General information for g2845.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 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.t1 | isoform | g2845.t1 | 20559905 | 20597223 |
| chr_3 | g2845 | g2845.t1 | exon | g2845.t1.exon1 | 20559905 | 20560115 |
| chr_3 | g2845 | g2845.t1 | cds | g2845.t1.CDS1 | 20559905 | 20560115 |
| chr_3 | g2845 | g2845.t1 | exon | g2845.t1.exon2 | 20561835 | 20562025 |
| chr_3 | g2845 | g2845.t1 | cds | g2845.t1.CDS2 | 20561835 | 20562025 |
| chr_3 | g2845 | g2845.t1 | exon | g2845.t1.exon3 | 20562086 | 20562257 |
| chr_3 | g2845 | g2845.t1 | cds | g2845.t1.CDS3 | 20562086 | 20562257 |
| chr_3 | g2845 | g2845.t1 | exon | g2845.t1.exon4 | 20562325 | 20562452 |
| chr_3 | g2845 | g2845.t1 | cds | g2845.t1.CDS4 | 20562325 | 20562452 |
| chr_3 | g2845 | g2845.t1 | exon | g2845.t1.exon5 | 20562720 | 20562830 |
| chr_3 | g2845 | g2845.t1 | cds | g2845.t1.CDS5 | 20562720 | 20562830 |
| chr_3 | g2845 | g2845.t1 | exon | g2845.t1.exon6 | 20562990 | 20563125 |
| chr_3 | g2845 | g2845.t1 | cds | g2845.t1.CDS6 | 20562990 | 20563125 |
| chr_3 | g2845 | g2845.t1 | exon | g2845.t1.exon7 | 20570793 | 20570897 |
| chr_3 | g2845 | g2845.t1 | cds | g2845.t1.CDS7 | 20570793 | 20570897 |
| chr_3 | g2845 | g2845.t1 | exon | g2845.t1.exon8 | 20570960 | 20571276 |
| chr_3 | g2845 | g2845.t1 | cds | g2845.t1.CDS8 | 20570960 | 20571276 |
| chr_3 | g2845 | g2845.t1 | exon | g2845.t1.exon9 | 20572109 | 20572204 |
| chr_3 | g2845 | g2845.t1 | cds | g2845.t1.CDS9 | 20572109 | 20572204 |
| chr_3 | g2845 | g2845.t1 | exon | g2845.t1.exon10 | 20576284 | 20576512 |
| chr_3 | g2845 | g2845.t1 | cds | g2845.t1.CDS10 | 20576284 | 20576512 |
| chr_3 | g2845 | g2845.t1 | exon | g2845.t1.exon11 | 20576593 | 20576720 |
| chr_3 | g2845 | g2845.t1 | cds | g2845.t1.CDS11 | 20576593 | 20576720 |
| chr_3 | g2845 | g2845.t1 | exon | g2845.t1.exon12 | 20596379 | 20596408 |
| chr_3 | g2845 | g2845.t1 | cds | g2845.t1.CDS12 | 20596379 | 20596408 |
| chr_3 | g2845 | g2845.t1 | exon | g2845.t1.exon13 | 20596471 | 20597223 |
| chr_3 | g2845 | g2845.t1 | cds | g2845.t1.CDS13 | 20596471 | 20597223 |
| chr_3 | g2845 | g2845.t1 | TSS | g2845.t1 | NA | NA |
| chr_3 | g2845 | g2845.t1 | TTS | g2845.t1 | NA | NA |
Sequences
>g2845.t1 Gene=g2845 Length=2607
ATGGAAAGTGCAGAAGAGAATGAAAAAATATTATCAACGACAGCAGCAAACACATCCTCA
GTGTCACCGGATGAAACATCAAAATTGCTGAGTGAGACAATCTCGAAAGTTTTTAATAAT
GGACCAACAGCTAATGGCAACCAACAACAACAGCAAGAGACCAACAATGCCACAACTGCT
ACCTCTACATCAACATCAACAAAGCCCATGCTTATACGACAGGATCGAACATATCTGGCG
AGTCCGCAATTATCCGTTACGGGTACTAATCTGGGCGGTTCGGAAGAGAGCACAGAGGAT
TATCGTAGTGACGAACAAAATCGCTCTGCTCCGGACATGCTACAGAATTTTAATCATCCT
CTCTCACCCTATCCTCAAATATCCGTCTCATCTGAAAATTATAATGGTGAAGAGAGTCAA
ATTCTTTCGCCATTGCCTACAACAAGGTGTCGAACGTGTCGACGTTCATCCACCTCACCT
ACCTCAATAATTTACCTTGATCGTTCAACATCAAAGGACAGCATTGTTCATGGTCATTTA
CGACCGCATTTGCTTGTTCATCATCATTCAACGACAATCCCACCTGTTTATGTCACTGGT
TCACCATCACGTTCATCACGAGTCATTCGACAAAGTTCACAGCCTGAGCCGAGTATGTAT
GGTCATTCAAGTCACACACATCAGACGGCCTCATTAAGTCAATTGAAAAACACAAGTGAT
