Gene loci information

Transcript annotation

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

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_2 g8216 g8216.t1 TSS g8216.t1 29093634 29093634
chr_2 g8216 g8216.t1 isoform g8216.t1 29094059 29096122
chr_2 g8216 g8216.t1 exon g8216.t1.exon1 29094059 29094134
chr_2 g8216 g8216.t1 cds g8216.t1.CDS1 29094059 29094134
chr_2 g8216 g8216.t1 exon g8216.t1.exon2 29094215 29094409
chr_2 g8216 g8216.t1 cds g8216.t1.CDS2 29094215 29094409
chr_2 g8216 g8216.t1 exon g8216.t1.exon3 29094472 29094939
chr_2 g8216 g8216.t1 cds g8216.t1.CDS3 29094472 29094939
chr_2 g8216 g8216.t1 exon g8216.t1.exon4 29095002 29095115
chr_2 g8216 g8216.t1 cds g8216.t1.CDS4 29095002 29095115
chr_2 g8216 g8216.t1 exon g8216.t1.exon5 29095169 29095559
chr_2 g8216 g8216.t1 cds g8216.t1.CDS5 29095169 29095559
chr_2 g8216 g8216.t1 exon g8216.t1.exon6 29095633 29096122
chr_2 g8216 g8216.t1 cds g8216.t1.CDS6 29095633 29096122
chr_2 g8216 g8216.t1 TTS g8216.t1 29096588 29096588

Sequences

>g8216.t1 Gene=g8216 Length=1734
ATGTCTAATTTAAAGAAGATAGCAAATGAGGACCGTGAGTCAAAATTCGGCTATGTATTT
GCCGTTTCAGGACCTGTCGTCACTGCTGAACGAATGGCTGGATCAGCTATGTACGAGTTG
GTGCGTGTAGGCTATTATGAATTGGTTGGTGAAATTATTCGTTTAGAAGGTGATATGGCA
ACAATTCAAGTCTATGAAGAAACATCAGGTGTAACTGTTGGTGATCCTGTCTTGAGAACT
GGCAAACCTTTATCAGTCGAATTGGGTCCAGGTATTATGGGTAGTATTTTTGACGGTATT
CAACGTCCATTAAAAGACATTAATGAATTGACACAATCAATTTATATCCCAAAGGGAATT
AATATTCCTTCACTTTCTCGTACTCAATCATGGGATTTTAATCCATTAAATGTAAAAGTC
GGATCGCACATAACTGGAGGTGATTTGTATGGTGTAGTTCATGAAAATACTTTAGTCAAA
CATAAATTGATTGTACCACCGAGAGCGAAAGGAACAGTTCGTTATATTGCACCACCAGGC
AATTATACAGTGGATGATATCATTCTTGAGACAGAATTTGATGGTGAAATCAATAAATAT
TCCATGTTGCAAGTGTGGCCTGTTCGTCAGCCACGTCCAGTCACTGAAAAATTGCCAGCA
AATCATCCCTTGCTGACTGGTCAGCGTGTCTTGGATTCATTGTTTCCATGTGTTCAAGGA
GGAACAACTGCTATACCTGATGTCATTATTTATGTCGGTTGCGGAGAACGTGGAAATGAA
ATGTCTGAAGTACTTCGTGATTTCCCAAGATTGTCTGTTGAAATTGATGGCGTAACTGAG
TCTATCATGAAGCCTTCCATTTATACTGGTATTACACTTTCTGAATACTTCCGTGATATG
GGTTATAATGTCTCTATGATGGCTGATTCGACTTCTCGTTGGGCTGAGGCTCTTCGTGAA
ATTTCAGGTCGTCTCGCTGAAATGCCTGCTGATTCAGGTTATCCAGCTTATTTGGGAGCT
CGTCTTGCCTCATTTTACGAACGTGCTGGTCGTGTTAAATGTTTGGGTAATCCAGAACGT
GAAGGTTCAGTATCAATTGTCGGCGCTGTATCGCCACCTGGCGGTGACTTCTCAGATCCT
GTTACATCTGCTACTTTAGGTATTGTTCAAGTGTTTTGGGGTTTGGATAAAAAATTGGCC
CAACGTAAACATTTTCCATCTATCAATTGGCTCATTTCATACAGTAAATATATGCGTGCA
CTTGATGATTTTTATGATAAAAACTTCCCCGAATTCGTTCCATTACGTACAAAAGTGAAG
GAAATTCTTCAAGAAGAAGAAGACTTGTCAGAAATTGTGCAACTCGTTGGTAAAGCATCA
TTGGCTGAAACTGATAAGATCACATTAGAAGTTGCTAAGCTTCTTAAGGATGACTTTTTA
CAACAAAATTCTTATTCATCATATGATCGTTTCTGTCCATTCTATAAAACTGTCGGCATG
TTAAGAAATTTTATTGCATTCTACGATATGGCTCGTCACGCTGTTGAATCAACAGCACAA
TCAGAAAATAAAATTACATGGAACATCATTCGTGATTCAATGGGCAACATGCTTTATCAA
TTATCATCTATGAAATTTAAAGATCCAGTCAAAGACGGTGAAGCAAAAATCAAAGCTGAT
TTCGATCAATTGCATGAAGAATTACAACAAGCTTTCCGCAATCTAGAGGATTAA

