Gene loci information

Transcript annotation

  • This transcript has been annotated as Potassium voltage-gated channel protein Shal.

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_2 g8730 g8730.t1 isoform g8730.t1 32656172 32660496
chr_2 g8730 g8730.t1 exon g8730.t1.exon1 32656172 32656195
chr_2 g8730 g8730.t1 cds g8730.t1.CDS1 32656172 32656195
chr_2 g8730 g8730.t1 exon g8730.t1.exon2 32656378 32656536
chr_2 g8730 g8730.t1 cds g8730.t1.CDS2 32656378 32656536
chr_2 g8730 g8730.t1 exon g8730.t1.exon3 32656659 32656847
chr_2 g8730 g8730.t1 cds g8730.t1.CDS3 32656659 32656847
chr_2 g8730 g8730.t1 exon g8730.t1.exon4 32657256 32657418
chr_2 g8730 g8730.t1 cds g8730.t1.CDS4 32657256 32657418
chr_2 g8730 g8730.t1 exon g8730.t1.exon5 32657490 32657763
chr_2 g8730 g8730.t1 cds g8730.t1.CDS5 32657490 32657763
chr_2 g8730 g8730.t1 exon g8730.t1.exon6 32657843 32657879
chr_2 g8730 g8730.t1 cds g8730.t1.CDS6 32657843 32657879
chr_2 g8730 g8730.t1 exon g8730.t1.exon7 32658620 32658774
chr_2 g8730 g8730.t1 cds g8730.t1.CDS7 32658620 32658774
chr_2 g8730 g8730.t1 exon g8730.t1.exon8 32658883 32658912
chr_2 g8730 g8730.t1 cds g8730.t1.CDS8 32658883 32658912
chr_2 g8730 g8730.t1 exon g8730.t1.exon9 32658975 32659224
chr_2 g8730 g8730.t1 cds g8730.t1.CDS9 32658975 32659224
chr_2 g8730 g8730.t1 exon g8730.t1.exon10 32660128 32660496
chr_2 g8730 g8730.t1 cds g8730.t1.CDS10 32660128 32660496
chr_2 g8730 g8730.t1 TSS g8730.t1 NA NA
chr_2 g8730 g8730.t1 TTS g8730.t1 NA NA

Sequences

>g8730.t1 Gene=g8730 Length=1650
ATGGCTTCAGTTGCAGCTTGGCTTCCTTTAGCGCGTGCAACGGCTATAGGATGGATTCCC
ATCGCTAGTAATCCACTGCCACCACCTCCATTAGTAAAAGATCGACGAAGAGCTGAAGAT
GAAAAGCTGATAATCAATATATCAGGTCACCGTTTTGAAACATGGCGAAATACATTAGAA
AAATATCCCGACACACTTCTTGGCTCAAACGAGCGAGAATTTTTCTTCGATGAGGAAAGC
AAAGAATACTTTTTTGATCGTGACCCCGACATTTTTAGGCACATTCTCAATTATTATAGA
ACAGGGAAATTGCATTATCCTCGTCATGAATGTCTAATGAGTTTTGATGAGGAACTGACG
TTTTTCGGGGTTTTACCCGATGTAATTGGTGATTGCTGTTATGAAGAATATAGGGATCGA
AAACGTGAAAATGCTGAACGCCTGCTAGATGATAATTTATCAGAAAAATCAGACACAAAT
CTTCCGCCACTGACGAATATAAGACAGCGTATGTGGAGAGCATTTGAGAATCCTCATACA
TCCACAGCAGCATTAGTGTTCTATTATGTCACTGGTTTCTTCATTGCTGTTTCAGTAATG
GCTAACGTTGTAGAAACTGTACCTTGCGGATTGAGGCCAGGAAGAGCAGGCACATTGTCA
TGCGGTGAACGCTACAAAATTGTTTTCTTCTGCTTAGATACAGCCTGTGTGATGATTTTT
ACTGCTGAATATTTACTTCGACTATTTGCTGCACCATCGCGGTGGAAATTTATGCGTAGC
GTTATGTCGATTATTGATGTTGTGGCGATTATGCCTTATTACATCGGTTTATTTATGCAA
GATAACGATGATGTATCAGGGGCTTTTGTCACTCTTCGAGTATTTCGTGTATTTCGTATT
TTTAAATTTTCGAGGCACTCGCAAGGGTTACGTATTCTTGGTTACACGTTAAAGAGTTGT
GCTTCCGAACTTGGCTTTCTCGTGTTTTCTCTTGCAATGGCCATCATTATTTTTGCAACT
GTGATGTTTTATGCTGAAAAAAATGTCGATGGCACAAATTTTACATCAATTCCGGCAGCT
TTCTGGTATACAATTGTGACAATGACAACATTAGGATATGGTGATATGGTGCCAGAAACA
ATAGCGGGTAAAGTTGTGGGCGGCGTATGCTCACTTAGCGGTGTGTTGGTCATCGCTCTT
CCCGTTCCCGTCATTGTGTCAAACTTTAGTCGAATTTATCATCAGAGTCAACGCGCTGAC
AAACGAAAAGCTCAAAGGAAAGCACGATTGGTACGAATTAAAATGGCAAAAGCATCGTCA
GGAGCAGCATTTATTAATAAAAAGAGAGCAGCTGAAGCACGTCTTGCTGCTCAAGAGAGC
GGAATCGACATGGATGACAGTTATAATGATGAAGATATCTTTGAATTACAACATCATCAT
CTGTTGCGATGCCTTGAGAAGACAACCGATCGAGAATTTCTTGACCTAGATCACGGTTTT
AATGGTATCACACAGCCAAAAAGGCCTGGCTCACCATCACCAATGGCAAGTCCATCACAT
TCGACTAATACCACTGCCGGATTATTACAATCATGTTGTGGACGATGTTGCTCACAGCGA
TATCAGAGCTACACTTCAGCGAATCAATGA

