Gene loci information

Transcript annotation

  • This transcript has been annotated as Calcium-activated potassium channel slowpoke.

Parent gene

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 g2813 g2813.t2 isoform g2813.t2 20393495 20420634
chr_3 g2813 g2813.t2 exon g2813.t2.exon1 20393495 20393554
chr_3 g2813 g2813.t2 cds g2813.t2.CDS1 20393495 20393554
chr_3 g2813 g2813.t2 exon g2813.t2.exon2 20393633 20393646
chr_3 g2813 g2813.t2 cds g2813.t2.CDS2 20393633 20393646
chr_3 g2813 g2813.t2 exon g2813.t2.exon3 20393705 20393846
chr_3 g2813 g2813.t2 cds g2813.t2.CDS3 20393705 20393846
chr_3 g2813 g2813.t2 exon g2813.t2.exon4 20393908 20394270
chr_3 g2813 g2813.t2 cds g2813.t2.CDS4 20393908 20394270
chr_3 g2813 g2813.t2 exon g2813.t2.exon5 20394339 20394752
chr_3 g2813 g2813.t2 cds g2813.t2.CDS5 20394339 20394752
chr_3 g2813 g2813.t2 exon g2813.t2.exon6 20394817 20395041
chr_3 g2813 g2813.t2 cds g2813.t2.CDS6 20394817 20395041
chr_3 g2813 g2813.t2 exon g2813.t2.exon7 20395100 20395274
chr_3 g2813 g2813.t2 cds g2813.t2.CDS7 20395100 20395274
chr_3 g2813 g2813.t2 exon g2813.t2.exon8 20395520 20395585
chr_3 g2813 g2813.t2 cds g2813.t2.CDS8 20395520 20395585
chr_3 g2813 g2813.t2 exon g2813.t2.exon9 20395834 20395990
chr_3 g2813 g2813.t2 cds g2813.t2.CDS9 20395834 20395990
chr_3 g2813 g2813.t2 exon g2813.t2.exon10 20396105 20396137
chr_3 g2813 g2813.t2 cds g2813.t2.CDS10 20396105 20396137
chr_3 g2813 g2813.t2 exon g2813.t2.exon11 20396702 20396773
chr_3 g2813 g2813.t2 cds g2813.t2.CDS11 20396702 20396773
chr_3 g2813 g2813.t2 exon g2813.t2.exon12 20398443 20398508
chr_3 g2813 g2813.t2 cds g2813.t2.CDS12 20398443 20398508
chr_3 g2813 g2813.t2 exon g2813.t2.exon13 20402216 20402292
chr_3 g2813 g2813.t2 cds g2813.t2.CDS13 20402216 20402292
chr_3 g2813 g2813.t2 exon g2813.t2.exon14 20402355 20402513
chr_3 g2813 g2813.t2 cds g2813.t2.CDS14 20402355 20402513
chr_3 g2813 g2813.t2 exon g2813.t2.exon15 20402942 20403054
chr_3 g2813 g2813.t2 cds g2813.t2.CDS15 20402942 20403054
chr_3 g2813 g2813.t2 exon g2813.t2.exon16 20403890 20404198
chr_3 g2813 g2813.t2 cds g2813.t2.CDS16 20403890 20404198
chr_3 g2813 g2813.t2 exon g2813.t2.exon17 20405508 20405613
chr_3 g2813 g2813.t2 cds g2813.t2.CDS17 20405508 20405613
chr_3 g2813 g2813.t2 exon g2813.t2.exon18 20407037 20407147
chr_3 g2813 g2813.t2 cds g2813.t2.CDS18 20407037 20407147
chr_3 g2813 g2813.t2 exon g2813.t2.exon19 20415040 20415081
chr_3 g2813 g2813.t2 cds g2813.t2.CDS19 20415040 20415081
chr_3 g2813 g2813.t2 exon g2813.t2.exon20 20415166 20415215
chr_3 g2813 g2813.t2 cds g2813.t2.CDS20 20415166 20415215
chr_3 g2813 g2813.t2 exon g2813.t2.exon21 20418184 20418351
chr_3 g2813 g2813.t2 cds g2813.t2.CDS21 20418184 20418351
chr_3 g2813 g2813.t2 exon g2813.t2.exon22 20418424 20418575
chr_3 g2813 g2813.t2 cds g2813.t2.CDS22 20418424 20418575
chr_3 g2813 g2813.t2 exon g2813.t2.exon23 20418638 20418749
chr_3 g2813 g2813.t2 cds g2813.t2.CDS23 20418638 20418749
chr_3 g2813 g2813.t2 exon g2813.t2.exon24 20418819 20418976
chr_3 g2813 g2813.t2 cds g2813.t2.CDS24 20418819 20418976
chr_3 g2813 g2813.t2 exon g2813.t2.exon25 20420349 20420634
chr_3 g2813 g2813.t2 cds g2813.t2.CDS25 20420349 20420634
chr_3 g2813 g2813.t2 TSS g2813.t2 NA NA
chr_3 g2813 g2813.t2 TTS g2813.t2 NA NA

