General information for g2844.t1
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.t1 | isoform | g2844.t1 | 20527778 | 20553616 |
| chr_3 | g2844 | g2844.t1 | exon | g2844.t1.exon1 | 20527778 | 20528542 |
| chr_3 | g2844 | g2844.t1 | cds | g2844.t1.CDS1 | 20527778 | 20528542 |
| chr_3 | g2844 | g2844.t1 | exon | g2844.t1.exon2 | 20528638 | 20528664 |
| chr_3 | g2844 | g2844.t1 | cds | g2844.t1.CDS2 | 20528638 | 20528664 |
| chr_3 | g2844 | g2844.t1 | exon | g2844.t1.exon3 | 20542226 | 20542359 |
| chr_3 | g2844 | g2844.t1 | cds | g2844.t1.CDS3 | 20542226 | 20542359 |
| chr_3 | g2844 | g2844.t1 | exon | g2844.t1.exon4 | 20542578 | 20542794 |
| chr_3 | g2844 | g2844.t1 | cds | g2844.t1.CDS4 | 20542578 | 20542794 |
| chr_3 | g2844 | g2844.t1 | exon | g2844.t1.exon5 | 20544920 | 20545015 |
| chr_3 | g2844 | g2844.t1 | cds | g2844.t1.CDS5 | 20544920 | 20545015 |
| chr_3 | g2844 | g2844.t1 | exon | g2844.t1.exon6 | 20545639 | 20545955 |
| chr_3 | g2844 | g2844.t1 | cds | g2844.t1.CDS6 | 20545639 | 20545955 |
| chr_3 | g2844 | g2844.t1 | exon | g2844.t1.exon7 | 20546222 | 20546326 |
| chr_3 | g2844 | g2844.t1 | cds | g2844.t1.CDS7 | 20546222 | 20546326 |
| chr_3 | g2844 | g2844.t1 | exon | g2844.t1.exon8 | 20548996 | 20549131 |
| chr_3 | g2844 | g2844.t1 | cds | g2844.t1.CDS8 | 20548996 | 20549131 |
| chr_3 | g2844 | g2844.t1 | exon | g2844.t1.exon9 | 20550508 | 20550618 |
| chr_3 | g2844 | g2844.t1 | cds | g2844.t1.CDS9 | 20550508 | 20550618 |
| chr_3 | g2844 | g2844.t1 | exon | g2844.t1.exon10 | 20550825 | 20550952 |
| chr_3 | g2844 | g2844.t1 | cds | g2844.t1.CDS10 | 20550825 | 20550952 |
| chr_3 | g2844 | g2844.t1 | exon | g2844.t1.exon11 | 20551328 | 20551397 |
| chr_3 | g2844 | g2844.t1 | cds | g2844.t1.CDS11 | 20551328 | 20551397 |
| chr_3 | g2844 | g2844.t1 | exon | g2844.t1.exon12 | 20551596 | 20551697 |
| chr_3 | g2844 | g2844.t1 | cds | g2844.t1.CDS12 | 20551596 | 20551697 |
| chr_3 | g2844 | g2844.t1 | exon | g2844.t1.exon13 | 20552228 | 20552424 |
| chr_3 | g2844 | g2844.t1 | cds | g2844.t1.CDS13 | 20552228 | 20552424 |
| chr_3 | g2844 | g2844.t1 | exon | g2844.t1.exon14 | 20553337 | 20553616 |
| chr_3 | g2844 | g2844.t1 | cds | g2844.t1.CDS14 | 20553337 | 20553616 |
| chr_3 | g2844 | g2844.t1 | TSS | g2844.t1 | NA | NA |
| chr_3 | g2844 | g2844.t1 | TTS | g2844.t1 | NA | NA |
Sequences
>g2844.t1 Gene=g2844 Length=2685
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
CTATGGATAATTGCATCGTGGACGTTGCGGCAGTGTGAGCGGTTTCATGATGACGAGCAT
GCCAATTTATTGAACTCAATGTGGCTGATTGCTATAACATTCTTAAGTGTTGGATTCGGT
GACATTGTTCCTAATACATATTGTGGACGTGGCATAGCTGTCAGTACGGGCATTATGGGC
GCCGGTTGTACTGCTCTTTTGGTTGCTGTCGTTTCACGAAAATTAGAATTGACGAGAGCT
GAAAAGCACGTTCATAATTTTATGATGGATACTCAACTTACAAAGCGATTGAAAAATGCC
GCAGCAAATGTTTTACGCGAAACATGGCTCATATACAAACATACAAGGCTCGTGAAGCGT
GTCAATCCTGGACGAGTGCGAACACATCAAAGAAAGTTTCTTCTTGCAATTTACGCATTG
AGAAAAGTCAAGATGGATCAACGAAAATTAATGGATAATGCAAATACAATAACAGATATG
GCGAAGACATCTAACACAGTGTATGAAATTGTTTCGGATATGTCATCGCGTCAAGATGCT
TTAGAAGAGAGATTATCTGGTCTTGAAGAGAAATTGCAAATGTTACAAGAACAACTCGAA
TCTCTTCCTGATGTATTGTCGCGATGTTTAACGCAACATCAAGATCGAGTAGAGCAACGC
CGTAATTTCCTTCATCCGGATATGGCAAATTCTAGTTCATCGCCTCAAGTTGGTATGTCT
TTGCCTCCACCTCCACCATTGCTACCATCTGCACCAATAGGTTCGCCTTTATTTCCACAT
TCTAGTATCCCTTATAGAAGCGCACTATCGTCAAACACAAACAATTCAGCAGTTTCTTAT
CAATGGCCGCCAAGTCCAATATTGCCATCAATATCCAGAAGAACACCTAATTTGATACCC
GAAACTTTCTTGCCAACATCAAATGAGCACAATAATACACTTAATAGCAATCACACGACT
GCTCTAGACCAAAATAATGAATTAGTGCAACAACAGCGACAACAGAGTGAATCTGCCGGT
TCAACAGTCGTAATACATAGCACTAATAATCGTGCTAATAGCTGA
>g2844.t1 Gene=g2844 Length=894
MSLQQEQQNMEVESVGSKTLISSEESSKLLAETAPVSLPSGKNNNNNNAAKLQKAHSYSA
SNGPTNTAATSARASSSSILVTQHSLSSGTTNKPVLIRQDRTSTYLTSPQLSILGTSASE
ETSDDDYSKSIAYQLLPSKSSTEGCRTCHKRERRSSASPSSVIYMPRSSSKESLSLRSPG
STVQLQSSSSVIPPVLITGSPTNASTSSPRIIRQSSQPESSTLSCCNNACSHAQQTSSLR
