General information for g2844.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 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.t3 | isoform | g2844.t3 | 20527778 | 20553616 |
| chr_3 | g2844 | g2844.t3 | exon | g2844.t3.exon1 | 20527778 | 20528542 |
| chr_3 | g2844 | g2844.t3 | cds | g2844.t3.CDS1 | 20527778 | 20528542 |
| chr_3 | g2844 | g2844.t3 | exon | g2844.t3.exon2 | 20528638 | 20528664 |
| chr_3 | g2844 | g2844.t3 | cds | g2844.t3.CDS2 | 20528638 | 20528664 |
| chr_3 | g2844 | g2844.t3 | exon | g2844.t3.exon3 | 20542226 | 20542359 |
| chr_3 | g2844 | g2844.t3 | cds | g2844.t3.CDS3 | 20542226 | 20542359 |
| chr_3 | g2844 | g2844.t3 | exon | g2844.t3.exon4 | 20542578 | 20542794 |
| chr_3 | g2844 | g2844.t3 | cds | g2844.t3.CDS4 | 20542578 | 20542794 |
| chr_3 | g2844 | g2844.t3 | exon | g2844.t3.exon5 | 20544920 | 20545015 |
| chr_3 | g2844 | g2844.t3 | cds | g2844.t3.CDS5 | 20544920 | 20545015 |
| chr_3 | g2844 | g2844.t3 | exon | g2844.t3.exon6 | 20545639 | 20545955 |
| chr_3 | g2844 | g2844.t3 | cds | g2844.t3.CDS6 | 20545639 | 20545955 |
| chr_3 | g2844 | g2844.t3 | exon | g2844.t3.exon7 | 20546222 | 20546326 |
| chr_3 | g2844 | g2844.t3 | cds | g2844.t3.CDS7 | 20546222 | 20546326 |
| chr_3 | g2844 | g2844.t3 | exon | g2844.t3.exon8 | 20548659 | 20548794 |
| chr_3 | g2844 | g2844.t3 | cds | g2844.t3.CDS8 | 20548659 | 20548794 |
| chr_3 | g2844 | g2844.t3 | exon | g2844.t3.exon9 | 20549012 | 20549131 |
| chr_3 | g2844 | g2844.t3 | cds | g2844.t3.CDS9 | 20549012 | 20549131 |
| chr_3 | g2844 | g2844.t3 | exon | g2844.t3.exon10 | 20550508 | 20550618 |
| chr_3 | g2844 | g2844.t3 | cds | g2844.t3.CDS10 | 20550508 | 20550618 |
| chr_3 | g2844 | g2844.t3 | exon | g2844.t3.exon11 | 20550825 | 20550952 |
| chr_3 | g2844 | g2844.t3 | cds | g2844.t3.CDS11 | 20550825 | 20550952 |
| chr_3 | g2844 | g2844.t3 | exon | g2844.t3.exon12 | 20551328 | 20551397 |
| chr_3 | g2844 | g2844.t3 | cds | g2844.t3.CDS12 | 20551328 | 20551397 |
| chr_3 | g2844 | g2844.t3 | exon | g2844.t3.exon13 | 20551596 | 20551697 |
| chr_3 | g2844 | g2844.t3 | cds | g2844.t3.CDS13 | 20551596 | 20551697 |
| chr_3 | g2844 | g2844.t3 | exon | g2844.t3.exon14 | 20552228 | 20552424 |
| chr_3 | g2844 | g2844.t3 | cds | g2844.t3.CDS14 | 20552228 | 20552424 |
| chr_3 | g2844 | g2844.t3 | exon | g2844.t3.exon15 | 20552681 | 20552743 |
| chr_3 | g2844 | g2844.t3 | cds | g2844.t3.CDS15 | 20552681 | 20552743 |
| chr_3 | g2844 | g2844.t3 | exon | g2844.t3.exon16 | 20553349 | 20553616 |
| chr_3 | g2844 | g2844.t3 | cds | g2844.t3.CDS16 | 20553349 | 20553616 |
| chr_3 | g2844 | g2844.t3 | TSS | g2844.t3 | NA | NA |
| chr_3 | g2844 | g2844.t3 | TTS | g2844.t3 | NA | NA |
Sequences
>g2844.t3 Gene=g2844 Length=2856
ATGTCGCTGCAACAAGAACAGCAGAATATGGAAGTAGAGAGTGTTGGAAGCAAAACTTTA
