General information for g3827.t1
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.t1 | TTS | g3827.t1 | 28222850 | 28222850 |
| chr_3 | g3827 | g3827.t1 | isoform | g3827.t1 | 28223545 | 28225593 |
| chr_3 | g3827 | g3827.t1 | exon | g3827.t1.exon1 | 28223545 | 28223682 |
| chr_3 | g3827 | g3827.t1 | cds | g3827.t1.CDS1 | 28223545 | 28223682 |
| chr_3 | g3827 | g3827.t1 | exon | g3827.t1.exon2 | 28223742 | 28224677 |
| chr_3 | g3827 | g3827.t1 | cds | g3827.t1.CDS2 | 28223742 | 28224677 |
| chr_3 | g3827 | g3827.t1 | exon | g3827.t1.exon3 | 28224734 | 28225059 |
| chr_3 | g3827 | g3827.t1 | cds | g3827.t1.CDS3 | 28224734 | 28225059 |
| chr_3 | g3827 | g3827.t1 | exon | g3827.t1.exon4 | 28225503 | 28225593 |
| chr_3 | g3827 | g3827.t1 | cds | g3827.t1.CDS4 | 28225503 | 28225593 |
| chr_3 | g3827 | g3827.t1 | TSS | g3827.t1 | 28225632 | 28225632 |
Sequences
>g3827.t1 Gene=g3827 Length=1491
ATGTCGTACTCTTCTGGTTTAAGTGCAAGACAAGCTGCAAAGGAACATGTCCTTGCTGTT
TCTCGTGATTTCATCTCTCAGCCACGATTAACTTATAAGACAGTATCGGGTGTGAATGGT
CCATTAGTTATTCTCGATGAAGTGAAATTTCCAAAATTCGCCGAAATCGTTCAATTGAGA
TTGAATGATGGCACAATTCGATCGGGTCAAGTTCTGGAAGTTAGTGGTTCAAAGGCTGTC
GTTCAAGTGTTCGAGGGTACTTCGGGTATTGATGCAAAGAACACTGTTTGCGAGTTTACA
GGAGATATTTTAAGAACACCTGTATCAGAAGATATGTTAGGTCGTGTATTTAACGGTTCA
GGCAAACCAATTGATAAAGGTCCACCAATTTTGGCTGAAGATTATCTTGATATTCAAGGA
CAACCAATTAATCCATGGTCACGTATTTATCCAGAAGAAATGATTCAGACTGGTATCTCT
GCCATCGATGTTATGAACTCAATTGCTCGTGGTCAGAAAATTCCAATTTTCTCAGCTGCT
GGTTTGCCTCACAACGAAATTGCTGCACAAATTTGTAGACAAGCTGGTCTTGTAAAGATT
CCAGGAAAATCAGTTTTGGATGATCATGAAGACAACTTTGCCATTGTTTTCGCAGCTATG
GGTGTGAACATGGAAACTGCTCGTTTCTTCAAACAAGATTTCGAAGAGAACGGTTCAATG
GAAAATGTGTGCTTGTTCTTGAACTTGGCTAACGATCCAACTATTGAAAGAATTATTACA
CCACGTTTAGCATTGACAGCTGCCGAATTCATGGCCTACCAATGTGAGAAGCACGTGTTG
GTCATCTTAACTGACATGTCATCATATGCTGAAGCTTTGCGTGAAGTCTCAGCTGCTCGT
GAAGAAGTACCTGGTCGTCGTGGTTTTCCAGGTTATATGTACACTGATTTGGCTACAATC
TATGAGCGTGCTGGTCGTGTTGAAGGTCGCAATGGATCAATCACACAAATTCCAATTCTT
ACTATGCCCAACGACGATATTACCCATCCAATTCCCGATTTGACAGGATACATTACTGAG
GGACAAATCTACGTCGATCGTCAACTTCACAACAGACAAATCTATCCACCAATTAACGTA
TTGCCATCATTGTCGCGTTTGATGAAGTCTGCTATTGGTGAAGGAATGACACGAAAGGAT
CATTCTGATGTTTCAAATCAATTGTATGCATGTTATGCTATTGGTAAAGATGTGCAAGCA
ATGAAGGCTGTCGTTGGTGAAGAGGCTTTGACACCTGATGACTTGTTATATTTGGAATTC
TTAGGCAAATTCGAAAAGAACTTTATTGCACAAGGAAACTACGAAAATCGTACAGTTTTT
