General information for g3827.t4
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.t4 | TTS | g3827.t4 | 28222850 | 28222850 |
| chr_3 | g3827 | g3827.t4 | isoform | g3827.t4 | 28223545 | 28225049 |
| chr_3 | g3827 | g3827.t4 | exon | g3827.t4.exon1 | 28223545 | 28223682 |
| chr_3 | g3827 | g3827.t4 | cds | g3827.t4.CDS1 | 28223545 | 28223682 |
| chr_3 | g3827 | g3827.t4 | exon | g3827.t4.exon2 | 28223742 | 28224677 |
| chr_3 | g3827 | g3827.t4 | cds | g3827.t4.CDS2 | 28223742 | 28224677 |
| chr_3 | g3827 | g3827.t4 | exon | g3827.t4.exon3 | 28224734 | 28225049 |
| chr_3 | g3827 | g3827.t4 | cds | g3827.t4.CDS3 | 28224734 | 28224817 |
| chr_3 | g3827 | g3827.t4 | TSS | g3827.t4 | 28225632 | 28225632 |
Sequences
>g3827.t4 Gene=g3827 Length=1390
AGTATCGGGTGTGAATGGTCCATTAGTTATTCTCGATGAAGTGAAATTTCCAAAATTCGC
CGAAATCGTTCAATTGAGATTGAATGATGGCACAATTCGATCGGGTCAAGTTCTGGAAGT
TAGTGGTTCAAAGGCTGTCGTTCAAGTGTTCGAGGGTACTTCGGGTATTGATGCAAAGAA
CACTGTTTGCGAGTTTACAGGAGATATTTTAAGAACACCTGTATCAGAAGATATGTTAGG
TCGTGTATTTAACGGTTCAGGCAAACCAATTGATAAAGGTCCACCAATTTTGGCTGAAGA
TTATCTTGATATTCAAGGACAACCAATTAATCCATGGTCACGTATTTATCCAGAAGAAAT
GATTCAGACTGGTATCTCTGCCATCGATGTTATGAACTCAATTGCTCGTGGTCAGAAAAT
TCCAATTTTCTCAGCTGCTGGTTTGCCTCACAACGAAATTGCTGCACAAATTTGTAGACA
AGCTGGTCTTGTAAAGATTCCAGGAAAATCAGTTTTGGATGATCATGAAGACAACTTTGC
CATTGTTTTCGCAGCTATGGGTGTGAACATGGAAACTGCTCGTTTCTTCAAACAAGATTT
CGAAGAGAACGGTTCAATGGAAAATGTGTGCTTGTTCTTGAACTTGGCTAACGATCCAAC
TATTGAAAGAATTATTACACCACGTTTAGCATTGACAGCTGCCGAATTCATGGCCTACCA
ATGTGAGAAGCACGTGTTGGTCATCTTAACTGACATGTCATCATATGCTGAAGCTTTGCG
TGAAGTCTCAGCTGCTCGTGAAGAAGTACCTGGTCGTCGTGGTTTTCCAGGTTATATGTA
CACTGATTTGGCTACAATCTATGAGCGTGCTGGTCGTGTTGAAGGTCGCAATGGATCAAT
CACACAAATTCCAATTCTTACTATGCCCAACGACGATATTACCCATCCAATTCCCGATTT
GACAGGATACATTACTGAGGGACAAATCTACGTCGATCGTCAACTTCACAACAGACAAAT
CTATCCACCAATTAACGTATTGCCATCATTGTCGCGTTTGATGAAGTCTGCTATTGGTGA
AGGAATGACACGAAAGGATCATTCTGATGTTTCAAATCAATTGTATGCATGTTATGCTAT
TGGTAAAGATGTGCAAGCAATGAAGGCTGTCGTTGGTGAAGAGGCTTTGACACCTGATGA
CTTGTTATATTTGGAATTCTTAGGCAAATTCGAAAAGAACTTTATTGCACAAGGAAACTA
CGAAAATCGTACAGTTTTTGAATCTTTGGATATTGGCTGGCAATTGCTTCGAATCTTCCC
TAAAGAAATGTTGAAACGTATTCCAGCTTCCATTTTAGCTGAATTCTATCCAAGAGACTC
ACGTCACTAA
>g3827.t4 Gene=g3827 Length=385
MLGRVFNGSGKPIDKGPPILAEDYLDIQGQPINPWSRIYPEEMIQTGISAIDVMNSIARG
QKIPIFSAAGLPHNEIAAQICRQAGLVKIPGKSVLDDHEDNFAIVFAAMGVNMETARFFK
QDFEENGSMENVCLFLNLANDPTIERIITPRLALTAAEFMAYQCEKHVLVILTDMSSYAE
ALREVSAAREEVPGRRGFPGYMYTDLATIYERAGRVEGRNGSITQIPILTMPNDDITHPI
PDLTGYITEGQIYVDRQLHNRQIYPPINVLPSLSRLMKSAIGEGMTRKDHSDVSNQLYAC
YAIGKDVQAMKAVVGEEALTPDDLLYLEFLGKFEKNFIAQGNYENRTVFESLDIGWQLLR
IFPKEMLKRIPASILAEFYPRDSRH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g3827.t4 | CDD | cd01135 | V_A-ATPase_B | 1 | 276 | 0.0 |
| 8 | g3827.t4 | CDD | cd18112 | ATP-synt_V_A-type_beta_C | 284 | 378 | 8.58283E-63 |
| 6 | g3827.t4 | Gene3D | G3DSA:3.40.50.12240 | - | 1 | 385 | 6.4E-173 |
| 2 | g3827.t4 | PANTHER | PTHR43389:SF5 | V-TYPE PROTON ATPASE SUBUNIT B, BRAIN ISOFORM | 1 | 383 | 1.7E-241 |
| 3 | g3827.t4 | PANTHER | PTHR43389 | V-TYPE PROTON ATPASE SUBUNIT B | 1 | 383 | 1.7E-241 |
| 1 | g3827.t4 | Pfam | PF00006 | ATP synthase alpha/beta family, nucleotide-binding domain | 47 | 274 | 1.8E-64 |
| 5 | g3827.t4 | ProSitePatterns | PS00152 | ATP synthase alpha and beta subunits signature. | 265 | 274 | - |
| 4 | g3827.t4 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 1 | 280 | 1.01E-82 |
| 7 | g3827.t4 | TIGRFAM | TIGR01040 | V-ATPase_V1_B: V-type ATPase, B subunit | 1 | 384 | 2.9E-254 |
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:1902600 | proton transmembrane transport | BP |
| GO:0005524 | ATP binding | MF |
| GO:0033180 | proton-transporting V-type ATPase, V1 domain | CC |
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.