QLRDPIAGIATETLRFNGAMRFKQLRKPVSTLSIPSMKTGVGNRETNREAACNEEAGLAL
VDVRSEYPRYMEERGLGGTFKESQDKTGTKQKPNVGYRLGRRKALFEKRKRISDYALVMG
MFGIIVMVIENELSSAGVYTKSDFYSYALKTLISVSTVILLGLIVAYHALEVQLFMIDNC
ADDWRIAMTWQRMAQIGLELLICAIHPIPGDNTFEWKTKLSNKNKEIKSEIVPLDVALSL
PMFFRLYLICRVMLLHSKLFTDASSRSIGALNRINFNTRFVLKTLMTICPGTVLLVFMVS
LWIIASWTLRQCERFHDDEHANLLNSMWLIAITFLSVGFGDIVPNTYCGRGIAVSTGIMG
AGCTALLVAVVSRKLELTRAEKHVHNFMMDTQLTKRLKNAAANVLRETWLIYKHTRLVKR
VNPGRVRTHQRKFLLAIYALRKVKMDQRKLMDNANTITDMAKTSNTVYEIVSDMSSRQDA
LEERLSGLEEKLQMLQEQLESLPDVLSRCLTQHQDRVEQRRNFLHPDMANSSSSPQVGMS
LPPPPPLLPSAPIGSPLFPHSSIPYRSALSSNTNNSAVSYQWPPSPILPSISRRTPNLIP
ETFLPTSNEHNNTLNSNHTTALDQNNELVQQQRQQSESAGSTVVIHSTNNRANS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g2844.t1 | Coils | Coil | Coil | 711 | 745 | - |
| 10 | g2844.t1 | Gene3D | G3DSA:1.10.287.70 | - | 515 | 613 | 2.2E-14 |
| 11 | g2844.t1 | Gene3D | G3DSA:1.10.287.70 | - | 614 | 710 | 6.3E-46 |
| 32 | g2844.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 27 | - |
| 35 | g2844.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 142 | 187 | - |
| 34 | g2844.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 157 | 187 | - |
| 33 | g2844.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 864 | 894 | - |
| 4 | g2844.t1 | PANTHER | PTHR10153 | SMALL CONDUCTANCE CALCIUM-ACTIVATED POTASSIUM CHANNEL | 316 | 757 | 7.2E-236 |
| 5 | g2844.t1 | PANTHER | PTHR10153:SF43 | SMALL CONDUCTANCE CALCIUM-ACTIVATED POTASSIUM CHANNEL PROTEIN 2 | 316 | 757 | 7.2E-236 |
| 7 | g2844.t1 | PRINTS | PR01451 | Calcium-activated SK potassium channel signature | 338 | 358 | 7.6E-15 |
| 6 | g2844.t1 | PRINTS | PR01451 | Calcium-activated SK potassium channel signature | 439 | 457 | 7.6E-15 |
| 1 | g2844.t1 | Pfam | PF03530 | Calcium-activated SK potassium channel | 338 | 451 | 1.2E-47 |
| 3 | g2844.t1 | Pfam | PF07885 | Ion channel | 538 | 615 | 2.5E-12 |
| 2 | g2844.t1 | Pfam | PF02888 | Calmodulin binding domain | 630 | 703 | 5.9E-35 |
| 13 | g2844.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 351 | - |
| 22 | g2844.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 352 | 369 | - |
| 18 | g2844.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 370 | 383 | - |
| 25 | g2844.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 384 | 407 | - |
| 16 | g2844.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 408 | 470 | - |
| 21 | g2844.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 471 | 494 | - |
| 17 | g2844.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 495 | 524 | - |
| 24 | g2844.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 525 | 549 | - |
| 14 | g2844.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 550 | 560 | - |
| 23 | g2844.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 561 | 580 | - |
| 19 | g2844.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 581 | 591 | - |
| 20 | g2844.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 592 | 612 | - |
| 15 | g2844.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 613 | 894 | - |
| 31 | g2844.t1 | SMART | SM01053 | CaMBD_2 | 630 | 706 | 6.3E-48 |
| 8 | g2844.t1 | SUPERFAMILY | SSF81324 | Voltage-gated potassium channels | 485 | 655 | 6.67E-25 |
| 9 | g2844.t1 | SUPERFAMILY | SSF81327 | Small-conductance potassium channel | 613 | 703 | 9.81E-40 |
| 27 | g2844.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 352 | 369 | - |
| 26 | g2844.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 384 | 406 | - |
| 30 | g2844.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 524 | 546 | - |
| 29 | g2844.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 561 | 583 | - |
| 28 | g2844.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 590 | 612 | - |
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.
