Gene loci information

Transcript annotation

  • This transcript has been annotated as H(+)/Cl(-) exchange transporter 5.

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.t2 isoform g11830.t2 18612956 18615954
chr_1 g11830 g11830.t2 exon g11830.t2.exon1 18612956 18613525
chr_1 g11830 g11830.t2 exon g11830.t2.exon2 18613619 18613679
chr_1 g11830 g11830.t2 cds g11830.t2.CDS1 18613669 18613679
chr_1 g11830 g11830.t2 exon g11830.t2.exon3 18615203 18615954
chr_1 g11830 g11830.t2 cds g11830.t2.CDS2 18615203 18615932
chr_1 g11830 g11830.t2 TSS g11830.t2 NA NA
chr_1 g11830 g11830.t2 TTS g11830.t2 NA NA

Sequences

>g11830.t2 Gene=g11830 Length=1383
ACCATTCATATTTCTTGGAGTGATGGGTGGTTGTATAGGAACACTATTCATTAAAGCGAA
CATTTATTGGTGTAAATTCAGAAAATGTAGCAAATTAGGACAATATCCAGTTGCTGAAGT
ACTCATTGTCACGCTTATTACTGCTGTCATTGCATTTCCAAATCCCTACACACGAATGAA
TACAAGTGAACTCATTTATTTACTCTTCAGTCAATGCGGTATTTCAAGTGGTGATCCAAT
ATGTGACTACAAGAGAAATTTTACAAATGTGAATCAAGCAATTGAGATAGCTGCTGCTGG
TCCTGGTGTTTATAAAGCCATCTGGCTTTTAATACTTGCAATGATTGTAAAACTTATTAT
GACAATCTTTACATTTGGAATCAAAGTTCCCTGTGGTTTATTCATTCCATCCTTGTGCTT
AGGAGCGATTATGGGTCGAATCGTTGGAATTTGTATGGAACAATTGGCATATAATTATTC
AAAGAATTGGATATTTTCGGGTGAATGTACTCAAGGTGATGATTGTATTCAGCCTGGTTT
GTATGCAATGGTGGGAGCTGCTGCAGTTTTAGGTGGAGTAACACGAATGACAGTTTCTTT
AGTTGTTATAATGTTTGAACTAACTGGCGGTGTTCGATATATTGTGCCATTGATGGCTGC
GGCAATGGCTTCAAAATGGGTTGGCGATGCATTAGGAAGACAAGGTATTTACGATGCACA
TATCGCACTAAATGGCTATCCCTTCCTTGATACACAATTTTAAAACTTTCAAGAATTTTA
TAATTTTTTTGTTTCCGCACATTGATTATATATCATACCTGAGACAGTTACAATGTTACT
GACGTTATTATCAACGACGTTATTTACTTCTGATGGTGATTTTTTTAGGTAAGGACACTC
GACGATTTTTACAATTTTTTGCGATCTTTTGCAATCTTTTGCAATCTTTCAATCTTCGTT
AAATTTTGTCATTTTAAAACATTTTCTTACTCGTCTCACTATAGATTAGCATCTATTATC
ATATGTTTTACATTTATTAAACGTTTAGATGAAGAATCAGTTGATGAATCAAGAGTAAAT
CAACAAAATTTTAAATTGATTTCTTTGTTTACAAATTTCGAATTTTTTTAAAAAAAATTT
CCGAACACAAACAAAAAGAAATTTGCAATTTTAGCTAAAATACAGCCTTAAACTGTAATA
TTCTATTAGAAAAGGATAATAAGGGACGGCAAAAGACTTTTCTGTGTACATTAGATCATT
TAATTCAACGAAAAATGCAAATTTTACCAAAACCAAATTTTACGATTTTTTGCAATCTTT
TGAGATCTTTCGCGATTTTTTTTCGAGTGTCCTAGTCTGGGATTTTTTCTACTTCTATAT
CTT

>g11830.t2 Gene=g11830 Length=246
MGGCIGTLFIKANIYWCKFRKCSKLGQYPVAEVLIVTLITAVIAFPNPYTRMNTSELIYL
LFSQCGISSGDPICDYKRNFTNVNQAIEIAAAGPGVYKAIWLLILAMIVKLIMTIFTFGI
KVPCGLFIPSLCLGAIMGRIVGICMEQLAYNYSKNWIFSGECTQGDDCIQPGLYAMVGAA
AVLGGVTRMTVSLVVIMFELTGGVRYIVPLMAAAMASKWVGDALGRQGIYDAHIALNGYP
FLDTQF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g11830.t2 Gene3D G3DSA:1.10.3080.10 Clc chloride channel 1 244 2.6E-62
2 g11830.t2 PANTHER PTHR45711 CHLORIDE CHANNEL PROTEIN 2 244 6.0E-107
3 g11830.t2 PANTHER PTHR45711:SF8 H(+)/CL(-) EXCHANGE TRANSPORTER 3 2 244 6.0E-107
7 g11830.t2 PRINTS PR00762 Chloride channel signature 122 142 6.1E-39
6 g11830.t2 PRINTS PR00762 Chloride channel signature 172 188 6.1E-39
4 g11830.t2 PRINTS PR00762 Chloride channel signature 190 209 6.1E-39
5 g11830.t2 PRINTS PR00762 Chloride channel signature 229 243 6.1E-39
1 g11830.t2 Pfam PF00654 Voltage gated chloride channel 2 222 5.2E-43
15 g11830.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 27 -
20 g11830.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 28 45 -
19 g11830.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 46 98 -
22 g11830.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 99 119 -
17 g11830.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 120 125 -
21 g11830.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 126 150 -
18 g11830.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 151 172 -
23 g11830.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 173 198 -
16 g11830.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 199 246 -
13 g11830.t2 SUPERFAMILY SSF81340 Clc chloride channel 2 244 2.49E-53
10 g11830.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 28 50 -
9 g11830.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 99 120 -
12 g11830.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 127 149 -
11 g11830.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 169 186 -
8 g11830.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 193 215 -

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