Gene loci information

Transcript annotation

  • This transcript has been annotated as Small conductance calcium-activated potassium channel protein.

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 g2845 g2845.t2 isoform g2845.t2 20559905 20597223
chr_3 g2845 g2845.t2 exon g2845.t2.exon1 20559905 20560115
chr_3 g2845 g2845.t2 cds g2845.t2.CDS1 20559905 20560115
chr_3 g2845 g2845.t2 exon g2845.t2.exon2 20561835 20562025
chr_3 g2845 g2845.t2 cds g2845.t2.CDS2 20561835 20562025
chr_3 g2845 g2845.t2 exon g2845.t2.exon3 20562086 20562257
chr_3 g2845 g2845.t2 cds g2845.t2.CDS3 20562086 20562257
chr_3 g2845 g2845.t2 exon g2845.t2.exon4 20562325 20562452
chr_3 g2845 g2845.t2 cds g2845.t2.CDS4 20562325 20562452
chr_3 g2845 g2845.t2 exon g2845.t2.exon5 20562720 20562830
chr_3 g2845 g2845.t2 cds g2845.t2.CDS5 20562720 20562830
chr_3 g2845 g2845.t2 exon g2845.t2.exon6 20562990 20563265
chr_3 g2845 g2845.t2 cds g2845.t2.CDS6 20562990 20563265
chr_3 g2845 g2845.t2 exon g2845.t2.exon7 20563324 20563459
chr_3 g2845 g2845.t2 cds g2845.t2.CDS7 20563324 20563459
chr_3 g2845 g2845.t2 exon g2845.t2.exon8 20570793 20570897
chr_3 g2845 g2845.t2 cds g2845.t2.CDS8 20570793 20570897
chr_3 g2845 g2845.t2 exon g2845.t2.exon9 20570960 20571276
chr_3 g2845 g2845.t2 cds g2845.t2.CDS9 20570960 20571276
chr_3 g2845 g2845.t2 exon g2845.t2.exon10 20572109 20572204
chr_3 g2845 g2845.t2 cds g2845.t2.CDS10 20572109 20572204
chr_3 g2845 g2845.t2 exon g2845.t2.exon11 20576284 20576512
chr_3 g2845 g2845.t2 cds g2845.t2.CDS11 20576284 20576512
chr_3 g2845 g2845.t2 exon g2845.t2.exon12 20576593 20576720
chr_3 g2845 g2845.t2 cds g2845.t2.CDS12 20576593 20576720
chr_3 g2845 g2845.t2 exon g2845.t2.exon13 20596379 20596408
chr_3 g2845 g2845.t2 cds g2845.t2.CDS13 20596379 20596408
chr_3 g2845 g2845.t2 exon g2845.t2.exon14 20596471 20597223
chr_3 g2845 g2845.t2 cds g2845.t2.CDS14 20596471 20597223
chr_3 g2845 g2845.t2 TSS g2845.t2 NA NA
chr_3 g2845 g2845.t2 TTS g2845.t2 NA NA

