Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Protein salvador homolog 1.

Parent gene

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.t4 TSS g2963.t4 21604744 21604744
chr_3 g2963 g2963.t4 isoform g2963.t4 21604825 21606424
chr_3 g2963 g2963.t4 exon g2963.t4.exon1 21604825 21604882
chr_3 g2963 g2963.t4 exon g2963.t4.exon2 21605027 21605675
chr_3 g2963 g2963.t4 cds g2963.t4.CDS1 21605204 21605675
chr_3 g2963 g2963.t4 exon g2963.t4.exon3 21605740 21605793
chr_3 g2963 g2963.t4 cds g2963.t4.CDS2 21605740 21605793
chr_3 g2963 g2963.t4 exon g2963.t4.exon4 21605857 21605944
chr_3 g2963 g2963.t4 cds g2963.t4.CDS3 21605857 21605944
chr_3 g2963 g2963.t4 exon g2963.t4.exon5 21606006 21606305
chr_3 g2963 g2963.t4 cds g2963.t4.CDS4 21606006 21606305
chr_3 g2963 g2963.t4 exon g2963.t4.exon6 21606361 21606424
chr_3 g2963 g2963.t4 cds g2963.t4.CDS5 21606361 21606424
chr_3 g2963 g2963.t4 TTS g2963.t4 21606529 21606529

Sequences

>g2963.t4 Gene=g2963 Length=1213
ATGCTTTCTAGGAAAAAGGACAAATCCTCCAAAACTGGTTTAGCAGGAAAATACATAAAT
AAAGTCACTTTTAGTCATAAATGTATGGACAACAAATACTGATCAAAAAAATACAAAATC
TAAAACTCGACAGAGCGAAGAAAAATCAAAATTAAGTATCAACAATGGTTCAACGAGCAG
TAGTAGTAATATTGGTCAAGGAAAATTTTTACAAAACTCATCGCTTGCCTTAAACATGCT
CGCGAGTCAAAAATATCATATGCAGCCAAGTAGTAGTTCATCAATAAATTCTGAACCATC
TTATTTTCATCGAACTCTTGCACATCATCATCATCCAATCAGCAATAATAACAGTGCACT
CGCGAGTGATAGTCAAAATAATTATGTAGAAATAGATACTCTAGAAACGTTTTTATCTGA
ACAACAGAATGAGCAGCAACAGCAATATTCAAATGCTCCGTATGAAATCAATAATTACAA
AGACAATAATCAACAAGTTTCAATCGACATGGCATTATCCTCTCCAATTTATGAAAATCA
AGCAGTAGTTCGACGATCTGAATCGCCTATTTATACAAATACAAATCATCAAAACTCATT
ATATTCGACATCACAAAACTTGTACTCAAATCTACCACCGAGCAATTCAAATACATCAGC
TTATGCAAATTTGCCTTCCAGTATCAGTTTAAATTTAGTTCCAGCAATTCGTAGCACGCC
ACAATTTAATGTGAACGTTGAAGAATTGCCATTACCTCCGGGCTGGTCAGTCGATTATAC
ATTAAAAGGAAGAAGAAAATATTATATTGACCACAATACTGCAACTACACATTGGTCTCA
TCCACTAGACTATATAACGAGACAAGTGCAATTGCACAATCCCTATTTCGCATATTATTT
GCCAGGCTATCATCAATATCAAGCACAACCGACTCTCATTCATCATCAAGCATTAGTTCC
TGCTAATCCATTACTTCACGTTGAAGTGCCTCACTGGCTAAAAGTATATTGTGCTTCCTC
ACATGAAAAAGATCACATAATTAAATGGAATATGTTCCAAGTTAATCAACTTATGACTAT
TAATGAAATGATTACAAAGCTTTTCAAAGAAGAGCTACATAATATTGTATTGAAATTTGA
GTCAATGAGAATTGCTATAAGCTTTGAAATGGAGAAGCGCAAGCAGCAACAAGGACCGCA
TTATAACAATTAA

>g2963.t4 Gene=g2963 Length=325
MLASQKYHMQPSSSSSINSEPSYFHRTLAHHHHPISNNNSALASDSQNNYVEIDTLETFL
SEQQNEQQQQYSNAPYEINNYKDNNQQVSIDMALSSPIYENQAVVRRSESPIYTNTNHQN
SLYSTSQNLYSNLPPSNSNTSAYANLPSSISLNLVPAIRSTPQFNVNVEELPLPPGWSVD
YTLKGRRKYYIDHNTATTHWSHPLDYITRQVQLHNPYFAYYLPGYHQYQAQPTLIHHQAL
VPANPLLHVEVPHWLKVYCASSHEKDHIIKWNMFQVNQLMTINEMITKLFKEELHNIVLK
FESMRIAISFEMEKRKQQQGPHYNN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g2963.t4 CDD cd00201 WW 174 205 0.0000008
6 g2963.t4 Gene3D G3DSA:2.20.70.10 - 166 216 0.0000000
3 g2963.t4 PANTHER PTHR47522 SALVADOR FAMILY WW DOMAIN-CONTAINING PROTEIN 1 13 205 0.0000000
2 g2963.t4 PANTHER PTHR47522 SALVADOR FAMILY WW DOMAIN-CONTAINING PROTEIN 1 224 322 0.0000000
1 g2963.t4 Pfam PF00397 WW domain 173 203 0.0000008
8 g2963.t4 ProSiteProfiles PS50020 WW/rsp5/WWP domain profile. 171 205 15.0920000
7 g2963.t4 ProSiteProfiles PS50951 SARAH domain profile. 268 315 10.5140000
5 g2963.t4 SMART SM00456 ww_5 172 205 0.0000470
4 g2963.t4 SUPERFAMILY SSF51045 WW domain 167 203 0.0000000

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

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.

Raw TPM values