Sequences

>g2813.t2 Gene=g2813 Length=3630
ATGTCGGGTTGTGACGAAGAAGTAATAACCACAGAACCATCTTTTGATAATTGCCTTCAA
GTTCGAAAATGGTGGTGTTTTCTACTGTCAAGTATTTTCACATTCTTGGCGGGGCTTCTT
ATAGTTCTATTATGGAGAGCTTTTGCATTTATTTGTTGTCGTAAAGAGCCAGAACTATCA
CCAAATGATCCCAAACAGAAAGAGCAAAAAGCCAATCGTGGCAAACAAGAGTTCGAGGGA
ACTTTTATGACAGAAGCTAAAGATTGGGCTGGAGAATTGATATCAGTGGTTCTTGTTTTT
ATCCTCAGTATCGCATCACTTATCATTTACTTTATTGATGCATCAAATGATAAAGTGGAG
CATTGTGAAAAATGGAGCAACAATATTACACAACAAATCGATCTTGCATTCAATATATTT
TTTATGGTGTACTTTTTTATACGATTCATAGCAGCATCTGATAAGTTTTGGTTTATGTTA
GAAATGTACAGTTTTGTCGACTATTTCACAATTCCCCCGTCCTTTGTGTCGATATATTTA
GACCGTACGTGGATTGGTCTACGTTTCCTTCGAGCGCTAAGACTTATGACTGTCCCAGAT
ATACTCCAATATCTAAATATATTAAAAACTTCAAGTTCTATTCGTTTAGCACAACTAGTA
TCAATTTTTATATCCGTATGGTTAACAGCTGCCGGAATTATTCATTTACTCGAAAATTCT
GGTGATCCATTGGAATTTAATAATCCACATCAGTTATCATATTGGACATGTGTTTATTTT
CTCATCGTAACAATGTCCACTGTCGGTTATGGTGATGTGTTTTGTGAGACAGTTCTCGGT
CGAACATTTCTTGTGTTTTTCCTACTCGTCGGTTTGGCTATGTTTGCGAGCTCTATTCCG
GAAATTATTGAACTCGTCGGTTCAGGGAGCAAATATTCGGGTGAACTGAAAAGAGAACAT
GGAAAGAGACACATCGTCGTATGTGGACACATAACTTATGAATCTGTTTCACATTTTCTA
AAAGACTTTTTACATGAGGATCGAGAAGATGTGGATGTGGAAGTTGTGTTTCTCCATAGG
CATGTCCCTGGCCTTGAACTAGAAGGGCTTTTCAAAAGACATTTTACTACAGTGGAGTTT
TTTCAAGGCACAATCATGAACCCAATTGATTTACAACGAGTCAAGGTGCACGAAGCTGAT
GCATGTTTAGTGTTAGCAAATAAATATTGTCAGGATCCCGATGCAGAAGATGCTGCTAAC
ATTATGCGCGTTATTTCAATCAAAAACTATAGCGATGACATTCGAGTTATCATTCAATTG
ATGCAATATCATAATAAAGCATACTTACTAAATATTCCATCATGGGACTGGAAACAAGGT
GATGATGTCATTTGTTTGGCTGAATTAAAATTAGGTTTCATCGCTCAGAGTTGTCTCGCA
CCTGGATTCTCAACAATGATGGCCAACTTGTTCGCTATGAGATCATTTAAAACGTCTCCT
GACATGCAAATTTGGCAAAATGATTACTTGCAAGGTACCGGATGTGAGATGTATACAGAA
ACCCTTTCACCTTCTTTTACCGGAATGACATTTCCACAAGCCAGCGAGCTTTGTTTTACA
AAATTAAAGTTGTTATTGCTAGCGATAGAAATTAAAGGCGGAGAAGAGGGAAATGATAGC
AAAATTTCGATCAATCCAAGAGGTGCTAAAATTCTGGCTAACACGCAAGGATTCTTTATT
GCGCAAAGTGCGGATGAAGTGAAAAGGGCATGGTTTTATTGTAAAGCATGTCATGATGAT
