t3 | PRINTS | PR01349 | Wnt protein signature | 145 | 159 | 2.8E-27 |
| 8 | g5739.t3 | PRINTS | PR01349 | Wnt protein signature | 164 | 177 | 2.8E-27 |
| 10 | g5739.t3 | PRINTS | PR01349 | Wnt protein signature | 240 | 252 | 2.8E-27 |
| 7 | g5739.t3 | PRINTS | PR01349 | Wnt protein signature | 294 | 308 | 2.8E-27 |
| 9 | g5739.t3 | PRINTS | PR01349 | Wnt protein signature | 385 | 396 | 2.8E-27 |
| 1 | g5739.t3 | Pfam | PF00110 | wnt family | 81 | 467 | 5.6E-116 |
| 12 | g5739.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 11 | - |
| 14 | g5739.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 29 | - |
| 13 | g5739.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 30 | 467 | - |
| 17 | g5739.t3 | ProSitePatterns | PS00246 | Wnt-1 family signature. | 293 | 302 | - |
| 18 | g5739.t3 | SMART | SM00097 | wnt1_3 | 80 | 467 | 5.6E-120 |
| 16 | g5739.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 29 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5739/g5739.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5739.t3.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 K01357 (wingless-type MMTV integration site family, member 10)
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