General information for g3827.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as V-type proton ATPase subunit B.
Parent gene
- The parent gene g3827 is located on chr_3: 28224173..28225593 (- 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 | g3827 | g3827.t6 | TTS | g3827.t6 | 28223455 | 28223455 |
| chr_3 | g3827 | g3827.t6 | isoform | g3827.t6 | 28224173 | 28225058 |
| chr_3 | g3827 | g3827.t6 | exon | g3827.t6.exon1 | 28224173 | 28224677 |
| chr_3 | g3827 | g3827.t6 | cds | g3827.t6.CDS1 | 28224174 | 28224677 |
| chr_3 | g3827 | g3827.t6 | exon | g3827.t6.exon2 | 28224734 | 28225058 |
| chr_3 | g3827 | g3827.t6 | cds | g3827.t6.CDS2 | 28224734 | 28224817 |
| chr_3 | g3827 | g3827.t6 | TSS | g3827.t6 | 28225632 | 28225632 |
Sequences
>g3827.t6 Gene=g3827 Length=830
TTATAAGACAGTATCGGGTGTGAATGGTCCATTAGTTATTCTCGATGAAGTGAAATTTCC
AAAATTCGCCGAAATCGTTCAATTGAGATTGAATGATGGCACAATTCGATCGGGTCAAGT
TCTGGAAGTTAGTGGTTCAAAGGCTGTCGTTCAAGTGTTCGAGGGTACTTCGGGTATTGA
TGCAAAGAACACTGTTTGCGAGTTTACAGGAGATATTTTAAGAACACCTGTATCAGAAGA
TATGTTAGGTCGTGTATTTAACGGTTCAGGCAAACCAATTGATAAAGGTCCACCAATTTT
GGCTGAAGATTATCTTGATATTCAAGGACAACCAATTAATCCATGGTCACGTATTTATCC
AGAAGAAATGATTCAGACTGGTATCTCTGCCATCGATGTTATGAACTCAATTGCTCGTGG
TCAGAAAATTCCAATTTTCTCAGCTGCTGGTTTGCCTCACAACGAAATTGCTGCACAAAT
TTGTAGACAAGCTGGTCTTGTAAAGATTCCAGGAAAATCAGTTTTGGATGATCATGAAGA
CAACTTTGCCATTGTTTTCGCAGCTATGGGTGTGAACATGGAAACTGCTCGTTTCTTCAA
ACAAGATTTCGAAGAGAACGGTTCAATGGAAAATGTGTGCTTGTTCTTGAACTTGGCTAA
CGATCCAACTATTGAAAGAATTATTACACCACGTTTAGCATTGACAGCTGCCGAATTCAT
GGCCTACCAATGTGAGAAGCACGTGTTGGTCATCTTAACTGACATGTCATCATATGCTGA
AGCTTTGCGTGAAGTCTCAGCTGCTCGTGAAGAAGTACCTGGTCGTCGTG
>g3827.t6 Gene=g3827 Length=196
MLGRVFNGSGKPIDKGPPILAEDYLDIQGQPINPWSRIYPEEMIQTGISAIDVMNSIARG
QKIPIFSAAGLPHNEIAAQICRQAGLVKIPGKSVLDDHEDNFAIVFAAMGVNMETARFFK
QDFEENGSMENVCLFLNLANDPTIERIITPRLALTAAEFMAYQCEKHVLVILTDMSSYAE
ALREVSAAREEVPGRR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g3827.t6 | CDD | cd01135 | V_A-ATPase_B | 1 | 196 | 0 |
| 5 | g3827.t6 | Gene3D | G3DSA:3.40.50.12240 | - | 1 | 196 | 0 |
| 2 | g3827.t6 | PANTHER | PTHR43389 | V-TYPE PROTON ATPASE SUBUNIT B | 1 | 196 | 0 |
| 3 | g3827.t6 | PANTHER | PTHR43389:SF2 | VACUOLAR PROTON PUMP SUBUNIT B | 1 | 196 | 0 |
| 1 | g3827.t6 | Pfam | PF00006 | ATP synthase alpha/beta family, nucleotide-binding domain | 47 | 195 | 0 |
| 4 | g3827.t6 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 1 | 196 | 0 |
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:0005524 | ATP 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.
