General information for g10660.t1
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.t1 | isoform | g10660.t1 | 11205086 | 11230664 |
| chr_1 | g10660 | g10660.t1 | exon | g10660.t1.exon1 | 11205086 | 11205177 |
| chr_1 | g10660 | g10660.t1 | cds | g10660.t1.CDS1 | 11205086 | 11205177 |
| chr_1 | g10660 | g10660.t1 | exon | g10660.t1.exon2 | 11219384 | 11220899 |
| chr_1 | g10660 | g10660.t1 | cds | g10660.t1.CDS2 | 11219384 | 11220899 |
| chr_1 | g10660 | g10660.t1 | exon | g10660.t1.exon3 | 11223512 | 11223596 |
| chr_1 | g10660 | g10660.t1 | cds | g10660.t1.CDS3 | 11223512 | 11223596 |
| chr_1 | g10660 | g10660.t1 | exon | g10660.t1.exon4 | 11228012 | 11228192 |
| chr_1 | g10660 | g10660.t1 | cds | g10660.t1.CDS4 | 11228012 | 11228192 |
| chr_1 | g10660 | g10660.t1 | exon | g10660.t1.exon5 | 11229481 | 11229724 |
| chr_1 | g10660 | g10660.t1 | cds | g10660.t1.CDS5 | 11229481 | 11229724 |
| chr_1 | g10660 | g10660.t1 | exon | g10660.t1.exon6 | 11229811 | 11229957 |
| chr_1 | g10660 | g10660.t1 | cds | g10660.t1.CDS6 | 11229811 | 11229957 |
| chr_1 | g10660 | g10660.t1 | exon | g10660.t1.exon7 | 11230051 | 11230153 |
| chr_1 | g10660 | g10660.t1 | cds | g10660.t1.CDS7 | 11230051 | 11230153 |
| chr_1 | g10660 | g10660.t1 | exon | g10660.t1.exon8 | 11230214 | 11230381 |
| chr_1 | g10660 | g10660.t1 | cds | g10660.t1.CDS8 | 11230214 | 11230381 |
| chr_1 | g10660 | g10660.t1 | exon | g10660.t1.exon9 | 11230477 | 11230664 |
| chr_1 | g10660 | g10660.t1 | cds | g10660.t1.CDS9 | 11230477 | 11230664 |
| chr_1 | g10660 | g10660.t1 | TSS | g10660.t1 | NA | NA |
| chr_1 | g10660 | g10660.t1 | TTS | g10660.t1 | NA | NA |
Sequences
>g10660.t1 Gene=g10660 Length=2724
ATGTCACATAATAAATTACTCTGGATTACACTTTGCTCCATCGTCTGGTTCATTCAGAGC
ATTCATGGATTACAAGGAGTGCCAACGTGGATGTGCTTAGGAATAAAATCACCATTCATA
GAATTCACAGCTGAATTTGAAATGCTTTCAAATATGACAGTGTCACTAAACCTCACAGAT
AAAAGTCCTGACTCGCGGCACCGAAAAAATGGTTTGCATAACTTGGGTAATTTCATAAAT
CCAATTGGAACAGCAAATCGTGATGATAAGACAATGGGTTTCAAGGGCATTAATAATACA
ACGTTTAGCATACAGAGTGATTTGCTTGAAACTAAAGATTCGAGAAAACATCAAGAACAG
CATTTATATGAATTGCAACAACAACAAATTCAAGAACTTCAGCAGCACAATTTGAACAAA
TCGGCAACTAACAAAATTTTAATGGACATTATAAAGCCAATTGTGACAGATAGCCATAAA
TCGGATGAAGACAACAAAAGTAGTACTGTTAGTGGCACAAGCAGTGAAGGAATCGATCAT
CCGACAATTCAAATAATTGCAAATGCTAACAATCACTATGAACAGATGAATTCTTATATG
GATGATTCAAGGAAAGTTATCATGCCATTAGCTTTGAAAACTACTCTAATCGAACGAGAT
CGTCCAGTGCCATCACCAACACCATTACCTAAGCCGCAAACAAACATAGAAGATTTAAAG
AAGCACTTGTTAATGCTACAAAACTACAGTGAAGTTGACAAAAGCTTTCAAAGTAAATTT
GTAGTTTTTAAAAAGCAAACATCTACCGCCGCACCAACCACAACTTCAACTACAACACCA
TCAACTCCATTTCCCACAAAAGCCCCGCAGACTACAACCACTATGCCGTTTCCCATGACA