>g8730.t1 Gene=g8730 Length=549
MASVAAWLPLARATAIGWIPIASNPLPPPPLVKDRRRAEDEKLIINISGHRFETWRNTLE
KYPDTLLGSNEREFFFDEESKEYFFDRDPDIFRHILNYYRTGKLHYPRHECLMSFDEELT
FFGVLPDVIGDCCYEEYRDRKRENAERLLDDNLSEKSDTNLPPLTNIRQRMWRAFENPHT
STAALVFYYVTGFFIAVSVMANVVETVPCGLRPGRAGTLSCGERYKIVFFCLDTACVMIF
TAEYLLRLFAAPSRWKFMRSVMSIIDVVAIMPYYIGLFMQDNDDVSGAFVTLRVFRVFRI
FKFSRHSQGLRILGYTLKSCASELGFLVFSLAMAIIIFATVMFYAEKNVDGTNFTSIPAA
FWYTIVTMTTLGYGDMVPETIAGKVVGGVCSLSGVLVIALPVPVIVSNFSRIYHQSQRAD
KRKAQRKARLVRIKMAKASSGAAFINKKRAAEARLAAQESGIDMDDSYNDEDIFELQHHH
LLRCLEKTTDREFLDLDHGFNGITQPKRPGSPSPMASPSHSTNTTAGLLQSCCGRCCSQR
YQSYTSANQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
50 g8730.t1 CDD cd18420 BTB_POZ_Shal-like 6 144 1.81853E-102
32 g8730.t1 Gene3D G3DSA:3.30.710.10 Potassium Channel Kv1.1; Chain A 1 144 7.8E-53
31 g8730.t1 Gene3D G3DSA:1.20.120.350 - 156 306 6.3E-38
30 g8730.t1 Gene3D G3DSA:1.10.287.70 - 307 417 2.3E-30
59 g8730.t1 MobiDBLite mobidb-lite consensus disorder prediction 502 522 -
58 g8730.t1 MobiDBLite mobidb-lite consensus disorder prediction 506 522 -
5 g8730.t1 PANTHER PTHR11537:SF265 POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY D MEMBER 2 23 540 6.8E-272
6 g8730.t1 PANTHER PTHR11537 VOLTAGE-GATED POTASSIUM CHANNEL 23 540 6.8E-272
25 g8730.t1 PRINTS PR01497 Shal voltage-gated K+ channel family signature 68 81 1.2E-61
7 g8730.t1 PRINTS PR01491 Voltage-gated potassium channel family signature 82 92 1.3E-20
17 g8730.t1 PRINTS PR00169 Potassium channel signature 82 101 2.6E-94
26 g8730.t1 PRINTS PR01497 Shal voltage-gated K+ channel family signature 143 159 1.2E-61
23 g8730.t1 PRINTS PR01497 Shal voltage-gated K+ channel family signature 161 175 1.2E-61
13 g8730.t1 PRINTS PR00169 Potassium channel signature 178 206 2.6E-94
21 g8730.t1 PRINTS PR01497 Shal voltage-gated K+ channel family signature 180 194 1.2E-61
24 g8730.t1 PRINTS PR01497 Shal voltage-gated K+ channel family signature 220 236 1.2E-61
11 g8730.t1 PRINTS PR00169 Potassium channel signature 231 254 2.6E-94
18 g8730.t1 PRINTS PR00169 Potassium channel signature 257 277 2.6E-94
12 g8730.t1 PRINTS PR00169 Potassium channel signature 294 320 2.6E-94
10 g8730.t1 PRINTS PR01491 Voltage-gated potassium channel family signature 299 307 1.3E-20
19 g8730.t1 PRINTS PR01497 Shal voltage-gated K+ channel family signature 318 337 1.2E-61
8 g8730.t1 PRINTS PR01491 Voltage-gated potassium channel family signature 323 337 1.3E-20
14 g8730.t1 PRINTS PR00169 Potassium channel signature 323 346 2.6E-94
16 g8730.t1 PRINTS PR00169 Potassium channel signature 354 376 2.6E-94
15 g8730.t1 PRINTS PR00169 Potassium channel signature 383 409 2.6E-94
9 g8730.t1 PRINTS PR01491 Voltage-gated potassium channel family signature 394 405 1.3E-20
