General information for g2844.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Small conductance calcium-activated potassium channel protein.
Parent gene
- The parent gene g2844 is located on chr_3: 20535778..20553616 (+ 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_3 | g2844 | g2844.t4 | TSS | g2844.t4 | 20535696 | 20535696 |
| chr_3 | g2844 | g2844.t4 | isoform | g2844.t4 | 20535778 | 20545955 |
| chr_3 | g2844 | g2844.t4 | exon | g2844.t4.exon1 | 20535778 | 20536004 |
| chr_3 | g2844 | g2844.t4 | cds | g2844.t4.CDS1 | 20535990 | 20536004 |
| chr_3 | g2844 | g2844.t4 | exon | g2844.t4.exon2 | 20542226 | 20542359 |
| chr_3 | g2844 | g2844.t4 | cds | g2844.t4.CDS2 | 20542226 | 20542359 |
| chr_3 | g2844 | g2844.t4 | exon | g2844.t4.exon3 | 20542578 | 20542794 |
| chr_3 | g2844 | g2844.t4 | cds | g2844.t4.CDS3 | 20542578 | 20542794 |
| chr_3 | g2844 | g2844.t4 | exon | g2844.t4.exon4 | 20544920 | 20545015 |
| chr_3 | g2844 | g2844.t4 | cds | g2844.t4.CDS4 | 20544920 | 20545015 |
| chr_3 | g2844 | g2844.t4 | exon | g2844.t4.exon5 | 20545639 | 20545955 |
| chr_3 | g2844 | g2844.t4 | cds | g2844.t4.CDS5 | 20545639 | 20545953 |
| chr_3 | g2844 | g2844.t4 | TTS | g2844.t4 | NA | NA |
Sequences
>g2844.t4 Gene=g2844 Length=991
GAAACGTTGCGGCACAGAGTAACGATAAAAATAAGAGCAAAATTGAGAAGAAAAGAAAAT
AAATAAAAAAATTGTCGTGATATATTTGATGTAATTTTTGTGAAATATTATATTAGTTTT
ATTTTCGATTGTTCATAAGTGACGATTGAGAAAAGAAATTTGTTCTTTTGATTGTGTTAA
AGTGTTCATCTTCTGCTTGATGATTTAGTGACATGAGTTTGAGAATTCTTCGAAAGCCTG
TATCCACTCTCTCGATACCTTCGATGAAAACTGGCGTTGGTAATCGAGAGACCAACAGAG
AAGCTGCATGCAACGAAGAAGCGGGTTTGGCGCTTGTTGATGTTCGATCAGAATATCCTA
GGTACATGGAGGAGCGCGGCTTAGGTGGCACCTTTAAAGAGTCACAAGATAAAACGGGCA
CAAAACAAAAGCCAAATGTCGGCTATCGATTGGGACGACGAAAAGCACTCTTTGAAAAGC
GAAAACGCATCAGTGACTACGCGCTTGTTATGGGAATGTTCGGTATAATTGTTATGGTTA
TTGAAAATGAGTTGAGTAGTGCTGGTGTCTATACGAAGAGTGATTTTTATTCATATGCAT
TAAAAACTTTGATATCTGTATCGACTGTGATTTTACTGGGACTTATTGTAGCTTATCATG
CTTTAGAAGTGCAGTTATTCATGATTGATAATTGCGCGGACGATTGGCGCATCGCAATGA
CATGGCAAAGAATGGCACAAATAGGTCTAGAATTACTTATATGTGCAATACATCCCATTC
CAGGAGACAACACATTCGAATGGAAGACAAAATTATCAAATAAAAACAAAGAAATTAAAA
GTGAAATCGTTCCATTGGATGTAGCTCTCTCATTGCCAATGTTTTTCCGTTTGTACCTGA
TCTGTCGTGTTATGCTGCTACATTCGAAACTTTTTACTGATGCTTCATCGCGAAGTATAG
GTGCATTAAATCGAATTAATTTTAATACTAG
>g2844.t4 Gene=g2844 Length=259
MSLRILRKPVSTLSIPSMKTGVGNRETNREAACNEEAGLALVDVRSEYPRYMEERGLGGT
FKESQDKTGTKQKPNVGYRLGRRKALFEKRKRISDYALVMGMFGIIVMVIENELSSAGVY
TKSDFYSYALKTLISVSTVILLGLIVAYHALEVQLFMIDNCADDWRIAMTWQRMAQIGLE
LLICAIHPIPGDNTFEWKTKLSNKNKEIKSEIVPLDVALSLPMFFRLYLICRVMLLHSKL
FTDASSRSIGALNRINFNT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g2844.t4 | PANTHER | PTHR10153 | SMALL CONDUCTANCE CALCIUM-ACTIVATED POTASSIUM CHANNEL | 57 | 259 | 1.7E-99 |
| 3 | g2844.t4 | PANTHER | PTHR10153:SF43 | SMALL CONDUCTANCE CALCIUM-ACTIVATED POTASSIUM CHANNEL PROTEIN 2 | 57 | 259 | 1.7E-99 |
| 5 | g2844.t4 | PRINTS | PR01451 | Calcium-activated SK potassium channel signature | 79 | 99 | 8.8E-16 |
| 4 | g2844.t4 | PRINTS | PR01451 | Calcium-activated SK potassium channel signature | 180 | 198 | 8.8E-16 |
| 1 | g2844.t4 | Pfam | PF03530 | Calcium-activated SK potassium channel | 79 | 192 | 1.3E-48 |
| 10 | g2844.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 92 | - |
| 13 | g2844.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 93 | 110 | - |
| 11 | g2844.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 111 | 124 | - |
| 12 | g2844.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 125 | 148 | - |
| 9 | g2844.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 149 | 259 | - |
| 8 | g2844.t4 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 10 | - |
| 7 | g2844.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 93 | 110 | - |
| 6 | g2844.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 125 | 147 | - |
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:0016021 | integral component of membrane | CC |
| GO:0016286 | small conductance calcium-activated potassium channel 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. There were no conditions that were differentially expressed