General information for g2963.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Protein salvador homolog 1.
Parent gene
- The parent gene g2963 is located on chr_3: 21606424..21606880 (+ 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_3 | g2963 | g2963.t1 | TSS | g2963.t1 | 21604744 | 21604744 |
| chr_3 | g2963 | g2963.t1 | isoform | g2963.t1 | 21604825 | 21606424 |
| chr_3 | g2963 | g2963.t1 | exon | g2963.t1.exon1 | 21604825 | 21604882 |
| chr_3 | g2963 | g2963.t1 | cds | g2963.t1.CDS1 | 21604825 | 21604882 |
| chr_3 | g2963 | g2963.t1 | exon | g2963.t1.exon2 | 21604960 | 21604986 |
| chr_3 | g2963 | g2963.t1 | cds | g2963.t1.CDS2 | 21604960 | 21604986 |
| chr_3 | g2963 | g2963.t1 | exon | g2963.t1.exon3 | 21605043 | 21605675 |
| chr_3 | g2963 | g2963.t1 | cds | g2963.t1.CDS3 | 21605043 | 21605675 |
| chr_3 | g2963 | g2963.t1 | exon | g2963.t1.exon4 | 21605740 | 21605793 |
| chr_3 | g2963 | g2963.t1 | cds | g2963.t1.CDS4 | 21605740 | 21605793 |
| chr_3 | g2963 | g2963.t1 | exon | g2963.t1.exon5 | 21605857 | 21605944 |
| chr_3 | g2963 | g2963.t1 | cds | g2963.t1.CDS5 | 21605857 | 21605944 |
| chr_3 | g2963 | g2963.t1 | exon | g2963.t1.exon6 | 21606006 | 21606305 |
| chr_3 | g2963 | g2963.t1 | cds | g2963.t1.CDS6 | 21606006 | 21606305 |
| chr_3 | g2963 | g2963.t1 | exon | g2963.t1.exon7 | 21606361 | 21606424 |
| chr_3 | g2963 | g2963.t1 | cds | g2963.t1.CDS7 | 21606361 | 21606424 |
| chr_3 | g2963 | g2963.t1 | TTS | g2963.t1 | 21606529 | 21606529 |
Sequences
>g2963.t1 Gene=g2963 Length=1224
ATGCTTTCTAGGAAAAAGGACAAATCCTCCAAAACTGGTTTAGCAGGAAAATACATAAAA
AAAGAATTGACTCCAGGAATTAAACTCATAAATGTATGGACAACAAATACTGATCAAAAA
AATACAAAATCTAAAACTCGACAGAGCGAAGAAAAATCAAAATTAAGTATCAACAATGGT
TCAACGAGCAGTAGTAGTAATATTGGTCAAGGAAAATTTTTACAAAACTCATCGCTTGCC
TTAAACATGCTCGCGAGTCAAAAATATCATATGCAGCCAAGTAGTAGTTCATCAATAAAT
TCTGAACCATCTTATTTTCATCGAACTCTTGCACATCATCATCATCCAATCAGCAATAAT
AACAGTGCACTCGCGAGTGATAGTCAAAATAATTATGTAGAAATAGATACTCTAGAAACG
TTTTTATCTGAACAACAGAATGAGCAGCAACAGCAATATTCAAATGCTCCGTATGAAATC
AATAATTACAAAGACAATAATCAACAAGTTTCAATCGACATGGCATTATCCTCTCCAATT
TATGAAAATCAAGCAGTAGTTCGACGATCTGAATCGCCTATTTATACAAATACAAATCAT
CAAAACTCATTATATTCGACATCACAAAACTTGTACTCAAATCTACCACCGAGCAATTCA
AATACATCAGCTTATGCAAATTTGCCTTCCAGTATCAGTTTAAATTTAGTTCCAGCAATT
CGTAGCACGCCACAATTTAATGTGAACGTTGAAGAATTGCCATTACCTCCGGGCTGGTCA
GTCGATTATACATTAAAAGGAAGAAGAAAATATTATATTGACCACAATACTGCAACTACA
CATTGGTCTCATCCACTAGACTATATAACGAGACAAGTGCAATTGCACAATCCCTATTTC
GCATATTATTTGCCAGGCTATCATCAATATCAAGCACAACCGACTCTCATTCATCATCAA
GCATTAGTTCCTGCTAATCCATTACTTCACGTTGAAGTGCCTCACTGGCTAAAAGTATAT
TGTGCTTCCTCACATGAAAAAGATCACATAATTAAATGGAATATGTTCCAAGTTAATCAA
CTTATGACTATTAATGAAATGATTACAAAGCTTTTCAAAGAAGAGCTACATAATATTGTA
TTGAAATTTGAGTCAATGAGAATTGCTATAAGCTTTGAAATGGAGAAGCGCAAGCAGCAA
CAAGGACCGCATTATAACAATTAA
>g2963.t1 Gene=g2963 Length=407
MLSRKKDKSSKTGLAGKYIKKELTPGIKLINVWTTNTDQKNTKSKTRQSEEKSKLSINNG
STSSSSNIGQGKFLQNSSLALNMLASQKYHMQPSSSSSINSEPSYFHRTLAHHHHPISNN
NSALASDSQNNYVEIDTLETFLSEQQNEQQQQYSNAPYEINNYKDNNQQVSIDMALSSPI
YENQAVVRRSESPIYTNTNHQNSLYSTSQNLYSNLPPSNSNTSAYANLPSSISLNLVPAI
RSTPQFNVNVEELPLPPGWSVDYTLKGRRKYYIDHNTATTHWSHPLDYITRQVQLHNPYF
AYYLPGYHQYQAQPTLIHHQALVPANPLLHVEVPHWLKVYCASSHEKDHIIKWNMFQVNQ
LMTINEMITKLFKEELHNIVLKFESMRIAISFEMEKRKQQQGPHYNN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g2963.t1 | CDD | cd00201 | WW | 256 | 287 | 6.49597E-7 |
| 5 | g2963.t1 | Gene3D | G3DSA:2.20.70.10 | - | 248 | 295 | 8.1E-13 |
| 9 | g2963.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 38 | 70 | - |
| 8 | g2963.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 53 | 70 | - |
| 3 | g2963.t1 | PANTHER | PTHR47522 | SALVADOR FAMILY WW DOMAIN-CONTAINING PROTEIN 1 | 1 | 287 | 5.5E-49 |
| 2 | g2963.t1 | PANTHER | PTHR47522 | SALVADOR FAMILY WW DOMAIN-CONTAINING PROTEIN 1 | 307 | 404 | 5.5E-49 |
| 1 | g2963.t1 | Pfam | PF00397 | WW domain | 255 | 285 | 1.1E-6 |
| 11 | g2963.t1 | ProSiteProfiles | PS50020 | WW/rsp5/WWP domain profile. | 253 | 287 | 15.092 |
| 10 | g2963.t1 | ProSiteProfiles | PS50951 | SARAH domain profile. | 350 | 397 | 10.514 |
| 7 | g2963.t1 | SMART | SM00456 | ww_5 | 254 | 287 | 4.7E-5 |
| 4 | g2963.t1 | SUPERFAMILY | SSF51045 | WW domain | 249 | 285 | 2.05E-9 |
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:0060090 | molecular adaptor activity | MF |
| GO:0035329 | hippo signaling | BP |
| GO:0007165 | signal transduction | BP |
| GO:0005515 | protein binding | MF |
| GO:0042127 | regulation of cell population proliferation | BP |
| GO:0006915 | apoptotic process | BP |
KEGG
Orthology
- This transcript has been annotated with K16686 (scaffold protein salvador)
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.