20 g8730.t1 PRINTS PR01497 Shal voltage-gated K+ channel family signature 415 426 1.2E-61
27 g8730.t1 PRINTS PR01497 Shal voltage-gated K+ channel family signature 429 445 1.2E-61
22 g8730.t1 PRINTS PR01497 Shal voltage-gated K+ channel family signature 475 489 1.2E-61
3 g8730.t1 Pfam PF11601 Shal-type voltage-gated potassium channels, N-terminal 2 29 8.3E-12
1 g8730.t1 Pfam PF02214 BTB/POZ domain 44 132 1.2E-27
2 g8730.t1 Pfam PF00520 Ion transport protein 186 416 3.4E-42
4 g8730.t1 Pfam PF11879 Domain of unknown function (DUF3399) 448 543 6.2E-17
40 g8730.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 15 -
41 g8730.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 1 -
42 g8730.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 2 10 -
49 g8730.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 11 15 -
37 g8730.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 16 226 -
46 g8730.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 227 249 -
35 g8730.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 250 260 -
44 g8730.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 261 279 -
39 g8730.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 280 284 -
43 g8730.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 285 303 -
34 g8730.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 304 323 -
48 g8730.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 324 345 -
36 g8730.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 346 356 -
45 g8730.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 357 373 -
33 g8730.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 374 384 -
47 g8730.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 385 406 -
38 g8730.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 407 549 -
57 g8730.t1 SMART SM00225 BTB_4 41 140 5.2E-18
29 g8730.t1 SUPERFAMILY SSF54695 POZ domain 40 145 5.61E-32
28 g8730.t1 SUPERFAMILY SSF81324 Voltage-gated potassium channels 181 411 3.08E-57
54 g8730.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 182 204 -
51 g8730.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 225 247 -
56 g8730.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 257 279 -
53 g8730.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 325 344 -
52 g8730.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 354 373 -
55 g8730.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 385 407 -

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:0005249 voltage-gated potassium channel activity MF
GO:0051260 protein homooligomerization BP
GO:0006811 ion transport BP
GO:0005216 ion channel activity MF
GO:0005515 protein binding MF
GO:0008076 voltage-gated potassium channel complex CC

KEGG

Orthology

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