ATCTCAAGTGAAGAATCGTCAAAACTTCTTGCCGAGACAGCACCGGTATCTTTGCCAAGT
GGTAAAAATAATAATAATAACAATGCCGCAAAGCTTCAAAAGGCACACTCATACAGTGCT
TCAAATGGGCCAACAAATACGGCAGCAACATCTGCCAGAGCATCTTCTTCCTCAATTCTC
GTGACACAGCATTCGCTTTCATCGGGAACAACAAATAAGCCGGTACTCATTCGTCAAGAC
CGTACTTCAACATATCTCACGAGTCCTCAACTGTCAATTCTCGGAACATCAGCCTCAGAA
GAGACGTCAGATGACGACTATTCAAAATCTATTGCATATCAGCTGTTGCCAAGCAAGTCA
AGCACTGAAGGTTGTCGCACGTGTCATAAACGTGAAAGACGTTCTTCTGCATCTCCCTCA
TCTGTGATTTATATGCCTCGTTCTTCATCAAAAGAAAGTCTCAGTCTAAGAAGTCCAGGT
TCGACTGTTCAACTACAATCTTCTTCTTCAGTAATTCCGCCTGTACTCATTACTGGTTCG
CCAACAAATGCAAGCACATCGTCGCCGCGAATTATTCGCCAAAGCTCACAACCAGAGTCA
AGTACGTTATCATGCTGTAACAATGCTTGTAGTCATGCGCAACAAACGTCCTCTTTACGT
CAACTACGAGATCCGATAGCTGGTATTGCGACTGAAACATTAAGGTTTAACGGAGCAATG
CGATTCAAACAGCTTCGAAAGCCTGTATCCACTCTCTCGATACCTTCGATGAAAACTGGC
GTTGGTAATCGAGAGACCAACAGAGAAGCTGCATGCAACGAAGAAGCGGGTTTGGCGCTT
GTTGATGTTCGATCAGAATATCCTAGGTACATGGAGGAGCGCGGCTTAGGTGGCACCTTT
AAAGAGTCACAAGATAAAACGGGCACAAAACAAAAGCCAAATGTCGGCTATCGATTGGGA
CGACGAAAAGCACTCTTTGAAAAGCGAAAACGCATCAGTGACTACGCGCTTGTTATGGGA
ATGTTCGGTATAATTGTTATGGTTATTGAAAATGAGTTGAGTAGTGCTGGTGTCTATACG
AAGAGTGATTTTTATTCATATGCATTAAAAACTTTGATATCTGTATCGACTGTGATTTTA
CTGGGACTTATTGTAGCTTATCATGCTTTAGAAGTGCAGTTATTCATGATTGATAATTGC
GCGGACGATTGGCGCATCGCAATGACATGGCAAAGAATGGCACAAATAGGTCTAGAATTA
CTTATATGTGCAATACATCCCATTCCAGGAGACAACACATTCGAATGGAAGACAAAATTA
TCAAATAAAAACAAAGAAATTAAAAGTGAAATCGTTCCATTGGATGTAGCTCTCTCATTG
CCAATGTTTTTCCGTTTGTACCTGATCTGTCGTGTTATGCTGCTACATTCGAAACTTTTT
ACTGATGCTTCATCGCGAAGTATAGGTGCATTAAATCGAATTAATTTTAATACTAGATTT
GTTTTGAAAACATTAATGACAATATGCCCTGGCACGGTATTATTAGTATTTATGGTTTCG
CTATGGATAATTGCATCGTGGACGTTGCGGCAGTGTGAGCGATTTCACGATGAAGAGCAT
GCAAATTTGCTCAATTCAATGTGGTTGACAGCAATAACGTTTCTCTGTGTTGGATATGGT
GATATTGTGCCGAACACTTATTGCGGTCGAGGAATTGCAATTACTTGTGGTGCAATGCAT
GCCAATTTATTGAACTCAATGTGGCTGATTGCTATAACATTCTTAAGTGTTGGATTCGGT
GACATTGTTCCTAATACATATTGTGGACGTGGCATAGCTGTCAGTACGGGCATTATGGGC
GCCGGTTGTACTGCTCTTTTGGTTGCTGTCGTTTCACGAAAATTAGAATTGACGAGAGCT
GAAAAGCACGTTCATAATTTTATGATGGATACTCAACTTACAAAGCGATTGAAAAATGCC
GCAGCAAATGTTTTACGCGAAACATGGCTCATATACAAACATACAAGGCTCGTGAAGCGT
GTCAATCCTGGACGAGTGCGAACACATCAAAGAAAGTTTCTTCTTGCAATTTACGCATTG
AGAAAAGTCAAGATGGATCAACGAAAATTAATGGATAATGCAAATACAATAACAGATATG
GCGAAGACATCTAACACAGTGTATGAAATTGTTTCGGATATGTCATCGCGTCAAGATGCT
TTAGAAGAGAGATTATCTGGTCTTGAAGAGAAATTGCAAATGTTACAAGAACAACTCGAA
TCTCTTCCTGATGTATTGTCGCGATGTTTAACGCAACATCAAGATCGAGTAGAGCAACGC
CGTAATTTCCTTCATCCGGATATGGCAAATTCTAGTTCATCGCCTCAAGTTGGTATGTCT
TTGCCTCCACCTCCACCATTGCTACCATCTGCACCAATAGGTTCGCCTTTATTTCCACAT
TCTAGCAACAGCAAAAACCCTCCCTTAGAAAATGAGACCAGCAATCAGGATTCATTGCAT
AATCAGCAAAGCGCACTATCGTCAAACACAAACAATTCAGCAGTTTCTTATCAATGGCCG
CCAAGTCCAATATTGCCATCAATATCCAGAAGAACACCTAATTTGATACCCGAAACTTTC
TTGCCAACATCAAATGAGCACAATAATACACTTAATAGCAATCACACGACTGCTCTAGAC
CAAAATAATGAATTAGTGCAACAACAGCGACAACAGAGTGAATCTGCCGGTTCAACAGTC
GTAATACATAGCACTAATAATCGTGCTAATAGCTGA
