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.t6 isoform g11830.t6 18613779 18615954
chr_1 g11830 g11830.t6 exon g11830.t6.exon1 18613779 18614512
chr_1 g11830 g11830.t6 exon g11830.t6.exon2 18614591 18614701
chr_1 g11830 g11830.t6 cds g11830.t6.CDS1 18614591 18614701
chr_1 g11830 g11830.t6 exon g11830.t6.exon3 18614762 18614868
chr_1 g11830 g11830.t6 cds g11830.t6.CDS2 18614762 18614868
chr_1 g11830 g11830.t6 exon g11830.t6.exon4 18614923 18615086
chr_1 g11830 g11830.t6 cds g11830.t6.CDS3 18614923 18615086
chr_1 g11830 g11830.t6 exon g11830.t6.exon5 18615151 18615954
chr_1 g11830 g11830.t6 cds g11830.t6.CDS4 18615151 18615932
chr_1 g11830 g11830.t6 TSS g11830.t6 NA NA
chr_1 g11830 g11830.t6 TTS g11830.t6 NA NA

Sequences

>g11830.t6 Gene=g11830 Length=1920
ACCATTCATATTTCTTGGAGTGATGGGTGGTTGTATAGGAACACTATTCATTAAAGCGAA
CATTTATTGGTGTAAATTCAGAAAATGTAGCAAATTAGGACAATATCCAGTTGCTGAAGT
ACTCATTGTCACGCTTATTACTGCTGTCATTGCATTTCCAAATCCCTACACACGAATGAA
TACAAGTGAACTCATTTATTTACTCTTCAGTCAATGCGGTATTTCAAGTGGTGATCCAAT
ATGTGACTACAAGAGAAATTTTACAAATGTGAATCAAGCAATTGAGATAGCTGCTGCTGG
TCCTGGTGTTTATAAAGCCATCTGGCTTTTAATACTTGCAATGATTGTAAAACTTATTAT
GACAATCTTTACATTTGGAATCAAAGTTCCCTGTGGTTTATTCATTCCATCCTTGTGCTT
AGGAGCGATTATGGGTCGAATCGTTGGAATTTGTATGGAACAATTGGCATATAATTATTC
AAAGAATTGGATATTTTCGGGTGAATGTACTCAAGGTGATGATTGTATTCAGCCTGGTTT
GTATGCAATGGTGGGAGCTGCTGCAGTTTTAGGTGGAGTAACACGAATGACAGTTTCTTT
AGTTGTTATAATGTTTGAACTAACTGGCGGTGTTCGATATATTGTGCCATTGATGGCTGC
GGCAATGGCTTCAAAATGGGTTGGCGATGCATTAGGAAGACAAGGTATTTACGATGCACA
TATCGCACTAAATGGCTATCCCTTCCTTGATAGTAAAGACGAATTTCAACACACAACATT
AGCGGGTGATGTCATGCAACCAAAACGTAATGAAGGATTAGCAGTTATAACTCAAGATTC
CATGACAATAGATGATATTGAAGTTCTTCTCAAAGACACTGAACATAATGGATATCCTGT
TGTTGTTTCACGTGAAAATCAATATTTAGTAGGATTTGTTTTAAGAAGAGACTTGAATTT
GGCATTAGCAAATGCAAAAAGAAATTTCGATGGAATTTCTGGTCAATCATTAGTGATATT
CACTAATAGTAGCAGTGTGCAAAATCTTGGCCCTGCACCACTTAAATTGAAAAAAATATT
GGATATGGCACCTATTACAGTAACTGATCAAACTCCTATGGAAACAGTTGTAGATATGTT
TAGAAAGTTAGGCTTACGACAAACTTTAGTCACTCATAACGGGTGATCGTCTATTGGGTG
TAATAACAAAGAAAGATGTTTTGAGACATGTTAAACAAATGGATAATGAAGATCCAACTA
CAATATTATTCAATTAAACACATCAATAACTTTTTTTTCTGTTATCAATGATAAAACTAA
TTGAAAGTTTTCCATAAGCTTATAATAATAGAATGTGACAGAGAAAGTAAAAAAGAACCT
ATATTTATTTATTTTTACTATAATTTCAATTTTTTTATATTTTTGCATGTTTTTCTGTTT
AATGTATTTGTAGCAAAAAAAGTATATCTGACTGAAAGTGATAATGTTTAAACTTTAAAG
ATACATACAAATGAAATTAAAATTTCCAAAAGAAACATAAGAAAGATCAATGTACATTAT
GATAATTAATCTACAGATCGAATAGTTCCAATTAATCTAATACTAGTTGTATACAAAAAA
AATATATCTATAATAAAAAGTATGTTTCAAACAAAACGTTTTCGCATCAAATTTTTCTTT
TAATTTATTCCTATGAATAAAAAGAAATGTATCTTCGTATGCATCCATCCATTTTACTCA
ACATGACGACAATCATTTATTAATAAACAAATTCAGACACGAGTTTGATTTAAATGAATG
AAATGATTCAAACATCCTACATATATAATTTCTTATTAGATGTCTAATTCAAGGATTGTC
ATACAATCGTCATTATAATTATATAATTTCGTCATTATGTAAAGATCTCGAACTCGAATC