ATCAAAGATGAAACGCTTATAAAGAAGTGCAAGTGTAAAAATTTGGCTTTAATGAGGAAA
AAGTTTCGAGCTCCTCCTCCTTCTCCATCAAAACTAATAAATTTATCAAATGATCATCCT
GCCGCACCGACATTTACTCCTCCCGAACTTCCTAAAAGAGTGCATGTGCGGGGCGTAACT
GGGGATGTCACAAGAGAACGAGATGAGATAAACCTCATAAATCGCAATAAGCGAATGCCA
TCAGTTAGTTCTGGATCTCATCAAATGTTAAACTCAATACAAACAAAACAAGTTAACAAA
GTTAAACCAAACGTTAATCGACCTCCCAATGGTGCCGAAGGTGTTGTTGTGTCTCCCTCA
TCATACAATCGACCTCCGGATACAGAAGCAAACCCATATGCGGGATATCAACTAGCATAT
GAAGTTAAAAAGCTCATGCCTACGGCGAGAGGTGGATCATCTACGCAAAATTCAAATGGA
GGTGTTACACTTCAAGCAGGCATTGCTGATGATCAATCTAAGGACTTTGACTTTGAAAAG
ACAGAAATGAAATACGATTCGACTGGAATGTTTCATTGGAGTCCTGCAAGGAGTCTTGAA
GATTGTATTTTGGATCGAAATCAAGCGGCTATGACAGTGTTAAATGGTCATGTTGTCGTT
TGTTTATTTGCCGATCCTGATAGTCCACTCATCGGTCTAAGAAATTTAGTTATGCCTTTA
CGCGCATCAAACTTTCATTATCATGAATTAAAACATGTTGTTATTGTTGGTTCTGTTGAT
TACATTCGTAGAGAATGGAAGATGTTACAAAACTTACCAAAAATATCTGTACTTAATGGA
TCACCACTTAGTCGCGCTGATTTGCGTGCGGTTAATGTAAATTTATGTGATATGTGCTGC
ATTTTATCGGCTAAAGTACCCTCAAACGATGATCCAACGTTGGCTGACAAAGAGGCCATT
TTAGCTTCTCTTAATATCAAGGCTATGACATTCGATGATACAATAGGTGTGCTTAGTCAG
CGCGGTGAACAAGACAATCTAACACCAGTTGGCAGTCCAATTGTTCTACAACGTCGAGGC
TCAGTATATGGTGCAAACGTTCCAATGATTACTGAATTGGTCAATGATAGCAACGTACAG
TTTCTCGATCAAGACGATGATGACGATCCCGATACAGAGCTTTACTTAACACAACCCTTT
GCTTGTGGTACTGCTTTTGCCGTTAGCGTACTAGATTCATTAATGTCAACGACATATTTT
AATCAAAACGCCTTAACATTAATTCGTTCATTAATCACTGGTGGTGCAACTCCCGAACTT
GAACTTATTTTGGCTGAAGGTGCTGGACTTCGTGGTGGTTATAGTACACCAGAAAGTCTT
AGTAATCGTGATAGATGTCGTGTTGGACAAATCTCGTTTTATGATGGACCTTTAGCACAA
TTTGGCGAAGCAGGAAAATATGGTGATTTGTTTGTAGCAGCACTCAAATCATATGGAATG
CTTTGCATTGGACTTTATAGATTTCGTGATACCAGTTCAAGTTGTGATGCTAGTAGTAAA
CGATATGTTATAACTAATCCACCAGATGATTTCTCATTGTTACCTACTGATCAGGTCTTT
GTGCTAATGCAATTTGATCCAGGTCTTGAGTATAAGCCTCAAACTCGACCAAATGCACAA
AACTCAGGCGGTGCAGTGGGAATCAACACAGGAAATATTGTTAGTAGTACTCGACAAACC
AATAATAATCAAGTAGTGCTCTTACTGATGGTCCTTACAGTTACATCTAACGTAAAGCTT
CAGTCTTTGTGCATAACATTGTTCATTTAA