>g2844.t3 Gene=g2844 Length=951
MSLQQEQQNMEVESVGSKTLISSEESSKLLAETAPVSLPSGKNNNNNNAAKLQKAHSYSA
SNGPTNTAATSARASSSSILVTQHSLSSGTTNKPVLIRQDRTSTYLTSPQLSILGTSASE
ETSDDDYSKSIAYQLLPSKSSTEGCRTCHKRERRSSASPSSVIYMPRSSSKESLSLRSPG
STVQLQSSSSVIPPVLITGSPTNASTSSPRIIRQSSQPESSTLSCCNNACSHAQQTSSLR
QLRDPIAGIATETLRFNGAMRFKQLRKPVSTLSIPSMKTGVGNRETNREAACNEEAGLAL
VDVRSEYPRYMEERGLGGTFKESQDKTGTKQKPNVGYRLGRRKALFEKRKRISDYALVMG
MFGIIVMVIENELSSAGVYTKSDFYSYALKTLISVSTVILLGLIVAYHALEVQLFMIDNC
ADDWRIAMTWQRMAQIGLELLICAIHPIPGDNTFEWKTKLSNKNKEIKSEIVPLDVALSL
PMFFRLYLICRVMLLHSKLFTDASSRSIGALNRINFNTRFVLKTLMTICPGTVLLVFMVS
LWIIASWTLRQCERFHDEEHANLLNSMWLTAITFLCVGYGDIVPNTYCGRGIAITCGAMH
ANLLNSMWLIAITFLSVGFGDIVPNTYCGRGIAVSTGIMGAGCTALLVAVVSRKLELTRA
EKHVHNFMMDTQLTKRLKNAAANVLRETWLIYKHTRLVKRVNPGRVRTHQRKFLLAIYAL
RKVKMDQRKLMDNANTITDMAKTSNTVYEIVSDMSSRQDALEERLSGLEEKLQMLQEQLE
SLPDVLSRCLTQHQDRVEQRRNFLHPDMANSSSSPQVGMSLPPPPPLLPSAPIGSPLFPH
SSNSKNPPLENETSNQDSLHNQQSALSSNTNNSAVSYQWPPSPILPSISRRTPNLIPETF
LPTSNEHNNTLNSNHTTALDQNNELVQQQRQQSESAGSTVVIHSTNNRANS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g2844.t3 | Coils | Coil | Coil | 751 | 785 | - |
| 15 | g2844.t3 | Gene3D | G3DSA:1.10.287.70 | - | 515 | 599 | 1.6E-11 |
| 16 | g2844.t3 | Gene3D | G3DSA:1.10.287.70 | - | 600 | 655 | 3.6E-10 |
| 14 | g2844.t3 | Gene3D | G3DSA:1.10.287.70 | - | 656 | 750 | 6.9E-46 |
| 43 | g2844.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 27 | - |
| 46 | g2844.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 142 | 187 | - |
| 44 | g2844.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 157 | 187 | - |
| 45 | g2844.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 841 | 875 | - |
| 42 | g2844.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 920 | 951 | - |
| 6 | g2844.t3 | PANTHER | PTHR10153 | SMALL CONDUCTANCE CALCIUM-ACTIVATED POTASSIUM CHANNEL | 316 | 601 | 2.9E-247 |
| 8 | g2844.t3 | PANTHER | PTHR10153:SF43 | SMALL CONDUCTANCE CALCIUM-ACTIVATED POTASSIUM CHANNEL PROTEIN 2 | 316 | 601 | 2.9E-247 |
| 5 | g2844.t3 | PANTHER | PTHR10153 | SMALL CONDUCTANCE CALCIUM-ACTIVATED POTASSIUM CHANNEL | 601 | 797 | 2.9E-247 |
| 7 | g2844.t3 | PANTHER | PTHR10153:SF43 | SMALL CONDUCTANCE CALCIUM-ACTIVATED POTASSIUM CHANNEL PROTEIN 2 | 601 | 797 | 2.9E-247 |
| 10 | g2844.t3 | PRINTS | PR01451 | Calcium-activated SK potassium channel signature | 338 | 358 | 8.5E-15 |
| 9 | g2844.t3 | PRINTS | PR01451 | Calcium-activated SK potassium channel signature | 439 | 457 | 8.5E-15 |
| 1 | g2844.t3 | Pfam | PF03530 | Calcium-activated SK potassium channel | 338 | 451 | 1.3E-47 |
| 3 | g2844.t3 | Pfam | PF07885 | Ion channel | 538 | 594 | 2.4E-8 |
| 4 | g2844.t3 | Pfam | PF07885 | Ion channel | 601 | 655 | 4.1E-10 |
| 2 | g2844.t3 | Pfam | PF02888 | Calmodulin binding domain | 670 | 743 | 6.4E-35 |