GAATCTTTGGATATTGGCTGGCAATTGCTTCGAATCTTCCCTAAAGAAATGTTGAAACGT
ATTCCAGCTTCCATTTTAGCTGAATTCTATCCAAGAGACTCACGTCACTAA
>g3827.t1 Gene=g3827 Length=496
MSYSSGLSARQAAKEHVLAVSRDFISQPRLTYKTVSGVNGPLVILDEVKFPKFAEIVQLR
LNDGTIRSGQVLEVSGSKAVVQVFEGTSGIDAKNTVCEFTGDILRTPVSEDMLGRVFNGS
GKPIDKGPPILAEDYLDIQGQPINPWSRIYPEEMIQTGISAIDVMNSIARGQKIPIFSAA
GLPHNEIAAQICRQAGLVKIPGKSVLDDHEDNFAIVFAAMGVNMETARFFKQDFEENGSM
ENVCLFLNLANDPTIERIITPRLALTAAEFMAYQCEKHVLVILTDMSSYAEALREVSAAR
EEVPGRRGFPGYMYTDLATIYERAGRVEGRNGSITQIPILTMPNDDITHPIPDLTGYITE
GQIYVDRQLHNRQIYPPINVLPSLSRLMKSAIGEGMTRKDHSDVSNQLYACYAIGKDVQA
MKAVVGEEALTPDDLLYLEFLGKFEKNFIAQGNYENRTVFESLDIGWQLLRIFPKEMLKR
IPASILAEFYPRDSRH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g3827.t1 | CDD | cd18118 | ATP-synt_V_A-type_beta_N | 31 | 102 | 5.45835E-39 |
| 10 | g3827.t1 | CDD | cd01135 | V_A-ATPase_B | 103 | 387 | 0.0 |
| 9 | g3827.t1 | CDD | cd18112 | ATP-synt_V_A-type_beta_C | 395 | 489 | 7.98182E-62 |
| 7 | g3827.t1 | Gene3D | G3DSA:3.40.50.12240 | - | 25 | 494 | 2.1E-201 |
| 5 | g3827.t1 | Hamap | MF_00310 | V-type ATP synthase beta chain [atpB]. | 29 | 494 | 54.659206 |
| 3 | g3827.t1 | PANTHER | PTHR43389:SF5 | V-TYPE PROTON ATPASE SUBUNIT B, BRAIN ISOFORM | 10 | 494 | 0.0 |
| 4 | g3827.t1 | PANTHER | PTHR43389 | V-TYPE PROTON ATPASE SUBUNIT B | 10 | 494 | 0.0 |
| 8 | g3827.t1 | PIRSF | PIRSF039114 | V-ATPsynth_beta/V-ATPase_B | 22 | 496 | 2.4E-240 |
| 1 | g3827.t1 | Pfam | PF02874 | ATP synthase alpha/beta family, beta-barrel domain | 35 | 101 | 1.3E-12 |
| 2 | g3827.t1 | Pfam | PF00006 | ATP synthase alpha/beta family, nucleotide-binding domain | 158 | 385 | 3.5E-64 |
| 12 | g3827.t1 | ProSitePatterns | PS00152 | ATP synthase alpha and beta subunits signature. | 376 | 385 | - |
| 6 | g3827.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 105 | 391 | 1.12E-84 |
| 13 | g3827.t1 | TIGRFAM | TIGR01040 | V-ATPase_V1_B: V-type ATPase, B subunit | 31 | 495 | 1.2E-300 |
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:0046034 | ATP metabolic process | BP |
| GO:1902600 | proton transmembrane transport | BP |
| GO:0005524 | ATP binding | MF |
| GO:0033180 | proton-transporting V-type ATPase, V1 domain | CC |
KEGG
Orthology
- This transcript has been annotated with K02147 (V-type H+-transporting ATPase subunit B)
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.
