General information for g2845.t3
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 g2845 is located on chr_3: 20562720..20597223 (- 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 | g2845 | g2845.t3 | isoform | g2845.t3 | 20562720 | 20576512 |
| chr_3 | g2845 | g2845.t3 | exon | g2845.t3.exon1 | 20562720 | 20562830 |
| chr_3 | g2845 | g2845.t3 | cds | g2845.t3.CDS1 | 20562720 | 20562830 |
| chr_3 | g2845 | g2845.t3 | exon | g2845.t3.exon2 | 20562990 | 20563125 |
| chr_3 | g2845 | g2845.t3 | cds | g2845.t3.CDS2 | 20562990 | 20563125 |
| chr_3 | g2845 | g2845.t3 | exon | g2845.t3.exon3 | 20570793 | 20570897 |
| chr_3 | g2845 | g2845.t3 | cds | g2845.t3.CDS3 | 20570793 | 20570897 |
| chr_3 | g2845 | g2845.t3 | exon | g2845.t3.exon4 | 20570960 | 20571276 |
| chr_3 | g2845 | g2845.t3 | cds | g2845.t3.CDS4 | 20570960 | 20571276 |
| chr_3 | g2845 | g2845.t3 | exon | g2845.t3.exon5 | 20572109 | 20572204 |
| chr_3 | g2845 | g2845.t3 | cds | g2845.t3.CDS5 | 20572109 | 20572204 |
| chr_3 | g2845 | g2845.t3 | exon | g2845.t3.exon6 | 20576284 | 20576512 |
| chr_3 | g2845 | g2845.t3 | cds | g2845.t3.CDS6 | 20576284 | 20576508 |
| chr_3 | g2845 | g2845.t3 | TSS | g2845.t3 | NA | NA |
| chr_3 | g2845 | g2845.t3 | TTS | g2845.t3 | NA | NA |
Sequences
>g2845.t3 Gene=g2845 Length=994
GTACATGGAGGAGCGCGGCTTAGGTGGTGGTGTATATAAAAGTGTATCAGGCTCACAAGA
CAAATCGAACGCCAAACAGAAACCAAATGTTGGCTATCGATTGGGTAGACGAAAAGCACT
CTTTGAAAAAAGAAAGCGCATCAGTGACTATGCCCTTGTGATGGGAATGTTCGGAATAAT
TGTTATGGTTATTGAAAATGAATTAAGTAGTGCCGGTGTCTATACGAAGGCGTCATTTTA
TTCAACTGCATTAAAAACGCTGATATCTGTATCGACTGTGATTTTACTTGGTCTTATAGT
TGCTTATCATGCTTTGGAAGTTCAGCTGTTTATGACAGATAATTGCGCAGACGATTGGCG
TATCGCAATGACGTGGCAACGTATCAGTCAAATAGGATTAGAATTACTTATATGTGCAAT
ACATCCTATTCCTGGCGAGTACTACTTTCGTTGGGAAACAAAATTATCAAATAAAAATAA
AGCTCCTGGCTTTGCTGATGTGCCATTCGATGTGGTGCTATCATTGCCAATGTTTCTTCG
TTTGTACCTGATCTGTCGTGTAATGCTACTACATTCGAAACTTTTTACTGACGCTTCATC
GCGAAGTATAGGTGCATTAAATCGAATTAATTTTAACACTAGATTTGTTTTCAAGACATT
AATGACAATATGCCCTGGCACGGTATTATTAGTATTCATGGTATCACTATGGATAATAGC
ATCGTGGACGTTGCGGCAATGTGAAAGGTTTCATGATGACGAGCATGCCAATTTATTGAA
CTCAATGTGGCTGATTGCTATAACATTCTTAAGTGTTGGATTCGGTGACATTGTTCCTAA
TACATATTGTGGACGTGGCATTGCTGTCAGTACGGGCATTATGGGCGCCGGCTGTACTGC
ATTCTTAGTAGCACTTTTGTCAAGGAAATTGGAATTGACAAGAGCGGAAAAACATGTGCA
TAATTTTATGATGGACACTCAGCTCACAAAGCGG
>g2845.t3 Gene=g2845 Length=330
MEERGLGGGVYKSVSGSQDKSNAKQKPNVGYRLGRRKALFEKRKRISDYALVMGMFGIIV
MVIENELSSAGVYTKASFYSTALKTLISVSTVILLGLIVAYHALEVQLFMTDNCADDWRI
AMTWQRISQIGLELLICAIHPIPGEYYFRWETKLSNKNKAPGFADVPFDVVLSLPMFLRL
YLICRVMLLHSKLFTDASSRSIGALNRINFNTRFVFKTLMTICPGTVLLVFMVSLWIIAS
WTLRQCERFHDDEHANLLNSMWLIAITFLSVGFGDIVPNTYCGRGIAVSTGIMGAGCTAF
LVALLSRKLELTRAEKHVHNFMMDTQLTKR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g2845.t3 | Gene3D | G3DSA:1.10.287.70 | - | 207 | 307 | 1.0E-14 |
| 9 | g2845.t3 | Gene3D | G3DSA:1.10.287.70 | - | 308 | 330 | 1.4E-10 |
| 29 | g2845.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 26 | - |
| 3 | g2845.t3 | PANTHER | PTHR10153 | SMALL CONDUCTANCE CALCIUM-ACTIVATED POTASSIUM CHANNEL | 5 | 330 | 3.6E-186 |
| 4 | g2845.t3 | PANTHER | PTHR10153:SF43 | SMALL CONDUCTANCE CALCIUM-ACTIVATED POTASSIUM CHANNEL PROTEIN 2 | 5 | 330 | 3.6E-186 |
| 5 | g2845.t3 | PRINTS | PR01451 | Calcium-activated SK potassium channel signature | 32 | 52 | 1.1E-16 |
| 6 | g2845.t3 | PRINTS | PR01451 | Calcium-activated SK potassium channel signature | 133 | 151 | 1.1E-16 |
| 1 | g2845.t3 | Pfam | PF03530 | Calcium-activated SK potassium channel | 32 | 145 | 1.2E-48 |
| 2 | g2845.t3 | Pfam | PF07885 | Ion channel | 232 | 309 | 3.9E-12 |
| 12 | g2845.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 45 | - |
| 22 | g2845.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 46 | 63 | - |
| 16 | g2845.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 64 | 82 | - |
| 20 | g2845.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 83 | 104 | - |
| 10 | g2845.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 105 | 165 | - |
| 21 | g2845.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 166 | 188 | - |
| 14 | g2845.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 189 | 218 | - |
| 18 | g2845.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 219 | 243 | - |
| 11 | g2845.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 244 | 254 | - |
| 17 | g2845.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 255 | 274 | - |
| 15 | g2845.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 275 | 285 | - |
| 19 | g2845.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 286 | 306 | - |
| 13 | g2845.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 307 | 330 | - |
| 7 | g2845.t3 | SUPERFAMILY | SSF81324 | Voltage-gated potassium channels | 178 | 327 | 2.22E-22 |
| 28 | g2845.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 46 | 63 | - |
| 27 | g2845.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 78 | 100 | - |
| 23 | g2845.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 167 | 189 | - |
| 24 | g2845.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 221 | 243 | - |
| 25 | g2845.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 255 | 277 | - |
| 26 | g2845.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 287 | 306 | - |
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