| 20 | g2844.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 351 | - |
| 33 | g2844.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 352 | 369 | - |
| 26 | g2844.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 370 | 388 | - |
| 31 | g2844.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 389 | 410 | - |
| 21 | g2844.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 411 | 429 | - |
| 30 | g2844.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 430 | 448 | - |
| 23 | g2844.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 449 | 481 | - |
| 28 | g2844.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 482 | 500 | - |
| 18 | g2844.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 501 | 519 | - |
| 32 | g2844.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 520 | 545 | - |
| 24 | g2844.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 546 | 564 | - |
| 34 | g2844.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 565 | 582 | - |
| 19 | g2844.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 583 | 602 | - |
| 29 | g2844.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 603 | 620 | - |
| 25 | g2844.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 621 | 631 | - |
| 27 | g2844.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 632 | 652 | - |
| 22 | g2844.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 653 | 951 | - |
| 41 | g2844.t3 | SMART | SM01053 | CaMBD_2 | 670 | 746 | 6.3E-48 |
| 12 | g2844.t3 | SUPERFAMILY | SSF81324 | Voltage-gated potassium channels | 473 | 596 | 1.83E-16 |
| 11 | g2844.t3 | SUPERFAMILY | SSF81324 | Voltage-gated potassium channels | 600 | 656 | 6.12E-12 |
| 13 | g2844.t3 | SUPERFAMILY | SSF81327 | Small-conductance potassium channel | 653 | 743 | 1.06E-39 |
| 36 | g2844.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 352 | 369 | - |
| 35 | g2844.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 384 | 406 | - |
| 39 | g2844.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 525 | 547 | - |
| 37 | g2844.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 567 | 589 | - |
| 38 | g2844.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 601 | 623 | - |
| 40 | g2844.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 633 | 652 | - |
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:0015269 | calcium-activated potassium channel activity | MF |
| GO:0016021 | integral component of membrane | CC |
| GO:0005516 | calmodulin binding | MF |
| GO:0016286 | small conductance calcium-activated potassium channel activity | MF |
KEGG
Orthology
- This transcript has been annotated with K04944 (potassium intermediate/small conductance calcium-activated channel subfamily N member 3)
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. There were no conditions that were differentially expressed