ACAATAGCAGGAATTGCTGGTGAAGCCCTCAAGATGTCAGGAGGAATGCGACCATTTAAG
CAACTGCGAAAGCCTCAATCAACACAGTCAATTCCATCGATGAAAAGTGGCAATCGTGAC
AGCAACAAAGAAGCTGCATGCAATGAAGAGGCCGGTGTAGCACTTGTCAACGTTCACTCT
GAATATCCTAGGTACATGGAGGAGCGCGGCTTAGGTGGTGGTGTATATAAAAGTGTATCA
GGCTCACAAGACAAATCGAACGCCAAACAGAAACCAAATGTTGGCTATCGATTGGGTAGA
CGAAAAGCACTCTTTGAAAAAAGAAAGCGCATCAGTGACTATGCCCTTGTGATGGGAATG
TTCGGAATAATTGTTATGGTTATTGAAAATGAATTAAGTAGTGCCGGTGTCTATACGAAG
GCGTCATTTTATTCAACTGCATTAAAAACGCTGATATCTGTATCGACTGTGATTTTACTT
GGTCTTATAGTTGCTTATCATGCTTTGGAAGTTCAGCTGTTTATGACAGATAATTGCGCA
GACGATTGGCGTATCGCAATGACGTGGCAACGTATCAGTCAAATAGGATTAGAATTACTT
ATATGTGCAATACATCCTATTCCTGGCGAGTACTACTTTCGTTGGGAAACAAAATTATCA
AATAAAAATAAAGCTCCTGGCTTTGCTGATGTGCCATTCGATGTGGTGCTATCATTGCCA
ATGTTTCTTCGTTTGTACCTGATCTGTCGTGTAATGCTACTACATTCGAAACTTTTTACT
GACGCTTCATCGCGAAGTATAGGTGCATTAAATCGAATTAATTTTAACACTAGATTTGTT
TTCAAGACATTAATGACAATATGCCCTGGCACGGTATTATTAGTATTCATGGTATCACTA
TGGATAATAGCATCGTGGACGTTGCGGCAATGTGAAAGGTTTCATGATGACGAGCATGCC
AATTTATTGAACTCAATGTGGCTGATTGCTATAACATTCTTAAGTGTTGGATTCGGTGAC
ATTGTTCCTAATACATATTGTGGACGTGGCATTGCTGTCAGTACGGGCATTATGGGCGCC
GGCTGTACTGCATTCTTAGTAGCACTTTTGTCAAGGAAATTGGAATTGACAAGAGCGGAA
AAACATGTGCATAATTTTATGATGGACACTCAGCTCACAAAGCGGCTGAAAAATGCCGCA
GCAAATGTTTTGCGTGAAACATGGCTTATATATAAACATACAAGGTTAGTGAAGCGAGTT
AATCCTGGTAGAGTGCGAACACATCAAAGAAAATTTCTTCTTGCTATTTACGCACTGAGA
AAAGTGAAAATGGATCAACGAAAACTTATGGATAATGCAAACACCATAACCGATATGGCA
AAAACACAAAATACTGTATATGAAATTGTATCAGATATGGCGACACGACAAGATGCCTTA
GAAGAGAGAATCGCTGGATTGGAAGAGAAAATTCAAACTATTAGGGATCAACTAGAGTCG
CTTCCAGAGGTGCTAACTCGATGTCTCTCACAACATCAAGAGCGAGTCGATCAACGAAGA
AATTTTCTTCATCCAGACACGGCTGCAACACTCAATACGACGTCTTCTGCTGGCGGTGGA
CTGCAAGTTGTTCAAGCATCTGCACCAATAGGTTCGCCTTTATTTCCACATTCTAGAAGC
ATTTCAACAAACACCACAACAAATACTTTCCAATGGCCCAGCACAAGTAGTCCCATACTG
CCCGTATCCAGCCGAACACCTCATCTGATACCAGAAACTCTGATGCCTGCATCAGTCGCT
AACAACAACAGCAACACGACAATTAATAACCAAACACTGCAACAACAACAGTTTCACATG
TACCATCACAAAAGTGCTGGTAGCTGA
>g2845.t1 Gene=g2845 Length=868
MESAEENEKILSTTAANTSSVSPDETSKLLSETISKVFNNGPTANGNQQQQQETNNATTA
TSTSTSTKPMLIRQDRTYLASPQLSVTGTNLGGSEESTEDYRSDEQNRSAPDMLQNFNHP
LSPYPQISVSSENYNGEESQILSPLPTTRCRTCRRSSTSPTSIIYLDRSTSKDSIVHGHL
RPHLLVHHHSTTIPPVYVTGSPSRSSRVIRQSSQPEPSMYGHSSHTHQTASLSQLKNTSD
TIAGIAGEALKMSGGMRPFKQLRKPQSTQSIPSMKSGNRDSNKEAACNEEAGVALVNVHS
EYPRYMEERGLGGGVYKSVSGSQDKSNAKQKPNVGYRLGRRKALFEKRKRISDYALVMGM
FGIIVMVIENELSSAGVYTKASFYSTALKTLISVSTVILLGLIVAYHALEVQLFMTDNCA
DDWRIAMTWQRISQIGLELLICAIHPIPGEYYFRWETKLSNKNKAPGFADVPFDVVLSLP
MFLRLYLICRVMLLHSKLFTDASSRSIGALNRINFNTRFVFKTLMTICPGTVLLVFMVSL
WIIASWTLRQCERFHDDEHANLLNSMWLIAITFLSVGFGDIVPNTYCGRGIAVSTGIMGA
GCTAFLVALLSRKLELTRAEKHVHNFMMDTQLTKRLKNAAANVLRETWLIYKHTRLVKRV
NPGRVRTHQRKFLLAIYALRKVKMDQRKLMDNANTITDMAKTQNTVYEIVSDMATRQDAL
EERIAGLEEKIQTIRDQLESLPEVLTRCLSQHQERVDQRRNFLHPDTAATLNTTSSAGGG
LQVVQASAPIGSPLFPHSRSISTNTTTNTFQWPSTSSPILPVSSRTPHLIPETLMPASVA
NNNSNTTINNQTLQQQQFHMYHHKSAGS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g2845.t1 | Coils | Coil | Coil | 710 | 737 | - |
| 11 | g2845.t1 | Gene3D | G3DSA:1.10.287.70 | - | 513 | 612 | 4.1E-14 |
