Gene loci information

Transcript annotation

  • This transcript has been annotated as V-type proton ATPase 21 kDa proteolipid subunit.

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 g5840 g5840.t1 TTS g5840.t1 12221859 12221859
chr_2 g5840 g5840.t1 isoform g5840.t1 12222368 12223553
chr_2 g5840 g5840.t1 exon g5840.t1.exon1 12222368 12222915
chr_2 g5840 g5840.t1 cds g5840.t1.CDS1 12222368 12222915
chr_2 g5840 g5840.t1 exon g5840.t1.exon2 12223058 12223068
chr_2 g5840 g5840.t1 cds g5840.t1.CDS2 12223058 12223068
chr_2 g5840 g5840.t1 exon g5840.t1.exon3 12223459 12223553
chr_2 g5840 g5840.t1 cds g5840.t1.CDS3 12223459 12223553
chr_2 g5840 g5840.t1 TSS g5840.t1 NA NA

Sequences

>g5840.t1 Gene=g5840 Length=654
ATGTGGGATTTTTTTGAAAATTCAAATTTAAGCGCTTTCAAAACTGCAGCAATTTTTCTG
AACTCGCACGTGACTGTGGGCATTTTTAAAAATTGGACTTTAGTCAGTCAAGGTGAACGA
ATTTCATTTGGATGGTTCTTAGAAGAAACAAGTCCTTATATGTGGGGTTGTCTTGGAATC
GGATTTTCCGTTGCATTCTCAGTAGTTGGTGCAGCTATTGGCATTCACACGACTGGTGTG
TCAATTGTCGGTGGTGGCGTAAAAGCGCCAAGAATCAAGACAAAGAACTTGATTTCAGTC
ATTTTCTGTGAAGCTGTCGCCATTTACGGTCTCATTACAGCCATTGTACTTTCCGGTATG
CTTGAACCATTTACAACAGAAACAGCAGCAACTGTTGATTCAGTGAGAGCAAACAATTGG
ATGGCAGGACATGTAATGTTTGGCGCAGGATTAGCCGTGGGTCTAGTCAATCTCTTCTGC
GGTTTAGCTGTCGGAATTGTTGGATCTGGAGCTGCATTAGCTGATGCTGCCAACTCAAGT
CTTTTTGTGAAAATTCTCATTGTAGAAATTTTCGGCTCAGCCATTGGTCTTTTCGGTCTT
ATTGTCGGAATTTATATGACCAGCAAAGTCAAAATGGGTGACAAGACAAATTAA

>g5840.t1 Gene=g5840 Length=217
MWDFFENSNLSAFKTAAIFLNSHVTVGIFKNWTLVSQGERISFGWFLEETSPYMWGCLGI
GFSVAFSVVGAAIGIHTTGVSIVGGGVKAPRIKTKNLISVIFCEAVAIYGLITAIVLSGM
LEPFTTETAATVDSVRANNWMAGHVMFGAGLAVGLVNLFCGLAVGIVGSGAALADAANSS
LFVKILIVEIFGSAIGLFGLIVGIYMTSKVKMGDKTN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g5840.t1 CDD cd18177 ATP-synt_Vo_c_ATP6F_rpt1 55 117 6.40972E-30
20 g5840.t1 CDD cd18178 ATP-synt_Vo_c_ATP6F_rpt2 142 206 1.21768E-25
9 g5840.t1 Gene3D G3DSA:1.20.120.610 - 52 213 1.1E-54
3 g5840.t1 PANTHER PTHR10263 V-TYPE PROTON ATPASE PROTEOLIPID SUBUNIT 37 211 9.8E-71
4 g5840.t1 PANTHER PTHR10263:SF18 V-TYPE PROTON ATPASE 21 KDA PROTEOLIPID SUBUNIT 37 211 9.8E-71
5 g5840.t1 PRINTS PR00122 Vacuolar ATP synthase 16kDa subunit signature 71 95 2.1E-9
6 g5840.t1 PRINTS PR00122 Vacuolar ATP synthase 16kDa subunit signature 185 208 2.1E-9
2 g5840.t1 Pfam PF00137 ATP synthase subunit C 58 117 2.0E-13
1 g5840.t1 Pfam PF00137 ATP synthase subunit C 147 206 8.7E-12
14 g5840.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 52 -
17 g5840.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 53 75 -
11 g5840.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 76 95 -
18 g5840.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 96 121 -
12 g5840.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 122 140 -
16 g5840.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 141 174 -
10 g5840.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 175 180 -
15 g5840.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 181 206 -
13 g5840.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 207 217 -
8 g5840.t1 SUPERFAMILY SSF81333 F1F0 ATP synthase subunit C 50 117 6.54E-15
7 g5840.t1 SUPERFAMILY SSF81333 F1F0 ATP synthase subunit C 139 209 1.83E-14
23 g5840.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 53 75 -
21 g5840.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 96 118 -
22 g5840.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 151 173 -
24 g5840.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 185 207 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5840/g5840.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5840.t1.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0033179 proton-transporting V-type ATPase, V0 domain CC
GO:1902600 proton transmembrane transport BP
GO:0033177 proton-transporting two-sector ATPase complex, proton-transporting domain CC
GO:0015078 proton transmembrane transporter activity 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