General information for g5739.t1
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.t1 | TTS | g5739.t1 | 11466846 | 11466846 |
| chr_2 | g5739 | g5739.t1 | isoform | g5739.t1 | 11467084 | 11476363 |
| chr_2 | g5739 | g5739.t1 | exon | g5739.t1.exon1 | 11467084 | 11467610 |
| chr_2 | g5739 | g5739.t1 | cds | g5739.t1.CDS1 | 11467084 | 11467610 |
| chr_2 | g5739 | g5739.t1 | exon | g5739.t1.exon2 | 11467673 | 11467700 |
| chr_2 | g5739 | g5739.t1 | cds | g5739.t1.CDS2 | 11467673 | 11467700 |
| chr_2 | g5739 | g5739.t1 | exon | g5739.t1.exon3 | 11467760 | 11468181 |
| chr_2 | g5739 | g5739.t1 | cds | g5739.t1.CDS3 | 11467760 | 11468181 |
| chr_2 | g5739 | g5739.t1 | exon | g5739.t1.exon4 | 11470423 | 11470501 |
| chr_2 | g5739 | g5739.t1 | cds | g5739.t1.CDS4 | 11470423 | 11470501 |
| chr_2 | g5739 | g5739.t1 | exon | g5739.t1.exon5 | 11470561 | 11470708 |
| chr_2 | g5739 | g5739.t1 | cds | g5739.t1.CDS5 | 11470561 | 11470708 |
| chr_2 | g5739 | g5739.t1 | exon | g5739.t1.exon6 | 11476284 | 11476363 |
| chr_2 | g5739 | g5739.t1 | cds | g5739.t1.CDS6 | 11476284 | 11476363 |
| chr_2 | g5739 | g5739.t1 | TSS | g5739.t1 | 11476549 | 11476549 |
Sequences
>g5739.t1 Gene=g5739 Length=1284
ATGGTCGAATCACAACGCTGGATTAAGGATTTGGGAGTTATTAAAATTATATACTTGCTT
GTAGTTTTTGTTATTCAGATCGTAAATTGTTTACCTGATGTTCGTGCATCATGCAAAACA
GTGCCGAATCTCACCAAATCTCAATTAGACTTGTGCTATAAAGCAAACGATGTGACATTG
GCTGCCATTGAGGGTTTAGAGTTGGCAATTTTTGAGTGTCAGCATCAATTCCGATGGAAT
CGATGGAATTGTTCATCTCTAAAAAGTAAAAGTCGAAATCCTCATTCATCAAATTTATTC
AAAAAAGGATACAGAGAAAGTGCCTTTGGGCATGCTATTACAGCAGCTGGTGTTGTTTTA
AGTGTGGCTCGAGCATGCAGTCAAGGACGTCTTCTCTCATGTGGTTGCGATCCAAATGCT
CATCGTAGAAGTCTTTCAAAATCATTACGTGATACACTTGAGGTTGAAAAATCACGATTT
TTGGACACAATCATTGACAATCCTTTCATTATCGACAAACGATTGGAGAGAAATTTCGGA
TTGGACACTAATGAAGTTGTTTCGAAAAAACGAATAAAACAGCAACTAGCAAATCGCTGG
AAATGGGCAGGATGTAGTCATAATATTGACTTTGGTGTTGAATTTTCAGAATTATTTTTG
GACTCGCGTGAAAAAGCCGGTGATTTGCAGTCACAAATTAATCTTCATAATAATAATGTT
GGACGATCTGTAGTTGAAAGAAATCTCGTAAGCAAATGTAAATGTCATGGACTCTCAGGT
TCCTGTCAATTAAAAACATGCTGGAAATCTTCGCCTGACTTTCGAACAGTAGGAAAAATT
TTGAAACAACAATTCCGACGTGCAGTGTTGGTGGATCAGTCCAATTTTGGAAATGGCATG
ATCATTTACAATGGAAACAATAAACGGCGAAAATCGAAATCAGCCAATTTTCGACCATCG
ATCGTACAAAATGAAATGCACAACAATGTGATGCTGCCAAAGCGTCGAAATAAGCGTAAT
AAGATGGAAAATTCGTTGTTTTACTTTCAAAAGTCACCAAATTTCTGTGAACGCGACACA
TTATCAGACATTGCAGGCACACATGGTCGTCGATGCAATCGAAATAGCACAGGAAGCGAC
TCATGTTCATCGCTTTGTTGTGGCCGCGGTTACAATCTTGTTAAAGAGGTGACAAATCAG
AGATGTAATTGTCGCTTTCATTGGTGTTGCTATGTTGAATGTCAAACATGTGAAGTGGTC
GAATGGATAAGCATATGCAATTAA
>g5739.t1 Gene=g5739 Length=427
MVESQRWIKDLGVIKIIYLLVVFVIQIVNCLPDVRASCKTVPNLTKSQLDLCYKANDVTL
AAIEGLELAIFECQHQFRWNRWNCSSLKSKSRNPHSSNLFKKGYRESAFGHAITAAGVVL
SVARACSQGRLLSCGCDPNAHRRSLSKSLRDTLEVEKSRFLDTIIDNPFIIDKRLERNFG
LDTNEVVSKKRIKQQLANRWKWAGCSHNIDFGVEFSELFLDSREKAGDLQSQINLHNNNV
GRSVVERNLVSKCKCHGLSGSCQLKTCWKSSPDFRTVGKILKQQFRRAVLVDQSNFGNGM
IIYNGNNKRRKSKSANFRPSIVQNEMHNNVMLPKRRNKRNKMENSLFYFQKSPNFCERDT
LSDIAGTHGRRCNRNSTGSDSCSSLCCGRGYNLVKEVTNQRCNCRFHWCCYVECQTCEVV
EWISICN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g5739.t1 | CDD | cd19342 | Wnt_Wnt10 | 38 | 427 | 3.11627E-175 |
| 9 | g5739.t1 | Gene3D | G3DSA:3.30.2460.20 | - | 367 | 427 | 2.4E-11 |
| 2 | g5739.t1 | PANTHER | PTHR12027:SF98 | PROTEIN WNT | 34 | 426 | 3.0E-138 |
| 3 | g5739.t1 | PANTHER | PTHR12027 | WNT RELATED | 34 | 426 | 3.0E-138 |
| 6 | g5739.t1 | PRINTS | PR01349 | Wnt protein signature | 105 | 119 | 1.9E-27 |
| 8 | g5739.t1 | PRINTS | PR01349 | Wnt protein signature | 124 | 137 | 1.9E-27 |
| 5 | g5739.t1 | PRINTS | PR01349 | Wnt protein signature | 200 | 212 | 1.9E-27 |
| 7 | g5739.t1 | PRINTS | PR01349 | Wnt protein signature | 254 | 268 | 1.9E-27 |
| 4 | g5739.t1 | PRINTS | PR01349 | Wnt protein signature | 345 | 356 | 1.9E-27 |
| 1 | g5739.t1 | Pfam | PF00110 | wnt family | 41 | 427 | 4.1E-116 |
| 10 | g5739.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 11 | - |
| 12 | g5739.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 29 | - |
| 11 | g5739.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 30 | 427 | - |
| 15 | g5739.t1 | ProSitePatterns | PS00246 | Wnt-1 family signature. | 253 | 262 | - |
| 16 | g5739.t1 | SMART | SM00097 | wnt1_3 | 40 | 427 | 5.6E-120 |
| 14 | g5739.t1 | 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.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5739.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 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