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.t7 isoform g11830.t7 18613779 18616693
chr_1 g11830 g11830.t7 exon g11830.t7.exon1 18613779 18614512
chr_1 g11830 g11830.t7 cds g11830.t7.CDS1 18614422 18614512
chr_1 g11830 g11830.t7 exon g11830.t7.exon2 18614595 18614701
chr_1 g11830 g11830.t7 cds g11830.t7.CDS2 18614595 18614701
chr_1 g11830 g11830.t7 exon g11830.t7.exon3 18614762 18614868
chr_1 g11830 g11830.t7 cds g11830.t7.CDS3 18614762 18614868
chr_1 g11830 g11830.t7 exon g11830.t7.exon4 18614923 18615086
chr_1 g11830 g11830.t7 cds g11830.t7.CDS4 18614923 18615086
chr_1 g11830 g11830.t7 exon g11830.t7.exon5 18615151 18616693
chr_1 g11830 g11830.t7 cds g11830.t7.CDS5 18615151 18616667
chr_1 g11830 g11830.t7 TSS g11830.t7 18617414 18617414
chr_1 g11830 g11830.t7 TTS g11830.t7 NA NA

Sequences

>g11830.t7 Gene=g11830 Length=2655
GTGTGATTGATATTGGTGCAAGTTGGATGACAGATTTGAAATTTGGAATTTGTCCACAAG
CATTTTGGTTAAATAGAGAACAATGTTGTTGGTCATCAAATGAAACGACTTTTGATGCAG
GAAATTGTTCACAATGGGTTACATGGTCTGAGATCCTTGTGAGTGCCAAAGAAGGTTTTG
GAGCGTATATTGTGATGTACTTTTTCTACATATTCTGGGCGTTGTTTTTCTCAACTCTTG
CTGCACTTCTTGTAAAAAATTTTGCTCCATATGCCTGTGGATCAGGTATTCCAGAAATAA
AAACTATTTTATCAGGATTTATAATACGAGGCTATTTGGGCAAATGGACACTTATCATTA
AATCTGTTGGAATCATACTGTCTGTATCAGCAGGTTTGAGTTTGGGAAAAGAAGGCCCAA
TGGTGCATATTGCCAGTTGTATTGGAAACATACTCTCTTATCTATTTCCCAAGTATGGTC
GGAATGAAGCAAAAAAGCGTGAAATTTTATCCGCTGCAGCTGCTGCAGGAGTCAGTGTTG
CTTTTGGCGCACCCATTGGAGGCGTTTTATTCAGTTTGGAAGAAGTATCATATTACTTTC
CTCTGAAAACACTTTGGAGATCATTCTTTTGTGCTCTAATCGCTGCCTTCATCTTACGCT
CTATCAATCCATTTGGAAATGAACATTCTGTATTGTTTTTCGTAGAATATTCAAAACCAT
GGATTTTTGTTGAACTTTTACCATTCATATTTCTTGGAGTGATGGGTGGTTGTATAGGAA
CACTATTCATTAAAGCGAACATTTATTGGTGTAAATTCAGAAAATGTAGCAAATTAGGAC
AATATCCAGTTGCTGAAGTACTCATTGTCACGCTTATTACTGCTGTCATTGCATTTCCAA
ATCCCTACACACGAATGAATACAAGTGAACTCATTTATTTACTCTTCAGTCAATGCGGTA
TTTCAAGTGGTGATCCAATATGTGACTACAAGAGAAATTTTACAAATGTGAATCAAGCAA
TTGAGATAGCTGCTGCTGGTCCTGGTGTTTATAAAGCCATCTGGCTTTTAATACTTGCAA
TGATTGTAAAACTTATTATGACAATCTTTACATTTGGAATCAAAGTTCCCTGTGGTTTAT
TCATTCCATCCTTGTGCTTAGGAGCGATTATGGGTCGAATCGTTGGAATTTGTATGGAAC
AATTGGCATATAATTATTCAAAGAATTGGATATTTTCGGGTGAATGTACTCAAGGTGATG
ATTGTATTCAGCCTGGTTTGTATGCAATGGTGGGAGCTGCTGCAGTTTTAGGTGGAGTAA
CACGAATGACAGTTTCTTTAGTTGTTATAATGTTTGAACTAACTGGCGGTGTTCGATATA
TTGTGCCATTGATGGCTGCGGCAATGGCTTCAAAATGGGTTGGCGATGCATTAGGAAGAC
AAGGTATTTACGATGCACATATCGCACTAAATGGCTATCCCTTCCTTGATAGTAAAGACG
AATTTCAACACACAACATTAGCGGGTGATGTCATGCAACCAAAACGTAATGAAGGATTAG
CAGTTATAACTCAAGATTCCATGACAATAGATGATATTGAAGTTCTTCTCAAAGACACTG
AACATAATGGATATCCTGTTGTTGTTTCACGTGAAAATCAATATTTAGTAGGATTTGTTT
TAAGAAGAGACTTGAATTTGGCATTAGCAAATGCAAAAAGAAATTTCGATGGAATTTCTG
GTCAATCATTAGTGATATTCACTAATAGTAGCAGTGTGCAAAATCTTGGCCCTGCACCAC
TTAAATTGAAAAAAATATTGGATATGGCACCTATTACAGTAACTGATCAAACTCCTATGG
AAACAGTTGTAGATATGTTTAGAAAGTTAGGCTTACGACAAACTTTAGTCACTCATAACG
GTCGTCTATTGGGTGTAATAACAAAGAAAGATGTTTTGAGACATGTTAAACAAATGGATA
ATGAAGATCCAACTACAATATTATTCAATTAAACACATCAATAACTTTTTTTTCTGTTAT
CAATGATAAAACTAATTGAAAGTTTTCCATAAGCTTATAATAATAGAATGTGACAGAGAA
AGTAAAAAAGAACCTATATTTATTTATTTTTACTATAATTTCAATTTTTTTATATTTTTG
CATGTTTTTCTGTTTAATGTATTTGTAGCAAAAAAAGTATATCTGACTGAAAGTGATAAT
GTTTAAACTTTAAAGATACATACAAATGAAATTAAAATTTCCAAAAGAAACATAAGAAAG
ATCAATGTACATTATGATAATTAATCTACAGATCGAATAGTTCCAATTAATCTAATACTA
GTTGTATACAAAAAAAATATATCTATAATAAAAAGTATGTTTCAAACAAAACGTTTTCGC
ATCAAATTTTTCTTTTAATTTATTCCTATGAATAAAAAGAAATGTATCTTCGTATGCATC
CATCCATTTTACTCAACATGACGACAATCATTTATTAATAAACAAATTCAGACACGAGTT
TGATTTAAATGAATGAAATGATTCAAACATCCTACATATATAATTTCTTATTAGATGTCT
AATTCAAGGATTGTCATACAATCGTCATTATAATTATATAATTTCGTCATTATGTAAAGA
TCTCGAACTCGAATC