GTTGGCACAATGTATCGCACTAAACCATCCATAAATATCCCAAACGTGCAGAACTCACAA
ATTTTACGCGATGTTTCTTATCCATATACGCGCATTGAAAGAGTTACTGTCGTACCGCAA
GTCTTTTTACAAAATGATCAGCAGCAACCAGAGACCGAGGAGGAGCGTCAACAACATACA
AATGCAGAACGTCGTAAAAATCGGAAGAACGAAAAGAAAGCAAAACGAGACAAAAAGAAA
AATCGGAACGGCAAGCAGGCAGCATCAAACGTGATTCCAACAACTATAGTTTTACCAACA
GCTATCCCGTTGCGGCCAATAAGACGCGAACAGCAGCGACAGCGACAAATGCGATCACAG
AATGGAAGTCAAATGTTTATTTCAACAACAACTGTGTCTAGTGCACCTTACATCATTAAT
TTGAGCGATAGCAAACCATTAGTGGATAGTAACAGTCAAAAATTATCACGAACGATCCGA
AGCAAGGGAAATAGAAGACGAAACCAAAATAAGATGCAACGTGACGCACTCATCATAGAC
TCATCAAATGGTGTTGTCGCAATAAAGAATGAAACGAGCGAGAAAATAGACATAAATCCA
AAACATTGCTATGATGTTAGCGGAATGAGTAAAGGACAGCAAAAGTTATGCGAGCAATTC
ACAAGCATTATGCCTGCAATATCACGTGGAGCACGTGCCGCTATACAGGAATGTCAACAT
CAATTTCAACATCGCCGTTGGAACTGTTCGACTGTTGATGATGACTCAGTTTTTGGACCG
GTCAGCGCTATCGGTTCGCCCGAAATGGCATTCGTATATGCTATGGCATCAGCAGCAGTT
ACAAGTTTTATTGCACGTGCATGTCGCGATGGACAACTGGCATCTTGTGGCTGTTCGCGT
TCTGCACGTCCAAAGCAGTTGCACGAAGATTGGACGTGGGGTGGTTGTGGTGACGATCTC
GAATTTGGATACAAATTCTCACAAAATTTCATTGACATCCGTGAAAAAGAGCGAAAAAGA
GGCGCAAGAGGATTAATATCTAAAATACCCGAACATTTGGGAAATGATACAGCTGCCGAT
AATACCACTATAACCTCCACCACTACGATGAGTCCTGAAGAGCAAATTAAGGCAGATGAA
ATGTTGAAACTTCAACAGAAAATTACACAAGAAATTTTAAATTCAAACCTCAAGGAAAAA
GAAATGAATGAATTGCAGGAAAAAATCAACAAAGAAATTCTCAACTCGAAAATCTTTAAC
GTCAATGCAGATGAGAACATTGGACGAAAGAAAAATCGCTTCAAGACAGCATCAGCAAAA
GCGCGTGCACTTATGAATCTTCACAATAATGAAGCTGGAAGGAGAGCAATATTAAAGAAG
CATAAAGTTCATTGCACATGTCATGGTATAAGTGGCTCATGTAGTTTAATTACGTGCTGG
CAGCAGCTGTCATCAATTCGTGAAATTGGTGATCATTTACGAGAGCAATATGAACAAGCC
ACTCAAGTAAAAATGAATAAGAGAGGCCGATTGCAGGTCAAAGATTCACGATATAAAGTC
CCTACCGCTCTTGATTTAGTGTATCTCGATGAAAGTCCTGACTGGTGCCGTGCTAATAAG
CAACTTCAATGGGCAGGTACACATGGTCGTAAATGTAATCGCACGTCAACAGGATTAGAC
AGCTGTTCAATCCTTTGTTGTGGACGTGGCTATAATACAAAGAAGATTGTTCTCTATGAG
CGATGCAATTGCAAATTTCAATGGTGTTGTAATGTGAGATGTGAAACATGTAAACGAGTT
ATTCAGGAATACACTTGTAAATAG
>g10660.t1 Gene=g10660 Length=907
MSHNKLLWITLCSIVWFIQSIHGLQGVPTWMCLGIKSPFIEFTAEFEMLSNMTVSLNLTD
KSPDSRHRKNGLHNLGNFINPIGTANRDDKTMGFKGINNTTFSIQSDLLETKDSRKHQEQ
HLYELQQQQIQELQQHNLNKSATNKILMDIIKPIVTDSHKSDEDNKSSTVSGTSSEGIDH
PTIQIIANANNHYEQMNSYMDDSRKVIMPLALKTTLIERDRPVPSPTPLPKPQTNIEDLK
KHLLMLQNYSEVDKSFQSKFVVFKKQTSTAAPTTTSTTTPSTPFPTKAPQTTTTMPFPMT
VGTMYRTKPSINIPNVQNSQILRDVSYPYTRIERVTVVPQVFLQNDQQQPETEEERQQHT
NAERRKNRKNEKKAKRDKKKNRNGKQAASNVIPTTIVLPTAIPLRPIRREQQRQRQMRSQ
NGSQMFISTTTVSSAPYIINLSDSKPLVDSNSQKLSRTIRSKGNRRRNQNKMQRDALIID
SSNGVVAIKNETSEKIDINPKHCYDVSGMSKGQQKLCEQFTSIMPAISRGARAAIQECQH
QFQHRRWNCSTVDDDSVFGPVSAIGSPEMAFVYAMASAAVTSFIARACRDGQLASCGCSR
SARPKQLHEDWTWGGCGDDLEFGYKFSQNFIDIREKERKRGARGLISKIPEHLGNDTAAD
