Gene loci information

Transcript annotation

  • This transcript has been annotated as Bumetanide-sensitive sodium-(potassium)-chloride cotransporter.

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_1 g11665 g11665.t2 isoform g11665.t2 17705578 17707855
chr_1 g11665 g11665.t2 exon g11665.t2.exon1 17705578 17705921
chr_1 g11665 g11665.t2 cds g11665.t2.CDS1 17705578 17705921
chr_1 g11665 g11665.t2 exon g11665.t2.exon2 17705977 17706091
chr_1 g11665 g11665.t2 cds g11665.t2.CDS2 17705977 17706091
chr_1 g11665 g11665.t2 exon g11665.t2.exon3 17707276 17707406
chr_1 g11665 g11665.t2 cds g11665.t2.CDS3 17707276 17707406
chr_1 g11665 g11665.t2 exon g11665.t2.exon4 17707479 17707855
chr_1 g11665 g11665.t2 cds g11665.t2.CDS4 17707479 17707854
chr_1 g11665 g11665.t2 TSS g11665.t2 NA NA
chr_1 g11665 g11665.t2 TTS g11665.t2 NA NA

Sequences

>g11665.t2 Gene=g11665 Length=967
ATGGCTGCAAAAGCAGAGAATTCCAATTCATTAGAACTCAGTTCTATGACACGATCGTCT
TCTGCTAATCGATTTCAAGTAAATCCAGTGAATAAGGATTCAAATGGTACTAACAATCAA
CATGAAGGTAATGAGGACGAAGTAGATCATTTCAGTGAAGATACTGAAATGGTTACACAG
AGAAGAACATCACGCATTCAATCACTTAAAAGTAGCTTCAGAGATTCCGAAAAGAAGCGA
AAAGAAAGCGTAACACGATTTAAAGTCAGCGATGAAAATTCTGATGAAGATGAAAATCTT
CTCGATGGAAATGAATATGACACGAAATATGGAAGAAGCTTTAGGCATTTTACACGTGAA
GCACTTCCACGTTTAGACAATTATCGAAATATTATGTCATTACAAGCTGGAACTCGACCG
ACACTCGAAGAGCTTCACAATGCATCGATAACAAATAAGGCACAAACATTTTCATCTAAT
GTAGATCCAGAAGGATTAACGGAAGGTGTTATCAAATTTGGATGGATCAAAGGCGTATTG
ATGAGATGTTTATTGAATATTTGGGGTGTTATGCTTTTCTTGCGACTTAGTTGGGTAGTT
GGTCAAGCAGGCATAATGCAGGGTCTAATTTTAATTTCAATAACAACATGTGTGACAGCA
ATTACTGCTTTAAGTATGAGCGCTATCAGCACAAATGGCATAATCAAGGGTGGTGGTACA
TATTTCATGATATCAAGAAGTCTTGGACCTGAATTTGGTGGCTCGATTGGATTAATTTTT
TCATTAGCAAATGCTGTTGCTGTGGCCATGTATATTGTTGGATTTTGTGAGTCGCTTCTC
GATCTTTTGTGGAACTCTTTCCAAATTCAAATATTTGATGGCGGTGTACAAGATACAAGA
ATTATTGGCAGCATTACTGTTGTCGTTTTACTTATTATTGTCGTTATCGGAATGGAATGG
GAAGCAA

>g11665.t2 Gene=g11665 Length=322
MAAKAENSNSLELSSMTRSSSANRFQVNPVNKDSNGTNNQHEGNEDEVDHFSEDTEMVTQ
RRTSRIQSLKSSFRDSEKKRKESVTRFKVSDENSDEDENLLDGNEYDTKYGRSFRHFTRE
ALPRLDNYRNIMSLQAGTRPTLEELHNASITNKAQTFSSNVDPEGLTEGVIKFGWIKGVL
MRCLLNIWGVMLFLRLSWVVGQAGIMQGLILISITTCVTAITALSMSAISTNGIIKGGGT
YFMISRSLGPEFGGSIGLIFSLANAVAVAMYIVGFCESLLDLLWNSFQIQIFDGGVQDTR
IIGSITVVVLLIIVVIGMEWEA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g11665.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 98 -
11 g11665.t2 MobiDBLite mobidb-lite consensus disorder prediction 7 38 -
12 g11665.t2 MobiDBLite mobidb-lite consensus disorder prediction 39 60 -
9 g11665.t2 MobiDBLite mobidb-lite consensus disorder prediction 71 94 -
3 g11665.t2 PANTHER PTHR11827:SF48 GH09711P 58 322 2.7E-83
4 g11665.t2 PANTHER PTHR11827 SOLUTE CARRIER FAMILY 12, CATION COTRANSPORTERS 58 322 2.7E-83
2 g11665.t2 Pfam PF08403 Amino acid permease N-terminal 107 152 1.0E-4
1 g11665.t2 Pfam PF00324 Amino acid permease 178 322 2.3E-32
15 g11665.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 178 -
19 g11665.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 179 198 -
16 g11665.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 199 209 -
21 g11665.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 210 235 -
14 g11665.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 236 255 -
18 g11665.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 256 280 -
17 g11665.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 281 299 -
20 g11665.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 300 320 -
13 g11665.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 321 322 -
5 g11665.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 183 205 -
8 g11665.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 209 231 -
7 g11665.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 252 274 -
6 g11665.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 301 318 -

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

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