| 10 | g2845.t1 | Gene3D | G3DSA:1.10.287.70 | - | 613 | 709 | 2.6E-46 |
| 34 | g2845.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 67 | - |
| 33 | g2845.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 8 | 67 | - |
| 36 | g2845.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 197 | 234 | - |
| 35 | g2845.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 261 | 284 | - |
| 32 | g2845.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 262 | 281 | - |
| 4 | g2845.t1 | PANTHER | PTHR10153 | SMALL CONDUCTANCE CALCIUM-ACTIVATED POTASSIUM CHANNEL | 227 | 755 | 3.5E-241 |
| 5 | g2845.t1 | PANTHER | PTHR10153:SF43 | SMALL CONDUCTANCE CALCIUM-ACTIVATED POTASSIUM CHANNEL PROTEIN 2 | 227 | 755 | 3.5E-241 |
| 6 | g2845.t1 | PRINTS | PR01451 | Calcium-activated SK potassium channel signature | 337 | 357 | 6.3E-16 |
| 7 | g2845.t1 | PRINTS | PR01451 | Calcium-activated SK potassium channel signature | 438 | 456 | 6.3E-16 |
| 1 | g2845.t1 | Pfam | PF03530 | Calcium-activated SK potassium channel | 337 | 450 | 6.5E-48 |
| 3 | g2845.t1 | Pfam | PF07885 | Ion channel | 537 | 614 | 6.0E-12 |
| 2 | g2845.t1 | Pfam | PF02888 | Calmodulin binding domain | 629 | 703 | 3.0E-35 |
| 16 | g2845.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 350 | - |
| 25 | g2845.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 351 | 368 | - |
| 19 | g2845.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 369 | 387 | - |
| 24 | g2845.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 388 | 409 | - |
| 15 | g2845.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 410 | 470 | - |
| 23 | g2845.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 471 | 493 | - |
| 18 | g2845.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 494 | 523 | - |
| 20 | g2845.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 524 | 548 | - |
| 13 | g2845.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 549 | 559 | - |
| 21 | g2845.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 560 | 579 | - |
| 17 | g2845.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 580 | 590 | - |
| 22 | g2845.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 591 | 611 | - |
| 14 | g2845.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 612 | 868 | - |
| 31 | g2845.t1 | SMART | SM01053 | CaMBD_2 | 629 | 705 | 1.7E-48 |
| 8 | g2845.t1 | SUPERFAMILY | SSF81324 | Voltage-gated potassium channels | 483 | 654 | 4.32E-25 |
| 9 | g2845.t1 | SUPERFAMILY | SSF81327 | Small-conductance potassium channel | 612 | 703 | 7.98E-40 |
| 30 | g2845.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 351 | 368 | - |
| 28 | g2845.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 383 | 405 | - |
| 29 | g2845.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 523 | 545 | - |
| 27 | g2845.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 560 | 579 | - |
| 26 | g2845.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 586 | 608 | - |
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