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.t4 isoform g5840.t4 12221436 12223553
chr_2 g5840 g5840.t4 exon g5840.t4.exon1 12221436 12223068
chr_2 g5840 g5840.t4 TTS g5840.t4 12221437 12221437
chr_2 g5840 g5840.t4 cds g5840.t4.CDS1 12222368 12222997
chr_2 g5840 g5840.t4 exon g5840.t4.exon2 12223459 12223553
chr_2 g5840 g5840.t4 TSS g5840.t4 NA NA

Sequences

>g5840.t4 Gene=g5840 Length=1728
ATGTGGGATTTTTTTGAAAATTCAAATTTAAGCGCTTTCAAAACTGCAGCAATTTTTCTG
AACTCGCACGTGACTGTGGGCATTTTTAAAAATTGGACTTTAGTCAGTGAGAAACTTCTC
TCTGTGATTAAGTACTCAAGATCAACGACCCACAAATTCAATCAAAATGCGTTATGCACT
TGGATATACTTTTACCGGAACAATTGTCACTCTATCATCGCTATGGATTCTTTATCATGT
TCTAACAGGTCAAGGTGAACGAATTTCATTTGGATGGTTCTTAGAAGAAACAAGTCCTTA
TATGTGGGGTTGTCTTGGAATCGGATTTTCCGTTGCATTCTCAGTAGTTGGTGCAGCTAT
TGGCATTCACACGACTGGTGTGTCAATTGTCGGTGGTGGCGTAAAAGCGCCAAGAATCAA
GACAAAGAACTTGATTTCAGTCATTTTCTGTGAAGCTGTCGCCATTTACGGTCTCATTAC
AGCCATTGTACTTTCCGGTATGCTTGAACCATTTACAACAGAAACAGCAGCAACTGTTGA
TTCAGTGAGAGCAAACAATTGGATGGCAGGACATGTAATGTTTGGCGCAGGATTAGCCGT
GGGTCTAGTCAATCTCTTCTGCGGTTTAGCTGTCGGAATTGTTGGATCTGGAGCTGCATT
AGCTGATGCTGCCAACTCAAGTCTTTTTGTGAAAATTCTCATTGTAGAAATTTTCGGCTC
AGCCATTGGTCTTTTCGGTCTTATTGTCGGAATTTATATGACCAGCAAAGTCAAAATGGG
TGACAAGACAAATTAAAAAGTTAGTGTGAAGTGATAGAGGCACATACATAAGAAAAATCC
TAAATCTATGTAGTTAATCAATATAATAATAATATTTGTGAAGAAATGAAGCTATCAATA
AGATTCAGTGCATAATCATTAATGGAATAAAAAGAAATTTAGATTTCTTTAATGATATCT
ATCGATTCCAAAAAGACACACAATCACACACATATATAAAATGAAAGAAAAAGAGAGAGA
TCAATATAATATATTCCAAATTTCAATTGTTGTAAATTTTTTGTTTGATTGACTTTTTAT
TAAATATATCGATATAATATAATTTAAACATTTCATCGTCGTTCAATGCTATAATATATT
ATCACATTCATTAGAAAGTATAAAATAAACACTTTTTTGGCTACAAAAGGCCAAAACAAA
TTGTTCTATTGCGATTAACAATTCTGTGTATTATAATAAAATTAAATTACTTATCATGCT
TTAGATCATCAAGAGAAAAGAGTGTGTAATAAATTTATTGAAATGAAAATTATTAGAAAT
ATATTTTAATGACTTATCTAATCTCATCTTCATTAAAGAAATTTGCTGTATAATCTAAAT
TAGATAAGAGACGAAAAAAGCTTGGCTAAAAAATATGTGTACCAGTCATGAATATTTTGT
CCTCTTCCTTTTTAATATATTTTAATAGTTTGTTTACTTGAGCTATGATGATTGATTTCT
TTTCAACAAGTGGTTCAAATGTGGCATATAACTCATAATTTGCTGTCACCCAAGCTAGTT
GAATTTCATGTTCATGCATTTCATATATTAATTTTAATGGTCTTGACACACGATGAATTC
TGTTATGTAAATCATAATACATTGCTTCAATACGTTCAAATTGTTCTGAAAAAAAATTGA
TAAAGTTCAAATTTAACTTGTCATTAAATTTTAATAATTTCTTACCTA

>g5840.t4 Gene=g5840 Length=209
MRYALGYTFTGTIVTLSSLWILYHVLTGQGERISFGWFLEETSPYMWGCLGIGFSVAFSV
VGAAIGIHTTGVSIVGGGVKAPRIKTKNLISVIFCEAVAIYGLITAIVLSGMLEPFTTET
AATVDSVRANNWMAGHVMFGAGLAVGLVNLFCGLAVGIVGSGAALADAANSSLFVKILIV
EIFGSAIGLFGLIVGIYMTSKVKMGDKTN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
21 g5840.t4 CDD cd18177 ATP-synt_Vo_c_ATP6F_rpt1 47 109 3.17771E-29
22 g5840.t4 CDD cd18178 ATP-synt_Vo_c_ATP6F_rpt2 134 198 3.05429E-25
9 g5840.t4 Gene3D G3DSA:1.20.120.610 - 44 205 1.0E-54
3 g5840.t4 PANTHER PTHR10263 V-TYPE PROTON ATPASE PROTEOLIPID SUBUNIT 32 203 1.2E-70
4 g5840.t4 PANTHER PTHR10263:SF18 V-TYPE PROTON ATPASE 21 KDA PROTEOLIPID SUBUNIT 32 203 1.2E-70
5 g5840.t4 PRINTS PR00122 Vacuolar ATP synthase 16kDa subunit signature 63 87 2.0E-9
6 g5840.t4 PRINTS PR00122 Vacuolar ATP synthase 16kDa subunit signature 177 200 2.0E-9
2 g5840.t4 Pfam PF00137 ATP synthase subunit C 50 109 1.9E-13
1 g5840.t4 Pfam PF00137 ATP synthase subunit C 139 198 8.1E-12
10 g5840.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 6 -
16 g5840.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 7 25 -
14 g5840.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 26 44 -
18 g5840.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 45 67 -
11 g5840.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 68 87 -
20 g5840.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 88 113 -
15 g5840.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 114 132 -
17 g5840.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 133 166 -
12 g5840.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 167 172 -
19 g5840.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 173 198 -
13 g5840.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 199 209 -
7 g5840.t4 SUPERFAMILY SSF81333 F1F0 ATP synthase subunit C 42 109 6.02E-15
8 g5840.t4 SUPERFAMILY SSF81333 F1F0 ATP synthase subunit C 131 201 1.7E-14
27 g5840.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 5 27 -
24 g5840.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 54 76 -
23 g5840.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 89 111 -
26 g5840.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 143 165 -
25 g5840.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 177 199 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5840/g5840.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5840.t4.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