General information for g10660.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein Wnt-5.
Parent gene
- The parent gene g10660 is located on chr_1: 11228012..11230664 (+ 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 | g10660 | g10660.t3 | isoform | g10660.t3 | 11228012 | 11230664 |
| chr_1 | g10660 | g10660.t3 | exon | g10660.t3.exon1 | 11228012 | 11228192 |
| chr_1 | g10660 | g10660.t3 | cds | g10660.t3.CDS1 | 11228023 | 11228192 |
| chr_1 | g10660 | g10660.t3 | exon | g10660.t3.exon2 | 11229481 | 11229724 |
| chr_1 | g10660 | g10660.t3 | cds | g10660.t3.CDS2 | 11229481 | 11229724 |
| chr_1 | g10660 | g10660.t3 | exon | g10660.t3.exon3 | 11229811 | 11229957 |
| chr_1 | g10660 | g10660.t3 | cds | g10660.t3.CDS3 | 11229811 | 11229957 |
| chr_1 | g10660 | g10660.t3 | exon | g10660.t3.exon4 | 11230051 | 11230153 |
| chr_1 | g10660 | g10660.t3 | cds | g10660.t3.CDS4 | 11230051 | 11230153 |
| chr_1 | g10660 | g10660.t3 | exon | g10660.t3.exon5 | 11230214 | 11230381 |
| chr_1 | g10660 | g10660.t3 | cds | g10660.t3.CDS5 | 11230214 | 11230381 |
| chr_1 | g10660 | g10660.t3 | exon | g10660.t3.exon6 | 11230477 | 11230664 |
| chr_1 | g10660 | g10660.t3 | cds | g10660.t3.CDS6 | 11230477 | 11230664 |
| chr_1 | g10660 | g10660.t3 | TSS | g10660.t3 | NA | NA |
| chr_1 | g10660 | g10660.t3 | TTS | g10660.t3 | NA | NA |
Sequences
>g10660.t3 Gene=g10660 Length=1031
GTTCGCCCGAAATGGCATTCGTATATGCTATGGCATCAGCAGCAGTTACAAGTTTTATTG
CACGTGCATGTCGCGATGGACAACTGGCATCTTGTGGCTGTTCGCGTTCTGCACGTCCAA
AGCAGTTGCACGAAGATTGGACGTGGGGTGGTTGTGGTGACGATCTCGAATTTGGATACA
AATTCTCACAAAATTTCATTGACATCCGTGAAAAAGAGCGAAAAAGAGGCGCAAGAGGAT
TAATATCTAAAATACCCGAACATTTGGGAAATGATACAGCTGCCGATAATACCACTATAA
CCTCCACCACTACGATGAGTCCTGAAGAGCAAATTAAGGCAGATGAAATGTTGAAACTTC
AACAGAAAATTACACAAGAAATTTTAAATTCAAACCTCAAGGAAAAAGAAATGAATGAAT
TGCAGGAAAAAATCAACAAAGAAATTCTCAACTCGAAAATCTTTAACGTCAATGCAGATG
AGAACATTGGACGAAAGAAAAATCGCTTCAAGACAGCATCAGCAAAAGCGCGTGCACTTA
TGAATCTTCACAATAATGAAGCTGGAAGGAGAGCAATATTAAAGAAGCATAAAGTTCATT
GCACATGTCATGGTATAAGTGGCTCATGTAGTTTAATTACGTGCTGGCAGCAGCTGTCAT
CAATTCGTGAAATTGGTGATCATTTACGAGAGCAATATGAACAAGCCACTCAAGTAAAAA
TGAATAAGAGAGGCCGATTGCAGGTCAAAGATTCACGATATAAAGTCCCTACCGCTCTTG
ATTTAGTGTATCTCGATGAAAGTCCTGACTGGTGCCGTGCTAATAAGCAACTTCAATGGG
CAGGTACACATGGTCGTAAATGTAATCGCACGTCAACAGGATTAGACAGCTGTTCAATCC
TTTGTTGTGGACGTGGCTATAATACAAAGAAGATTGTTCTCTATGAGCGATGCAATTGCA
AATTTCAATGGTGTTGTAATGTGAGATGTGAAACATGTAAACGAGTTATTCAGGAATACA
CTTGTAAATAG
>g10660.t3 Gene=g10660 Length=339
MAFVYAMASAAVTSFIARACRDGQLASCGCSRSARPKQLHEDWTWGGCGDDLEFGYKFSQ
NFIDIREKERKRGARGLISKIPEHLGNDTAADNTTITSTTTMSPEEQIKADEMLKLQQKI
TQEILNSNLKEKEMNELQEKINKEILNSKIFNVNADENIGRKKNRFKTASAKARALMNLH
NNEAGRRAILKKHKVHCTCHGISGSCSLITCWQQLSSIREIGDHLREQYEQATQVKMNKR
GRLQVKDSRYKVPTALDLVYLDESPDWCRANKQLQWAGTHGRKCNRTSTGLDSCSILCCG
RGYNTKKIVLYERCNCKFQWCCNVRCETCKRVIQEYTCK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g10660.t3 | Coils | Coil | Coil | 127 | 147 | - |
| 10 | g10660.t3 | Gene3D | G3DSA:3.30.2460.20 | - | 279 | 339 | 3.9E-15 |
| 3 | g10660.t3 | PANTHER | PTHR12027 | WNT RELATED | 1 | 339 | 2.4E-116 |
| 4 | g10660.t3 | PANTHER | PTHR12027:SF77 | PROTEIN WNT-5 | 1 | 339 | 2.4E-116 |
| 5 | g10660.t3 | PRINTS | PR01349 | Wnt protein signature | 18 | 31 | 3.9E-20 |
| 8 | g10660.t3 | PRINTS | PR01349 | Wnt protein signature | 43 | 55 | 3.9E-20 |
| 6 | g10660.t3 | PRINTS | PR01349 | Wnt protein signature | 198 | 212 | 3.9E-20 |
| 7 | g10660.t3 | PRINTS | PR01349 | Wnt protein signature | 257 | 268 | 3.9E-20 |
| 2 | g10660.t3 | Pfam | PF00110 | wnt family | 2 | 93 | 1.2E-21 |
| 1 | g10660.t3 | Pfam | PF00110 | wnt family | 164 | 339 | 6.0E-65 |
| 13 | g10660.t3 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 14 | g10660.t3 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 1 | - |
| 15 | g10660.t3 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 2 | 13 | - |
| 16 | g10660.t3 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 19 | - |
| 12 | g10660.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 339 | - |
| 9 | g10660.t3 | SMART | SM00097 | wnt1_3 | 2 | 339 | 1.6E-90 |
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: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 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. There were no conditions that were differentially expressed