>g2813.t2 Gene=g2813 Length=1209
MSGCDEEVITTEPSFDNCLQVRKWWCFLLSSIFTFLAGLLIVLLWRAFAFICCRKEPELS
PNDPKQKEQKANRGKQEFEGTFMTEAKDWAGELISVVLVFILSIASLIIYFIDASNDKVE
HCEKWSNNITQQIDLAFNIFFMVYFFIRFIAASDKFWFMLEMYSFVDYFTIPPSFVSIYL
DRTWIGLRFLRALRLMTVPDILQYLNILKTSSSIRLAQLVSIFISVWLTAAGIIHLLENS
GDPLEFNNPHQLSYWTCVYFLIVTMSTVGYGDVFCETVLGRTFLVFFLLVGLAMFASSIP
EIIELVGSGSKYSGELKREHGKRHIVVCGHITYESVSHFLKDFLHEDREDVDVEVVFLHR
HVPGLELEGLFKRHFTTVEFFQGTIMNPIDLQRVKVHEADACLVLANKYCQDPDAEDAAN
IMRVISIKNYSDDIRVIIQLMQYHNKAYLLNIPSWDWKQGDDVICLAELKLGFIAQSCLA
PGFSTMMANLFAMRSFKTSPDMQIWQNDYLQGTGCEMYTETLSPSFTGMTFPQASELCFT
KLKLLLLAIEIKGGEEGNDSKISINPRGAKILANTQGFFIAQSADEVKRAWFYCKACHDD
IKDETLIKKCKCKNLALMRKKFRAPPPSPSKLINLSNDHPAAPTFTPPELPKRVHVRGVT
GDVTRERDEINLINRNKRMPSVSSGSHQMLNSIQTKQVNKVKPNVNRPPNGAEGVVVSPS
SYNRPPDTEANPYAGYQLAYEVKKLMPTARGGSSTQNSNGGVTLQAGIADDQSKDFDFEK
TEMKYDSTGMFHWSPARSLEDCILDRNQAAMTVLNGHVVVCLFADPDSPLIGLRNLVMPL
RASNFHYHELKHVVIVGSVDYIRREWKMLQNLPKISVLNGSPLSRADLRAVNVNLCDMCC
ILSAKVPSNDDPTLADKEAILASLNIKAMTFDDTIGVLSQRGEQDNLTPVGSPIVLQRRG
SVYGANVPMITELVNDSNVQFLDQDDDDDPDTELYLTQPFACGTAFAVSVLDSLMSTTYF
NQNALTLIRSLITGGATPELELILAEGAGLRGGYSTPESLSNRDRCRVGQISFYDGPLAQ
FGEAGKYGDLFVAALKSYGMLCIGLYRFRDTSSSCDASSKRYVITNPPDDFSLLPTDQVF
VLMQFDPGLEYKPQTRPNAQNSGGAVGINTGNIVSSTRQTNNNQVVLLLMVLTVTSNVKL
QSLCITLFI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
29 g2813.t2 Gene3D G3DSA:1.20.120.350 - 29 205 3.6E-10
28 g2813.t2 Gene3D G3DSA:1.10.287.70 - 213 317 1.6E-17
26 g2813.t2 Gene3D G3DSA:3.40.50.720 - 318 453 5.8E-16
27 g2813.t2 Gene3D G3DSA:3.40.50.720 - 810 956 5.0E-7
4 g2813.t2 PANTHER PTHR10027 CALCIUM-ACTIVATED POTASSIUM CHANNEL ALPHA CHAIN 20 616 0.0
6 g2813.t2 PANTHER PTHR10027:SF28 CALCIUM-ACTIVATED POTASSIUM CHANNEL SUBUNIT ALPHA-1 20 616 0.0
3 g2813.t2 PANTHER PTHR10027 CALCIUM-ACTIVATED POTASSIUM CHANNEL ALPHA CHAIN 782 1146 0.0
5 g2813.t2 PANTHER PTHR10027:SF28 CALCIUM-ACTIVATED POTASSIUM CHANNEL SUBUNIT ALPHA-1 782 1146 0.0
16 g2813.t2 PRINTS PR00169 Potassium channel signature 132 155 4.4E-6
14 g2813.t2 PRINTS PR00169 Potassium channel signature 158 178 4.4E-6
15 g2813.t2 PRINTS PR00169 Potassium channel signature 251 273 4.4E-6
13 g2813.t2 PRINTS PR00169 Potassium channel signature 280 306 4.4E-6
7 g2813.t2 PRINTS PR01449 Calcium-activated BK potassium channel alpha subunit signature 354 374 4.2E-45
11 g2813.t2 PRINTS PR01449 Calcium-activated BK potassium channel alpha subunit signature 397 417 4.2E-45
12 g2813.t2 PRINTS PR01449 Calcium-activated BK potassium channel alpha subunit signature 430 443 4.2E-45
10 g2813.t2 PRINTS PR01449 Calcium-activated BK potassium channel alpha subunit signature 476 491 4.2E-45
