Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t6 isoform g5840.t6 12221843 12223058
chr_2 g5840 g5840.t6 exon g5840.t6.exon1 12221843 12222501
chr_2 g5840 g5840.t6 TTS g5840.t6 12221859 12221859
chr_2 g5840 g5840.t6 cds g5840.t6.CDS1 12222472 12222501
chr_2 g5840 g5840.t6 exon g5840.t6.exon2 12222590 12223058
chr_2 g5840 g5840.t6 cds g5840.t6.CDS2 12222590 12222997
chr_2 g5840 g5840.t6 TSS g5840.t6 12223482 12223482

Sequences

>g5840.t6 Gene=g5840 Length=1128
AGTGAGAAACTTCTCTCTGTGATTAAGTACTCAAGATCAACGACCCACAAATTCAATCAA
AATGCGTTATGCACTTGGATATACTTTTACCGGAACAATTGTCACTCTATCATCGCTATG
GATTCTTTATCATGTTCTAACAGGTCAAGGTGAACGAATTTCATTTGGATGGTTCTTAGA
AGAAACAAGTCCTTATATGTGGGGTTGTCTTGGAATCGGATTTTCCGTTGCATTCTCAGT
AGTTGGTGCAGCTATTGGCATTCACACGACTGGTGTGTCAATTGTCGGTGGTGGCGTAAA
AGCGCCAAGAATCAAGACAAAGAACTTGATTTCAGTCATTTTCTGTGAAGCTGTCGCCAT
TTACGGTCTCATTACAGCCATTGTACTTTCCGGTATGCTTGAACCATTTACAACAGAAAC
AGCAGCAACTGTTGATTCAGTGAGAGCAAACAATTGGATGGCAGGACATCTGATGCTGCC
AACTCAAGTCTTTTTGTGAAAATTCTCATTGTAGAAATTTTCGGCTCAGCCATTGGTCTT
TTCGGTCTTATTGTCGGAATTTATATGACCAGCAAAGTCAAAATGGGTGACAAGACAAAT
TAAAAAGTTAGTGTGAAGTGATAGAGGCACATACATAAGAAAAATCCTAAATCTATGTAG
TTAATCAATATAATAATAATATTTGTGAAGAAATGAAGCTATCAATAAGATTCAGTGCAT
AATCATTAATGGAATAAAAAGAAATTTAGATTTCTTTAATGATATCTATCGATTCCAAAA
AGACACACAATCACACACATATATAAAATGAAAGAAAAAGAGAGAGATCAATATAATATA
TTCCAAATTTCAATTGTTGTAAATTTTTTGTTTGATTGACTTTTTATTAAATATATCGAT
ATAATATAATTTAAACATTTCATCGTCGTTCAATGCTATAATATATTATCACATTCATTA
GAAAGTATAAAATAAACACTTTTTTGGCTACAAAAGGCCAAAACAAATTGTTCTATTGCG
ATTAACAATTCTGTGTATTATAATAAAATTAAATTACTTATCATGCTTTAGATCATCAAG
AGAAAAGAGTGTGTAATAAATTTATTGAAATGAAAATTATTAGAAATA

>g5840.t6 Gene=g5840 Length=145
MRYALGYTFTGTIVTLSSLWILYHVLTGQGERISFGWFLEETSPYMWGCLGIGFSVAFSV
VGAAIGIHTTGVSIVGGGVKAPRIKTKNLISVIFCEAVAIYGLITAIVLSGMLEPFTTET
AATVDSVRANNWMAGHLMLPTQVFL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g5840.t6 CDD cd18177 ATP-synt_Vo_c_ATP6F_rpt1 47 109 2.52847E-32
7 g5840.t6 Gene3D G3DSA:1.20.120.610 - 44 139 2.8E-25
2 g5840.t6 PANTHER PTHR10263 V-TYPE PROTON ATPASE PROTEOLIPID SUBUNIT 32 135 3.2E-37
3 g5840.t6 PANTHER PTHR10263:SF18 V-TYPE PROTON ATPASE 21 KDA PROTEOLIPID SUBUNIT 32 135 3.2E-37
5 g5840.t6 PRINTS PR00122 Vacuolar ATP synthase 16kDa subunit signature 63 87 2.7E-8
4 g5840.t6 PRINTS PR00122 Vacuolar ATP synthase 16kDa subunit signature 89 113 2.7E-8
1 g5840.t6 Pfam PF00137 ATP synthase subunit C 50 109 8.7E-14
8 g5840.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 6 -
13 g5840.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 7 25 -
11 g5840.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 26 44 -
14 g5840.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 45 67 -
9 g5840.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 68 87 -
12 g5840.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 88 109 -
10 g5840.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 110 145 -
6 g5840.t6 SUPERFAMILY SSF81333 F1F0 ATP synthase subunit C 42 109 2.62E-15
18 g5840.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 5 27 -
17 g5840.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 54 76 -
16 g5840.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 89 111 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5840/g5840.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5840.t6.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

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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