Gene loci information

Transcript annotation

  • This transcript has been annotated as V-type proton ATPase subunit B.

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 g3827 g3827.t5 TTS g3827.t5 28222850 28222850
chr_3 g3827 g3827.t5 isoform g3827.t5 28223545 28225593
chr_3 g3827 g3827.t5 exon g3827.t5.exon1 28223545 28224677
chr_3 g3827 g3827.t5 cds g3827.t5.CDS1 28223733 28224677
chr_3 g3827 g3827.t5 exon g3827.t5.exon2 28224734 28225059
chr_3 g3827 g3827.t5 cds g3827.t5.CDS2 28224734 28225059
chr_3 g3827 g3827.t5 exon g3827.t5.exon3 28225503 28225593
chr_3 g3827 g3827.t5 cds g3827.t5.CDS3 28225503 28225593
chr_3 g3827 g3827.t5 TSS g3827.t5 28225632 28225632

Sequences

>g3827.t5 Gene=g3827 Length=1550
ATGTCGTACTCTTCTGGTTTAAGTGCAAGACAAGCTGCAAAGGAACATGTCCTTGCTGTT
TCTCGTGATTTCATCTCTCAGCCACGATTAACTTATAAGACAGTATCGGGTGTGAATGGT
CCATTAGTTATTCTCGATGAAGTGAAATTTCCAAAATTCGCCGAAATCGTTCAATTGAGA
TTGAATGATGGCACAATTCGATCGGGTCAAGTTCTGGAAGTTAGTGGTTCAAAGGCTGTC
GTTCAAGTGTTCGAGGGTACTTCGGGTATTGATGCAAAGAACACTGTTTGCGAGTTTACA
GGAGATATTTTAAGAACACCTGTATCAGAAGATATGTTAGGTCGTGTATTTAACGGTTCA
GGCAAACCAATTGATAAAGGTCCACCAATTTTGGCTGAAGATTATCTTGATATTCAAGGA
CAACCAATTAATCCATGGTCACGTATTTATCCAGAAGAAATGATTCAGACTGGTATCTCT
GCCATCGATGTTATGAACTCAATTGCTCGTGGTCAGAAAATTCCAATTTTCTCAGCTGCT
GGTTTGCCTCACAACGAAATTGCTGCACAAATTTGTAGACAAGCTGGTCTTGTAAAGATT
CCAGGAAAATCAGTTTTGGATGATCATGAAGACAACTTTGCCATTGTTTTCGCAGCTATG
GGTGTGAACATGGAAACTGCTCGTTTCTTCAAACAAGATTTCGAAGAGAACGGTTCAATG
GAAAATGTGTGCTTGTTCTTGAACTTGGCTAACGATCCAACTATTGAAAGAATTATTACA
CCACGTTTAGCATTGACAGCTGCCGAATTCATGGCCTACCAATGTGAGAAGCACGTGTTG
GTCATCTTAACTGACATGTCATCATATGCTGAAGCTTTGCGTGAAGTCTCAGCTGCTCGT
GAAGAAGTACCTGGTCGTCGTGGTTTTCCAGGTTATATGTACACTGATTTGGCTACAATC
TATGAGCGTGCTGGTCGTGTTGAAGGTCGCAATGGATCAATCACACAAATTCCAATTCTT
ACTATGCCCAACGACGATATTACCCATCCAATTCCCGATTTGACAGGATACATTACTGAG
GGACAAATCTACGTCGATCGTCAACTTCACAACAGACAAATCTATCCACCAATTAACGTA
TTGCCATCATTGTCGCGTTTGATGAAGTCTGCTATTGGTGAAGGAATGACACGAAAGGAT
CATTCTGATGTTTCAAATCAATTGTATGCATGTTATGCTATTGGTAAAGATGTGCAAGCA
ATGAAGGCTGTCGTTGGTGAAGAGGCTTTGACACCTGATGACTTGTTATATTTGGAATTC
TTAGGCAAATTCGAAAAGAACTTTATTGCACAAGTAAGATAATTTTTACTTTTAATTTTA
GATTTATTACTAATTTTTATATTTTACAACAGGGAAACTACGAAAATCGTACAGTTTTTG
AATCTTTGGATATTGGCTGGCAATTGCTTCGAATCTTCCCTAAAGAAATGTTGAAACGTA
TTCCAGCTTCCATTTTAGCTGAATTCTATCCAAGAGACTCACGTCACTAA

>g3827.t5 Gene=g3827 Length=453
MSYSSGLSARQAAKEHVLAVSRDFISQPRLTYKTVSGVNGPLVILDEVKFPKFAEIVQLR
LNDGTIRSGQVLEVSGSKAVVQVFEGTSGIDAKNTVCEFTGDILRTPVSEDMLGRVFNGS
GKPIDKGPPILAEDYLDIQGQPINPWSRIYPEEMIQTGISAIDVMNSIARGQKIPIFSAA
GLPHNEIAAQICRQAGLVKIPGKSVLDDHEDNFAIVFAAMGVNMETARFFKQDFEENGSM
ENVCLFLNLANDPTIERIITPRLALTAAEFMAYQCEKHVLVILTDMSSYAEALREVSAAR
EEVPGRRGFPGYMYTDLATIYERAGRVEGRNGSITQIPILTMPNDDITHPIPDLTGYITE
GQIYVDRQLHNRQIYPPINVLPSLSRLMKSAIGEGMTRKDHSDVSNQLYACYAIGKDVQA
MKAVVGEEALTPDDLLYLEFLGKFEKNFIAQVR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g3827.t5 CDD cd18118 ATP-synt_V_A-type_beta_N 31 102 6.0797E-39
8 g3827.t5 CDD cd01135 V_A-ATPase_B 103 387 0.0
7 g3827.t5 Gene3D G3DSA:3.40.50.12240 - 25 453 2.4E-184
5 g3827.t5 Hamap MF_00310 V-type ATP synthase beta chain [atpB]. 29 453 48.482155
3 g3827.t5 PANTHER PTHR43389:SF5 V-TYPE PROTON ATPASE SUBUNIT B, BRAIN ISOFORM 10 451 3.9E-275
4 g3827.t5 PANTHER PTHR43389 V-TYPE PROTON ATPASE SUBUNIT B 10 451 3.9E-275
1 g3827.t5 Pfam PF02874 ATP synthase alpha/beta family, beta-barrel domain 35 101 1.1E-12
2 g3827.t5 Pfam PF00006 ATP synthase alpha/beta family, nucleotide-binding domain 158 385 2.8E-64
10 g3827.t5 ProSitePatterns PS00152 ATP synthase alpha and beta subunits signature. 376 385 -
6 g3827.t5 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 105 391 8.5E-85
11 g3827.t5 TIGRFAM TIGR01040 V-ATPase_V1_B: V-type ATPase, B subunit 31 451 1.2E-276

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

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