General information for g5840.t10
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as V-type proton ATPase 21 kDa proteolipid subunit.
Parent gene
- The parent gene g5840 is located on chr_2: 12222368..12223553 (- strand)
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.t10 | isoform | g5840.t10 | 12221843 | 12223553 |
| chr_2 | g5840 | g5840.t10 | exon | g5840.t10.exon1 | 12221843 | 12223060 |
| chr_2 | g5840 | g5840.t10 | TTS | g5840.t10 | 12221859 | 12221859 |
| chr_2 | g5840 | g5840.t10 | cds | g5840.t10.CDS1 | 12222368 | 12222997 |
| chr_2 | g5840 | g5840.t10 | exon | g5840.t10.exon2 | 12223415 | 12223553 |
| chr_2 | g5840 | g5840.t10 | TSS | g5840.t10 | NA | NA |
Sequences
>g5840.t10 Gene=g5840 Length=1357
ATGTGGGATTTTTTTGAAAATTCAAATTTAAGCGCTTTCAAAACTGCAGCAATTTTTCTG
AACTCGCACGTGACTGTGGGCATTTTTAAAAATTGGTAAATTTTAATTTTAATATTTTTT
ATAAAATTCTAAATAACTCTCAGTGAGAAACTTCTCTCTGTGATTAAGTACTCAAGATCA
ACGACCCACAAATTCAATCAAAATGCGTTATGCACTTGGATATACTTTTACCGGAACAAT
TGTCACTCTATCATCGCTATGGATTCTTTATCATGTTCTAACAGGTCAAGGTGAACGAAT
TTCATTTGGATGGTTCTTAGAAGAAACAAGTCCTTATATGTGGGGTTGTCTTGGAATCGG
ATTTTCCGTTGCATTCTCAGTAGTTGGTGCAGCTATTGGCATTCACACGACTGGTGTGTC
AATTGTCGGTGGTGGCGTAAAAGCGCCAAGAATCAAGACAAAGAACTTGATTTCAGTCAT
TTTCTGTGAAGCTGTCGCCATTTACGGTCTCATTACAGCCATTGTACTTTCCGGTATGCT
TGAACCATTTACAACAGAAACAGCAGCAACTGTTGATTCAGTGAGAGCAAACAATTGGAT
GGCAGGACATGTAATGTTTGGCGCAGGATTAGCCGTGGGTCTAGTCAATCTCTTCTGCGG
TTTAGCTGTCGGAATTGTTGGATCTGGAGCTGCATTAGCTGATGCTGCCAACTCAAGTCT
TTTTGTGAAAATTCTCATTGTAGAAATTTTCGGCTCAGCCATTGGTCTTTTCGGTCTTAT
TGTCGGAATTTATATGACCAGCAAAGTCAAAATGGGTGACAAGACAAATTAAAAAGTTAG
TGTGAAGTGATAGAGGCACATACATAAGAAAAATCCTAAATCTATGTAGTTAATCAATAT
AATAATAATATTTGTGAAGAAATGAAGCTATCAATAAGATTCAGTGCATAATCATTAATG
GAATAAAAAGAAATTTAGATTTCTTTAATGATATCTATCGATTCCAAAAAGACACACAAT
CACACACATATATAAAATGAAAGAAAAAGAGAGAGATCAATATAATATATTCCAAATTTC
AATTGTTGTAAATTTTTTGTTTGATTGACTTTTTATTAAATATATCGATATAATATAATT
TAAACATTTCATCGTCGTTCAATGCTATAATATATTATCACATTCATTAGAAAGTATAAA
ATAAACACTTTTTTGGCTACAAAAGGCCAAAACAAATTGTTCTATTGCGATTAACAATTC
TGTGTATTATAATAAAATTAAATTACTTATCATGCTTTAGATCATCAAGAGAAAAGAGTG
TGTAATAAATTTATTGAAATGAAAATTATTAGAAATA
>g5840.t10 Gene=g5840 Length=209
MRYALGYTFTGTIVTLSSLWILYHVLTGQGERISFGWFLEETSPYMWGCLGIGFSVAFSV
VGAAIGIHTTGVSIVGGGVKAPRIKTKNLISVIFCEAVAIYGLITAIVLSGMLEPFTTET
AATVDSVRANNWMAGHVMFGAGLAVGLVNLFCGLAVGIVGSGAALADAANSSLFVKILIV
EIFGSAIGLFGLIVGIYMTSKVKMGDKTN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 21 | g5840.t10 | CDD | cd18177 | ATP-synt_Vo_c_ATP6F_rpt1 | 47 | 109 | 3.17771E-29 |
| 22 | g5840.t10 | CDD | cd18178 | ATP-synt_Vo_c_ATP6F_rpt2 | 134 | 198 | 3.05429E-25 |
| 9 | g5840.t10 | Gene3D | G3DSA:1.20.120.610 | - | 44 | 205 | 1.0E-54 |
| 3 | g5840.t10 | PANTHER | PTHR10263 | V-TYPE PROTON ATPASE PROTEOLIPID SUBUNIT | 32 | 203 | 1.2E-70 |
| 4 | g5840.t10 | PANTHER | PTHR10263:SF18 | V-TYPE PROTON ATPASE 21 KDA PROTEOLIPID SUBUNIT | 32 | 203 | 1.2E-70 |
| 5 | g5840.t10 | PRINTS | PR00122 | Vacuolar ATP synthase 16kDa subunit signature | 63 | 87 | 2.0E-9 |
| 6 | g5840.t10 | PRINTS | PR00122 | Vacuolar ATP synthase 16kDa subunit signature | 177 | 200 | 2.0E-9 |
| 2 | g5840.t10 | Pfam | PF00137 | ATP synthase subunit C | 50 | 109 | 1.9E-13 |
| 1 | g5840.t10 | Pfam | PF00137 | ATP synthase subunit C | 139 | 198 | 8.1E-12 |
| 10 | g5840.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 6 | - |
| 16 | g5840.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 25 | - |
| 14 | g5840.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 26 | 44 | - |
| 18 | g5840.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 45 | 67 | - |
| 11 | g5840.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 68 | 87 | - |
| 20 | g5840.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 88 | 113 | - |
| 15 | g5840.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 114 | 132 | - |
| 17 | g5840.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 133 | 166 | - |
| 12 | g5840.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 167 | 172 | - |
| 19 | g5840.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 173 | 198 | - |
| 13 | g5840.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 199 | 209 | - |
| 7 | g5840.t10 | SUPERFAMILY | SSF81333 | F1F0 ATP synthase subunit C | 42 | 109 | 6.02E-15 |
| 8 | g5840.t10 | SUPERFAMILY | SSF81333 | F1F0 ATP synthase subunit C | 131 | 201 | 1.7E-14 |
| 27 | g5840.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 5 | 27 | - |
| 24 | g5840.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 54 | 76 | - |
| 23 | g5840.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 89 | 111 | - |
| 26 | g5840.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 143 | 165 | - |
| 25 | g5840.t10 | 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.t10; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5840.t10.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 transcript has been annotated with K03661 (V-type H+-transporting ATPase 21kDa proteolipid subunit)
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.