>g11830.t6 Gene=g11830 Length=387
MGGCIGTLFIKANIYWCKFRKCSKLGQYPVAEVLIVTLITAVIAFPNPYTRMNTSELIYL
LFSQCGISSGDPICDYKRNFTNVNQAIEIAAAGPGVYKAIWLLILAMIVKLIMTIFTFGI
KVPCGLFIPSLCLGAIMGRIVGICMEQLAYNYSKNWIFSGECTQGDDCIQPGLYAMVGAA
AVLGGVTRMTVSLVVIMFELTGGVRYIVPLMAAAMASKWVGDALGRQGIYDAHIALNGYP
FLDSKDEFQHTTLAGDVMQPKRNEGLAVITQDSMTIDDIEVLLKDTEHNGYPVVVSRENQ
YLVGFVLRRDLNLALANAKRNFDGISGQSLVIFTNSSSVQNLGPAPLKLKKILDMAPITV
TDQTPMETVVDMFRKLGLRQTLVTHNG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g11830.t6 CDD cd04591 CBS_pair_voltage-gated_CLC_euk_bac 253 387 4.34992E-37
12 g11830.t6 Gene3D G3DSA:1.10.3080.10 Clc chloride channel 1 244 1.1E-61
13 g11830.t6 Gene3D G3DSA:3.90.1280.20 - 250 387 2.6E-58
11 g11830.t6 Gene3D G3DSA:3.10.580.20 - 267 357 2.6E-58
3 g11830.t6 PANTHER PTHR45711 CHLORIDE CHANNEL PROTEIN 2 387 8.8E-172
4 g11830.t6 PANTHER PTHR45711:SF8 H(+)/CL(-) EXCHANGE TRANSPORTER 3 2 387 8.8E-172
8 g11830.t6 PRINTS PR00762 Chloride channel signature 122 142 2.7E-38
7 g11830.t6 PRINTS PR00762 Chloride channel signature 172 188 2.7E-38
5 g11830.t6 PRINTS PR00762 Chloride channel signature 190 209 2.7E-38
6 g11830.t6 PRINTS PR00762 Chloride channel signature 229 243 2.7E-38
2 g11830.t6 Pfam PF00654 Voltage gated chloride channel 2 222 2.2E-42
1 g11830.t6 Pfam PF00571 CBS domain 267 315 5.7E-4
14 g11830.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 27 -
19 g11830.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 28 45 -
18 g11830.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 46 98 -
21 g11830.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 99 119 -
15 g11830.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 120 125 -
20 g11830.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 126 150 -
17 g11830.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 151 172 -
22 g11830.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 173 198 -
16 g11830.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 199 387 -
10 g11830.t6 SUPERFAMILY SSF81340 Clc chloride channel 2 245 2.22E-53
9 g11830.t6 SUPERFAMILY SSF54631 CBS-domain pair 245 387 1.64E-20
26 g11830.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 28 50 -
25 g11830.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 99 120 -
28 g11830.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 127 149 -
27 g11830.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 169 186 -
24 g11830.t6 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