Gene loci information

Transcript annotation

  • This transcript has been annotated as H(+)/Cl(-) exchange transporter 3.

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 g11830 g11830.t8 isoform g11830.t8 18615954 18617265
chr_1 g11830 g11830.t8 exon g11830.t8.exon1 18615954 18616693
chr_1 g11830 g11830.t8 cds g11830.t8.CDS1 18615954 18616693
chr_1 g11830 g11830.t8 exon g11830.t8.exon2 18616754 18616823
chr_1 g11830 g11830.t8 cds g11830.t8.CDS2 18616754 18616823
chr_1 g11830 g11830.t8 exon g11830.t8.exon3 18616942 18617023
chr_1 g11830 g11830.t8 cds g11830.t8.CDS3 18616942 18617023
chr_1 g11830 g11830.t8 exon g11830.t8.exon4 18617147 18617265
chr_1 g11830 g11830.t8 cds g11830.t8.CDS4 18617147 18617265
chr_1 g11830 g11830.t8 TSS g11830.t8 18617414 18617414
chr_1 g11830 g11830.t8 TTS g11830.t8 NA NA

Sequences

>g11830.t8 Gene=g11830 Length=1011
ATGGACGAAAACGAATTTAAAATGTCGTCATCATCTTCTCAAGATTTTACTGGAGCCGAT
GCTTTTGAAGAGGATTGGTATCAAAATTCTCCTTATTCAGATTTCTACACAATTGATTGG
TTAAAAGATCTTGCAAGAGATCGTATGCGACATCGATATATTCTAAAGAGACGACAAAAT
TCATTATGGGAACTTATAAAGGGCGCTCACGACGCACTTTCAGGCTGGTTGTGTGTGTTA
CTCGTAGGATTAGTAACAGGATGTGTTGCAGGTGTGATTGATATTGGTGCAAGTTGGATG
ACAGATTTGAAATTTGGAATTTGTCCACAAGCATTTTGGTTAAATAGAGAACAATGTTGT
TGGTCATCAAATGAAACGACTTTTGATGCAGGAAATTGTTCACAATGGGTTACATGGTCT
GAGATCCTTGTGAGTGCCAAAGAAGGTTTTGGAGCGTATATTGTGATGTACTTTTTCTAC
ATATTCTGGGCGTTGTTTTTCTCAACTCTTGCTGCACTTCTTGTAAAAAATTTTGCTCCA
TATGCCTGTGGATCAGGTATTCCAGAAATAAAAACTATTTTATCAGGATTTATAATACGA
GGCTATTTGGGCAAATGGACACTTATCATTAAATCTGTTGGAATCATACTGTCTGTATCA
GCAGGTTTGAGTTTGGGAAAAGAAGGCCCAATGGTGCATATTGCCAGTTGTATTGGAAAC
ATACTCTCTTATCTATTTCCCAAGTATGGTCGGAATGAAGCAAAAAAGCGTGAAATTTTA
TCCGCTGCAGCTGCTGCAGGAGTCAGTGTTGCTTTTGGCGCACCCATTGGAGGCGTTTTA
TTCAGTTTGGAAGAAGTATCATATTACTTTCCTCTGAAAACACTTTGGAGATCATTCTTT
TGTGCTCTAATCGCTGCCTTCATCTTACGCTCTATCAATCCATTTGGAAATGAACATTCT
GTATTGTTTTTCGTAGAATATTCAAAACCATGGATTTTTGTTGAACTTTTA

>g11830.t8 Gene=g11830 Length=337
MDENEFKMSSSSSQDFTGADAFEEDWYQNSPYSDFYTIDWLKDLARDRMRHRYILKRRQN
SLWELIKGAHDALSGWLCVLLVGLVTGCVAGVIDIGASWMTDLKFGICPQAFWLNREQCC
WSSNETTFDAGNCSQWVTWSEILVSAKEGFGAYIVMYFFYIFWALFFSTLAALLVKNFAP
YACGSGIPEIKTILSGFIIRGYLGKWTLIIKSVGIILSVSAGLSLGKEGPMVHIASCIGN
ILSYLFPKYGRNEAKKREILSAAAAAGVSVAFGAPIGGVLFSLEEVSYYFPLKTLWRSFF
CALIAAFILRSINPFGNEHSVLFFVEYSKPWIFVELL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g11830.t8 Gene3D G3DSA:1.10.3080.10 Clc chloride channel 124 337 5.6E-72
2 g11830.t8 PANTHER PTHR45711 CHLORIDE CHANNEL PROTEIN 20 337 8.5E-151
3 g11830.t8 PANTHER PTHR45711:SF8 H(+)/CL(-) EXCHANGE TRANSPORTER 3 20 337 8.5E-151
5 g11830.t8 PRINTS PR00762 Chloride channel signature 180 197 6.2E-33
6 g11830.t8 PRINTS PR00762 Chloride channel signature 211 230 6.2E-33
4 g11830.t8 PRINTS PR00762 Chloride channel signature 265 284 6.2E-33
1 g11830.t8 Pfam PF00654 Voltage gated chloride channel 167 321 3.6E-49
15 g11830.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 72 -
27 g11830.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 73 93 -
21 g11830.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 94 149 -
22 g11830.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 150 175 -
18 g11830.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 176 207 -
23 g11830.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 208 225 -
19 g11830.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 226 230 -
24 g11830.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 231 247 -
17 g11830.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 248 258 -
26 g11830.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 259 283 -
20 g11830.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 284 294 -
25 g11830.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 295 312 -
16 g11830.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 313 337 -
13 g11830.t8 SUPERFAMILY SSF81340 Clc chloride channel 58 335 3.92E-63
12 g11830.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 73 95 -
11 g11830.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 153 175 -
10 g11830.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 202 224 -
8 g11830.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 229 246 -
9 g11830.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 259 281 -
7 g11830.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 296 313 -

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:0006821 chloride transport BP
GO:0005247 voltage-gated chloride 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.

Raw TPM values