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.t5 isoform g5840.t5 12221843 12222915
chr_2 g5840 g5840.t5 exon g5840.t5.exon1 12221843 12222156
chr_2 g5840 g5840.t5 TTS g5840.t5 12221859 12221859
chr_2 g5840 g5840.t5 exon g5840.t5.exon2 12222287 12222915
chr_2 g5840 g5840.t5 cds g5840.t5.CDS1 12222368 12222862
chr_2 g5840 g5840.t5 TSS g5840.t5 12223482 12223482

Sequences

>g5840.t5 Gene=g5840 Length=943
GTCAAGGTGAACGAATTTCATTTGGATGGTTCTTAGAAGAAACAAGTCCTTATATGTGGG
GTTGTCTTGGAATCGGATTTTCCGTTGCATTCTCAGTAGTTGGTGCAGCTATTGGCATTC
ACACGACTGGTGTGTCAATTGTCGGTGGTGGCGTAAAAGCGCCAAGAATCAAGACAAAGA
ACTTGATTTCAGTCATTTTCTGTGAAGCTGTCGCCATTTACGGTCTCATTACAGCCATTG
TACTTTCCGGTATGCTTGAACCATTTACAACAGAAACAGCAGCAACTGTTGATTCAGTGA
GAGCAAACAATTGGATGGCAGGACATGTAATGTTTGGCGCAGGATTAGCCGTGGGTCTAG
TCAATCTCTTCTGCGGTTTAGCTGTCGGAATTGTTGGATCTGGAGCTGCATTAGCTGATG
CTGCCAACTCAAGTCTTTTTGTGAAAATTCTCATTGTAGAAATTTTCGGCTCAGCCATTG
GTCTTTTCGGTCTTATTGTCGGAATTTATATGACCAGCAAAGTCAAAATGGGTGACAAGA
CAAATTAAAAAGTTAGTGTGAAGTGATAGAGGCACATACATAAGAAAAATCCTAAATCTA
TGTAGTTAATCAATATAATAATAATATTTAAAAAGAGAGAGATCAATATAATATATTCCA
AATTTCAATTGTTGTAAATTTTTTGTTTGATTGACTTTTTATTAAATATATCGATATAAT
ATAATTTAAACATTTCATCGTCGTTCAATGCTATAATATATTATCACATTCATTAGAAAG
TATAAAATAAACACTTTTTTGGCTACAAAAGGCCAAAACAAATTGTTCTATTGCGATTAA
CAATTCTGTGTATTATAATAAAATTAAATTACTTATCATGCTTTAGATCATCAAGAGAAA
AGAGTGTGTAATAAATTTATTGAAATGAAAATTATTAGAAATA

>g5840.t5 Gene=g5840 Length=164
MWGCLGIGFSVAFSVVGAAIGIHTTGVSIVGGGVKAPRIKTKNLISVIFCEAVAIYGLIT
AIVLSGMLEPFTTETAATVDSVRANNWMAGHVMFGAGLAVGLVNLFCGLAVGIVGSGAAL
ADAANSSLFVKILIVEIFGSAIGLFGLIVGIYMTSKVKMGDKTN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g5840.t5 CDD cd18177 ATP-synt_Vo_c_ATP6F_rpt1 2 64 6.85281E-28
20 g5840.t5 CDD cd18178 ATP-synt_Vo_c_ATP6F_rpt2 89 153 1.0014E-23
9 g5840.t5 Gene3D G3DSA:1.20.120.610 - 1 160 1.3E-54
3 g5840.t5 PANTHER PTHR10263 V-TYPE PROTON ATPASE PROTEOLIPID SUBUNIT 1 158 1.3E-63
4 g5840.t5 PANTHER PTHR10263:SF18 V-TYPE PROTON ATPASE 21 KDA PROTEOLIPID SUBUNIT 1 158 1.3E-63
6 g5840.t5 PRINTS PR00122 Vacuolar ATP synthase 16kDa subunit signature 18 42 1.4E-9
5 g5840.t5 PRINTS PR00122 Vacuolar ATP synthase 16kDa subunit signature 132 155 1.4E-9
2 g5840.t5 Pfam PF00137 ATP synthase subunit C 5 64 1.1E-13
1 g5840.t5 Pfam PF00137 ATP synthase subunit C 94 153 4.9E-12
13 g5840.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
18 g5840.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 32 -
10 g5840.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 33 43 -
17 g5840.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 44 68 -
14 g5840.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 69 87 -
15 g5840.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 88 121 -
11 g5840.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 122 127 -
16 g5840.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 128 153 -
12 g5840.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 154 164 -
8 g5840.t5 SUPERFAMILY SSF81333 F1F0 ATP synthase subunit C 2 64 1.57E-13
7 g5840.t5 SUPERFAMILY SSF81333 F1F0 ATP synthase subunit C 86 156 9.81E-15
24 g5840.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 10 32 -
23 g5840.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 44 66 -
22 g5840.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 98 120 -
21 g5840.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 132 154 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5840/g5840.t5; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5840.t5.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