>g8216.t1 Gene=g8216 Length=577
MSNLKKIANEDRESKFGYVFAVSGPVVTAERMAGSAMYELVRVGYYELVGEIIRLEGDMA
TIQVYEETSGVTVGDPVLRTGKPLSVELGPGIMGSIFDGIQRPLKDINELTQSIYIPKGI
NIPSLSRTQSWDFNPLNVKVGSHITGGDLYGVVHENTLVKHKLIVPPRAKGTVRYIAPPG
NYTVDDIILETEFDGEINKYSMLQVWPVRQPRPVTEKLPANHPLLTGQRVLDSLFPCVQG
GTTAIPDVIIYVGCGERGNEMSEVLRDFPRLSVEIDGVTESIMKPSIYTGITLSEYFRDM
GYNVSMMADSTSRWAEALREISGRLAEMPADSGYPAYLGARLASFYERAGRVKCLGNPER
EGSVSIVGAVSPPGGDFSDPVTSATLGIVQVFWGLDKKLAQRKHFPSINWLISYSKYMRA
LDDFYDKNFPEFVPLRTKVKEILQEEEDLSEIVQLVGKASLAETDKITLEVAKLLKDDFL
QQNSYSSYDRFCPFYKTVGMLRNFIAFYDMARHAVESTAQSENKITWNIIRDSMGNMLYQ
LSSMKFKDPVKDGEAKIKADFDQLHEELQQAFRNLED

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g8216.t1 CDD cd18119 ATP-synt_V_A-type_alpha_N 16 82 2.73407E-39
16 g8216.t1 CDD cd01134 V_A-ATPase_A 83 417 0.0
17 g8216.t1 CDD cd18111 ATP-synt_V_A-type_alpha_C 432 537 1.21311E-50
14 g8216.t1 Coils Coil Coil 558 577 -
12 g8216.t1 Gene3D G3DSA:2.40.30.20 - 15 84 3.1E-33
10 g8216.t1 Gene3D G3DSA:3.40.50.300 - 86 414 1.1E-137
11 g8216.t1 Gene3D G3DSA:2.40.50.100 - 129 200 1.1E-137
13 g8216.t1 Gene3D G3DSA:1.10.1140.10 - 416 575 1.4E-51
4 g8216.t1 PANTHER PTHR43607:SF1 V-TYPE PROTON ATPASE CATALYTIC SUBUNIT A 9 575 1.5E-288
5 g8216.t1 PANTHER PTHR43607 V-TYPE PROTON ATPASE CATALYTIC SUBUNIT A 9 575 1.5E-288
2 g8216.t1 Pfam PF02874 ATP synthase alpha/beta family, beta-barrel domain 19 81 5.9E-14
1 g8216.t1 Pfam PF16886 ATPsynthase alpha/beta subunit N-term extension 97 218 3.0E-44
3 g8216.t1 Pfam PF00006 ATP synthase alpha/beta family, nucleotide-binding domain 248 415 6.1E-70
9 g8216.t1 ProSitePatterns PS00152 ATP synthase alpha and beta subunits signature. 406 415 -
6 g8216.t1 SUPERFAMILY SSF50615 N-terminal domain of alpha and beta subunits of F1 ATP synthase 13 84 2.94E-15
7 g8216.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 195 420 3.49E-60
8 g8216.t1 SUPERFAMILY SSF47917 C-terminal domain of alpha and beta subunits of F1 ATP synthase 430 532 3.66E-26

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

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