Sequences

>g2845.t2 Gene=g2845 Length=2883
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
TGGATAATAGCATCGTGGACGTTGCGGCAATGTGAAAGATTTCACGATGAAGAGCATGCA
AATTTGCTCAATTCAATGTGGCTAACAGCAATAACGTTTTTGTGTGTAGGATATGGTGAT
ATTGTTCCAAATACGTACTGTGGTCGTGGAATAACGCTTACCTGCGGAATGGTGAGATCA
AAAAAAGTTCTATTTGGCAAAAAAGAAATGCGAGTAACTCAACGAGATGACATAGCAAAT
AATAATTTCGTCTTCCATATGGGATATATGAAAAATTTAGTTCTTCAATCAATTTTAACT
CAATCATCAATTAGGTTTCATGATGACGAGCATGCCAATTTATTGAACTCAATGTGGCTG
ATTGCTATAACATTCTTAAGTGTTGGATTCGGTGACATTGTTCCTAATACATATTGTGGA
CGTGGCATTGCTGTCAGTACGGGCATTATGGGCGCCGGCTGTACTGCATTCTTAGTAGCA
CTTTTGTCAAGGAAATTGGAATTGACAAGAGCGGAAAAACATGTGCATAATTTTATGATG
GACACTCAGCTCACAAAGCGGCTGAAAAATGCCGCAGCAAATGTTTTGCGTGAAACATGG
CTTATATATAAACATACAAGGTTAGTGAAGCGAGTTAATCCTGGTAGAGTGCGAACACAT
CAAAGAAAATTTCTTCTTGCTATTTACGCACTGAGAAAAGTGAAAATGGATCAACGAAAA
CTTATGGATAATGCAAACACCATAACCGATATGGCAAAAACACAAAATACTGTATATGAA
ATTGTATCAGATATGGCGACACGACAAGATGCCTTAGAAGAGAGAATCGCTGGATTGGAA
GAGAAAATTCAAACTATTAGGGATCAACTAGAGTCGCTTCCAGAGGTGCTAACTCGATGT
CTCTCACAACATCAAGAGCGAGTCGATCAACGAAGAAATTTTCTTCATCCAGACACGGCT
GCAACACTCAATACGACGTCTTCTGCTGGCGGTGGACTGCAAGTTGTTCAAGCATCTGCA
CCAATAGGTTCGCCTTTATTTCCACATTCTAGAAGCATTTCAACAAACACCACAACAAAT
ACTTTCCAATGGCCCAGCACAAGTAGTCCCATACTGCCCGTATCCAGCCGAACACCTCAT
CTGATACCAGAAACTCTGATGCCTGCATCAGTCGCTAACAACAACAGCAACACGACAATT
AATAACCAAACACTGCAACAACAACAGTTTCACATGTACCATCACAAAAGTGCTGGTAGC
TGA

