General information for g11996.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Sodium/potassium-transporting ATPase subunit beta-2.
Parent gene
- The parent gene g11996 is located on chr_1: 20238634..20239785 (+ 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_1 | g11996 | g11996.t6 | TSS | g11996.t6 | 20233096 | 20233096 |
| chr_1 | g11996 | g11996.t6 | isoform | g11996.t6 | 20233202 | 20239052 |
| chr_1 | g11996 | g11996.t6 | exon | g11996.t6.exon1 | 20233202 | 20233277 |
| chr_1 | g11996 | g11996.t6 | exon | g11996.t6.exon2 | 20235508 | 20235638 |
| chr_1 | g11996 | g11996.t6 | cds | g11996.t6.CDS1 | 20235509 | 20235638 |
| chr_1 | g11996 | g11996.t6 | exon | g11996.t6.exon3 | 20237916 | 20238086 |
| chr_1 | g11996 | g11996.t6 | cds | g11996.t6.CDS2 | 20237916 | 20238086 |
| chr_1 | g11996 | g11996.t6 | exon | g11996.t6.exon4 | 20238155 | 20238244 |
| chr_1 | g11996 | g11996.t6 | cds | g11996.t6.CDS3 | 20238155 | 20238244 |
| chr_1 | g11996 | g11996.t6 | exon | g11996.t6.exon5 | 20238306 | 20238487 |
| chr_1 | g11996 | g11996.t6 | cds | g11996.t6.CDS4 | 20238306 | 20238487 |
| chr_1 | g11996 | g11996.t6 | exon | g11996.t6.exon6 | 20238550 | 20238657 |
| chr_1 | g11996 | g11996.t6 | cds | g11996.t6.CDS5 | 20238550 | 20238657 |
| chr_1 | g11996 | g11996.t6 | exon | g11996.t6.exon7 | 20238718 | 20238886 |
| chr_1 | g11996 | g11996.t6 | cds | g11996.t6.CDS6 | 20238718 | 20238886 |
| chr_1 | g11996 | g11996.t6 | exon | g11996.t6.exon8 | 20238949 | 20239052 |
| chr_1 | g11996 | g11996.t6 | cds | g11996.t6.CDS7 | 20238949 | 20239052 |
| chr_1 | g11996 | g11996.t6 | TTS | g11996.t6 | 20239474 | 20239474 |
Sequences
>g11996.t6 Gene=g11996 Length=1031
ATGACTCATGAAAGGAAACATGTTAAAGCAACGGAAAAAACTGAAATGTCTTATCTATTA
GACAAAAATGGGAAGAGATGGCCGATAAAAATAAACAGGGTGAATACTATTCGAGACCAG
CCAAAATGGGCAAATGGGAAGGCTTCAAACATTTTCTTTGGAATAGTGAAACTAGTGAGC
TGTTAGGACGAACAGGAGGAAGTTGGGCTAAAATTCTATTATTCTACGTACTCTTCTATG
CTGCCCTTGCCGGTTTTTTTGCTGCTATCTTTGCTGTATTTTATCAAACACTTGATGCCA
ACAAACCGAAATGGCTTTTGGATAATGGTTTGATAGGCTCAAATCCCGGACTCGGATTTC
GTCCAATGCCTCCAGAGTCGAATGTAGAGAGCACACTCGTGTGGTTCGAAGCTTCAAAAG
AGTCTAACATTGAATATTGGATTTCTGCCCTTGATGAATTCTTGGAAGTTTATAAGAAAG
AAGATCGAGAAGTCGAGAAGAATCGAATGGAATGTAATGCTCAAAATCATCCAAAAGATG
GAAAAGTTTGTCGTGTCGATGTATCACCGAATGCATTTGGCGCGTGTACAAAGGAAAATC
AGTATGGTTATGCGAAAGCCTCACCATGTATTTTCCTCAAGCTAAATAAGATTTATGGAT
GGAATCCAGAATATTTTAATAGATCAAGTGAGCTGCCTTCAAAAATGCCAGAAGATTTGC
AAGAACAAATCAAGGGTATTCCAGAAGATGATAAAAATCATGAAATGATTTGGGTCTCAT
GTGAGGGTGAAAATCCTGCTGATATTGAAAATTTGGGACCTATTAACTACATACCTAAAC
GTGGATTCCCAGGATATTATTTCCCATTCATGAATCAAAAAGGTTATTTGCCACCAGTTT
TGGCAATCAATTTTGAGCGTCCAAAAACTGGTGTACTCATTAATATTGAATGCAAAGCAT
GGGCACGCAACATTATGCACGACAGAGCTGAACGTCGAGGATCAGTTCATTTTGAATTGA
TGGTTGATTAA
>g11996.t6 Gene=g11996 Length=317
MADKNKQGEYYSRPAKMGKWEGFKHFLWNSETSELLGRTGGSWAKILLFYVLFYAALAGF
FAAIFAVFYQTLDANKPKWLLDNGLIGSNPGLGFRPMPPESNVESTLVWFEASKESNIEY
WISALDEFLEVYKKEDREVEKNRMECNAQNHPKDGKVCRVDVSPNAFGACTKENQYGYAK
ASPCIFLKLNKIYGWNPEYFNRSSELPSKMPEDLQEQIKGIPEDDKNHEMIWVSCEGENP
ADIENLGPINYIPKRGFPGYYFPFMNQKGYLPPVLAINFERPKTGVLINIECKAWARNIM
HDRAERRGSVHFELMVD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11996.t6 | Gene3D | G3DSA:2.60.40.1660 | Na | 14 | 317 | 9.5E-104 |
| 2 | g11996.t6 | PANTHER | PTHR11523:SF46 | SODIUM/POTASSIUM-TRANSPORTING ATPASE SUBUNIT BETA-2 | 8 | 317 | 4.3E-123 |
| 3 | g11996.t6 | PANTHER | PTHR11523 | SODIUM/POTASSIUM-DEPENDENT ATPASE BETA SUBUNIT | 8 | 317 | 4.3E-123 |
| 1 | g11996.t6 | Pfam | PF00287 | Sodium / potassium ATPase beta chain | 17 | 312 | 4.8E-85 |
| 7 | g11996.t6 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 46 | - |
| 9 | g11996.t6 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 47 | 69 | - |
| 8 | g11996.t6 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 70 | 317 | - |
| 5 | g11996.t6 | ProSitePatterns | PS00390 | Sodium and potassium ATPases beta subunits signature 1. | 23 | 43 | - |
| 4 | g11996.t6 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 46 | 68 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0006813 | potassium ion transport | BP |
| GO:0005890 | sodium:potassium-exchanging ATPase complex | CC |
| GO:0006814 | sodium ion transport | BP |
KEGG
Orthology
- This transcript has been annotated with K01540 (sodium/potassium-transporting ATPase subunit beta)
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.
