General information for g3378.t9
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Protein phosphatase 1 regulatory subunit 3C.
Parent gene
- The parent gene g3378 is located on chr_3: 24971572..24977000 (- 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 | g3378 | g3378.t9 | TTS | g3378.t9 | 24969849 | 24969849 |
| chr_3 | g3378 | g3378.t9 | isoform | g3378.t9 | 24970871 | 24977000 |
| chr_3 | g3378 | g3378.t9 | exon | g3378.t9.exon1 | 24970871 | 24971079 |
| chr_3 | g3378 | g3378.t9 | cds | g3378.t9.CDS1 | 24970873 | 24971079 |
| chr_3 | g3378 | g3378.t9 | exon | g3378.t9.exon2 | 24971152 | 24971461 |
| chr_3 | g3378 | g3378.t9 | cds | g3378.t9.CDS2 | 24971152 | 24971461 |
| chr_3 | g3378 | g3378.t9 | exon | g3378.t9.exon3 | 24971529 | 24972146 |
| chr_3 | g3378 | g3378.t9 | cds | g3378.t9.CDS3 | 24971529 | 24972079 |
| chr_3 | g3378 | g3378.t9 | exon | g3378.t9.exon4 | 24976483 | 24977000 |
| chr_3 | g3378 | g3378.t9 | TSS | g3378.t9 | NA | NA |
Sequences
>g3378.t9 Gene=g3378 Length=1655
TCTCGCGATTTGACTTGCTCAAATGCACGAATGAAACTTGAAAACCGATTGTAGAACACA
GTTCTCCATAGAGGACGACAATTTTTATAAACTTGATCAATCGTGAAGATGCTCTTCTAG
CAACGAGACGCGAAAAATATTTAATCAAGTTAATTTATACGTGAATCAAATTCTTTATAC
AAAAATTTATTTTTTTAAATTTTTAATAAAATAAAATTTATTAAAAATTTGTCGGGTCTC
TCTACAATAAAAAATCAACCAAAAAAAGTCTTCAAGTTTACTAAGAGTTAAAAGCTATCC
CGATTAAAAATTAAAATAAAAGTGCCAAATTCAAATTAAATGCAGCAATTAATTAAATTG
CTGTGAAATATAGTGCCTTTAAAATAATAAAAATTATTTTCATGAGAATATTCAATTAAT
TAAATAATATAAGTGCTTATAGAAAGCAGAAAAAGAAAAAAAGTTGTAAAATAAATCCTA
AACAAAAAGTCAAAAGTTTTTATTGTACACAACAAGTAATTTTTATAAACAGTCAAAATT
TCGCCCTCAAAAACGGATTACATAACGCCTTCGCGCTCTATCCCAATGCCAGCTTATTAC
GAGATGCTGGTATCACAAAGTCCTCCACTATTCAGTCATAGTCCTCCGACTGGATTTCTA
TCAGAGTATGGACCTAATCGATTCTATGAATCGCCACGCTTTTGTCGATCAGCCGCTGTC
CTCTCGCCACTTTCACAACGCCGTTTTGCGCAAAACAATCCACAAACTTCCTTATATCAA
TCACATTTACAAAGTCTAACGCCATATAAACCATGCATTGTACCTAAACCACGCCGTTCA
TGCCTTATTGTTCGAAACGAGCCAGATCACTTGAAAAACGATACAACTAGCGATAGCAGC
GAAGATAGTGATGATTGCGACAGACAAGTACGTAAGCCAAAAAAGCGTGTCGTATTTGCG
GATGACAAAGGGCTCGAATTAGAACAAGTTAAAATAATGTCGGAGGCATCAACTCAACCG
CCAACGTGGTCACTGCAATTTCTCGCACACGTTACTCAGGGAATGATTTCGCCTGTGCCA
CAAGAGCAGTGGACTATTGATTTTAGGCAGCCAGCGTCAGATTATCTAGAGTTTAGGCGC
AAATTAGAAAATAATTTCGTGTCATTGGAAAATGTCATAATAAAAGAATCCGAATCAACT
GTTGTAGGAACAGTGAAAGTGAAAAACTTAAGTTATCATAAAGAAGTCATAATCCGATCA
TCTTGGGATAACTGGAAATCTGAAACTGATACACTCTGCACATACTCGAAAATTGTGGGC
GCTAGTGGAGCATATGTAATTTATGACACATTTTCATTTAAACTAACACTTCCACCGCAT
TCGCGATCGTTGGAGTTTTGTGTATGCTATAGAACAGATGGAAAAGAATTCTGGGACAAC
AATGGAGGTGTCAATTACAAGCTTACAAACCGCGTTTCAGCTCAACAGCAAGAAAATGAG
CTTGTGATAAGACTTAATAATACATCACTCAATGATCAACGTAAAGATTCAAAAGAGAAT
CAATCGCCAACTGACTCTGATGTACCAAAACCACATTTCGGCTCATGGTCAGAATTTAGT
ACACGACACTCTGAGACACCACTACCTTATTGGTA
>g3378.t9 Gene=g3378 Length=356
MPAYYEMLVSQSPPLFSHSPPTGFLSEYGPNRFYESPRFCRSAAVLSPLSQRRFAQNNPQ
TSLYQSHLQSLTPYKPCIVPKPRRSCLIVRNEPDHLKNDTTSDSSEDSDDCDRQVRKPKK
RVVFADDKGLELEQVKIMSEASTQPPTWSLQFLAHVTQGMISPVPQEQWTIDFRQPASDY
LEFRRKLENNFVSLENVIIKESESTVVGTVKVKNLSYHKEVIIRSSWDNWKSETDTLCTY
SKIVGASGAYVIYDTFSFKLTLPPHSRSLEFCVCYRTDGKEFWDNNGGVNYKLTNRVSAQ
QQENELVIRLNNTSLNDQRKDSKENQSPTDSDVPKPHFGSWSEFSTRHSETPLPYW
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g3378.t9 | Gene3D | G3DSA:2.60.40.2440 | - | 168 | 295 | 3.8E-39 |
| 6 | g3378.t9 | MobiDBLite | mobidb-lite | consensus disorder prediction | 91 | 118 | - |
| 5 | g3378.t9 | MobiDBLite | mobidb-lite | consensus disorder prediction | 310 | 356 | - |
| 4 | g3378.t9 | MobiDBLite | mobidb-lite | consensus disorder prediction | 316 | 330 | - |
| 2 | g3378.t9 | PANTHER | PTHR12307:SF47 | PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT | 52 | 344 | 4.1E-75 |
| 3 | g3378.t9 | PANTHER | PTHR12307 | PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT | 52 | 344 | 4.1E-75 |
| 1 | g3378.t9 | Pfam | PF03370 | Carbohydrate/starch-binding module (family 21) | 187 | 293 | 2.6E-29 |
| 8 | g3378.t9 | ProSiteProfiles | PS51159 | CBM21 (carbohydrate binding type-21) domain profile. | 184 | 294 | 25.708 |
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:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K07189 (protein phosphatase 1 regulatory subunit 3A/B/C/D/E)
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