9 g2813.t2 PRINTS PR01449 Calcium-activated BK potassium channel alpha subunit signature 526 543 4.2E-45
8 g2813.t2 PRINTS PR01449 Calcium-activated BK potassium channel alpha subunit signature 981 996 4.2E-45
2 g2813.t2 Pfam PF00520 Ion transport protein 98 304 3.3E-16
1 g2813.t2 Pfam PF03493 Calcium-activated BK potassium channel alpha subunit 453 549 8.8E-38
34 g2813.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 23 -
41 g2813.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 24 48 -
37 g2813.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 49 92 -
46 g2813.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 93 112 -
31 g2813.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 113 132 -
39 g2813.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 133 151 -
36 g2813.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 152 156 -
44 g2813.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 157 180 -
30 g2813.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 181 215 -
45 g2813.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 216 237 -
35 g2813.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 238 251 -
40 g2813.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 252 271 -
32 g2813.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 272 282 -
43 g2813.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 283 303 -
38 g2813.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 304 1184 -
42 g2813.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 1185 1208 -
33 g2813.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1209 1209 -
24 g2813.t2 SUPERFAMILY SSF81324 Voltage-gated potassium channels 96 305 3.85E-32
25 g2813.t2 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 322 487 1.97E-8
18 g2813.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 27 49 -
20 g2813.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 90 112 -
17 g2813.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 133 152 -
19 g2813.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 157 179 -
22 g2813.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 219 237 -
23 g2813.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 252 271 -
21 g2813.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 278 300 -

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:0016020 membrane CC
GO:0055085 transmembrane transport BP
GO:0006813 potassium ion transport BP
GO:0005216 ion channel activity MF
GO:0060072 large conductance calcium-activated potassium channel activity MF
GO:0006811 ion transport BP

KEGG

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.

Raw TPM values