NTTITSTTTMSPEEQIKADEMLKLQQKITQEILNSNLKEKEMNELQEKINKEILNSKIFN
VNADENIGRKKNRFKTASAKARALMNLHNNEAGRRAILKKHKVHCTCHGISGSCSLITCW
QQLSSIREIGDHLREQYEQATQVKMNKRGRLQVKDSRYKVPTALDLVYLDESPDWCRANK
QLQWAGTHGRKCNRTSTGLDSCSILCCGRGYNTKKIVLYERCNCKFQWCCNVRCETCKRV
IQEYTCK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 20 | g10660.t1 | CDD | cd19337 | Wnt_Wnt5 | 503 | 907 | 2.86769E-170 |
| 14 | g10660.t1 | Coils | Coil | Coil | 116 | 136 | - |
| 12 | g10660.t1 | Coils | Coil | Coil | 352 | 382 | - |
| 13 | g10660.t1 | Coils | Coil | Coil | 695 | 715 | - |
| 11 | g10660.t1 | Gene3D | G3DSA:3.30.2460.20 | - | 847 | 907 | 1.5E-14 |
| 22 | g10660.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 158 | 179 | - |
| 27 | g10660.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 267 | 287 | - |
| 26 | g10660.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 346 | 423 | - |
| 24 | g10660.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 349 | 367 | - |
| 23 | g10660.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 368 | 382 | - |
| 25 | g10660.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 452 | 471 | - |
| 3 | g10660.t1 | PANTHER | PTHR12027 | WNT RELATED | 483 | 907 | 3.8E-150 |
| 4 | g10660.t1 | PANTHER | PTHR12027:SF77 | PROTEIN WNT-5 | 483 | 907 | 3.8E-150 |
| 9 | g10660.t1 | PRINTS | PR01349 | Wnt protein signature | 567 | 581 | 2.9E-24 |
| 8 | g10660.t1 | PRINTS | PR01349 | Wnt protein signature | 586 | 599 | 2.9E-24 |
| 5 | g10660.t1 | PRINTS | PR01349 | Wnt protein signature | 611 | 623 | 2.9E-24 |
| 7 | g10660.t1 | PRINTS | PR01349 | Wnt protein signature | 766 | 780 | 2.9E-24 |
| 6 | g10660.t1 | PRINTS | PR01349 | Wnt protein signature | 825 | 836 | 2.9E-24 |
| 1 | g10660.t1 | Pfam | PF00110 | wnt family | 506 | 660 | 5.8E-44 |
| 2 | g10660.t1 | Pfam | PF00110 | wnt family | 732 | 907 | 5.6E-64 |
| 16 | g10660.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 26 | - |
| 17 | g10660.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 5 | - |
| 18 | g10660.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 6 | 18 | - |
| 19 | g10660.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 19 | 26 | - |
| 15 | g10660.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 27 | 907 | - |
| 21 | g10660.t1 | SMART | SM00097 | wnt1_3 | 505 | 907 | 1.3E-146 |
| 10 | g10660.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 23 | - |
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 transcript has been annotated with K00444 (wingless-type MMTV integration site family, member 5)
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.