>g2845.t2 Gene=g2845 Length=960
MESAEENEKILSTTAANTSSVSPDETSKLLSETISKVFNNGPTANGNQQQQQETNNATTA
TSTSTSTKPMLIRQDRTYLASPQLSVTGTNLGGSEESTEDYRSDEQNRSAPDMLQNFNHP
LSPYPQISVSSENYNGEESQILSPLPTTRCRTCRRSSTSPTSIIYLDRSTSKDSIVHGHL
RPHLLVHHHSTTIPPVYVTGSPSRSSRVIRQSSQPEPSMYGHSSHTHQTASLSQLKNTSD
TIAGIAGEALKMSGGMRPFKQLRKPQSTQSIPSMKSGNRDSNKEAACNEEAGVALVNVHS
EYPRYMEERGLGGGVYKSVSGSQDKSNAKQKPNVGYRLGRRKALFEKRKRISDYALVMGM
FGIIVMVIENELSSAGVYTKASFYSTALKTLISVSTVILLGLIVAYHALEVQLFMTDNCA
DDWRIAMTWQRISQIGLELLICAIHPIPGEYYFRWETKLSNKNKAPGFADVPFDVVLSLP
MFLRLYLICRVMLLHSKLFTDASSRSIGALNRINFNTRFVFKTLMTICPGTVLLVFMVSL
WIIASWTLRQCERFHDEEHANLLNSMWLTAITFLCVGYGDIVPNTYCGRGITLTCGMVRS
KKVLFGKKEMRVTQRDDIANNNFVFHMGYMKNLVLQSILTQSSIRFHDDEHANLLNSMWL
IAITFLSVGFGDIVPNTYCGRGIAVSTGIMGAGCTAFLVALLSRKLELTRAEKHVHNFMM
DTQLTKRLKNAAANVLRETWLIYKHTRLVKRVNPGRVRTHQRKFLLAIYALRKVKMDQRK
LMDNANTITDMAKTQNTVYEIVSDMATRQDALEERIAGLEEKIQTIRDQLESLPEVLTRC
LSQHQERVDQRRNFLHPDTAATLNTTSSAGGGLQVVQASAPIGSPLFPHSRSISTNTTTN
TFQWPSTSSPILPVSSRTPHLIPETLMPASVANNNSNTTINNQTLQQQQFHMYHHKSAGS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g2845.t2 Coils Coil Coil 802 829 -
16 g2845.t2 Gene3D G3DSA:1.10.287.70 - 511 603 3.2E-11
15 g2845.t2 Gene3D G3DSA:1.10.287.70 - 624 705 6.0E-12
14 g2845.t2 Gene3D G3DSA:1.10.287.70 - 706 801 3.0E-46
44 g2845.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 67 -
43 g2845.t2 MobiDBLite mobidb-lite consensus disorder prediction 8 67 -
46 g2845.t2 MobiDBLite mobidb-lite consensus disorder prediction 197 234 -
45 g2845.t2 MobiDBLite mobidb-lite consensus disorder prediction 261 284 -
42 g2845.t2 MobiDBLite mobidb-lite consensus disorder prediction 262 281 -
6 g2845.t2 PANTHER PTHR10153 SMALL CONDUCTANCE CALCIUM-ACTIVATED POTASSIUM CHANNEL 227 597 5.2E-255
8 g2845.t2 PANTHER PTHR10153:SF43 SMALL CONDUCTANCE CALCIUM-ACTIVATED POTASSIUM CHANNEL PROTEIN 2 227 597 5.2E-255
5 g2845.t2 PANTHER PTHR10153 SMALL CONDUCTANCE CALCIUM-ACTIVATED POTASSIUM CHANNEL 645 847 5.2E-255
7 g2845.t2 PANTHER PTHR10153:SF43 SMALL CONDUCTANCE CALCIUM-ACTIVATED POTASSIUM CHANNEL PROTEIN 2 645 847 5.2E-255
9 g2845.t2 PRINTS PR01451 Calcium-activated SK potassium channel signature 337 357 7.6E-16
10 g2845.t2 PRINTS PR01451 Calcium-activated SK potassium channel signature 438 456 7.6E-16
1 g2845.t2 Pfam PF03530 Calcium-activated SK potassium channel 337 450 7.5E-48
4 g2845.t2 Pfam PF07885 Ion channel 537 595 2.7E-8
3 g2845.t2 Pfam PF07885 Ion channel 635 706 1.2E-11
2 g2845.t2 Pfam PF02888 Calmodulin binding domain 721 795 3.4E-35
22 g2845.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 350 -
34 g2845.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 351 368 -
25 g2845.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 369 387 -
31 g2845.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 388 409 -
21 g2845.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 410 428 -
29 g2845.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 429 447 -
24 g2845.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 448 466 -
27 g2845.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 467 487 -
18 g2845.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 488 518 -
32 g2845.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 519 544 -
26 g2845.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 545 563 -
28 g2845.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 564 582 -
19 g2845.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 583 653 -
33 g2845.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 654 671 -
23 g2845.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 672 682 -
30 g2845.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 683 703 -
20 g2845.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 704 960 -
41 g2845.t2 SMART SM01053 CaMBD_2 721 797 1.7E-48
12 g2845.t2 SUPERFAMILY SSF81324 Voltage-gated potassium channels 472 597 5.49E-16
11 g2845.t2 SUPERFAMILY SSF81324 Voltage-gated potassium channels 635 706 1.26E-12
13 g2845.t2 SUPERFAMILY SSF81327 Small-conductance potassium channel 704 795 9.16E-40
40 g2845.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 351 368 -
38 g2845.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 383 405 -
39 g2845.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 524 546 -
36 g2845.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 566 588 -
35 g2845.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 652 674 -
37 g2845.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 684 703 -

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 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