>g11830.t7 Gene=g11830 Length=661
MTDLKFGICPQAFWLNREQCCWSSNETTFDAGNCSQWVTWSEILVSAKEGFGAYIVMYFF
YIFWALFFSTLAALLVKNFAPYACGSGIPEIKTILSGFIIRGYLGKWTLIIKSVGIILSV
SAGLSLGKEGPMVHIASCIGNILSYLFPKYGRNEAKKREILSAAAAAGVSVAFGAPIGGV
LFSLEEVSYYFPLKTLWRSFFCALIAAFILRSINPFGNEHSVLFFVEYSKPWIFVELLPF
IFLGVMGGCIGTLFIKANIYWCKFRKCSKLGQYPVAEVLIVTLITAVIAFPNPYTRMNTS
ELIYLLFSQCGISSGDPICDYKRNFTNVNQAIEIAAAGPGVYKAIWLLILAMIVKLIMTI
FTFGIKVPCGLFIPSLCLGAIMGRIVGICMEQLAYNYSKNWIFSGECTQGDDCIQPGLYA
MVGAAAVLGGVTRMTVSLVVIMFELTGGVRYIVPLMAAAMASKWVGDALGRQGIYDAHIA
LNGYPFLDSKDEFQHTTLAGDVMQPKRNEGLAVITQDSMTIDDIEVLLKDTEHNGYPVVV
SRENQYLVGFVLRRDLNLALANAKRNFDGISGQSLVIFTNSSSVQNLGPAPLKLKKILDM
APITVTDQTPMETVVDMFRKLGLRQTLVTHNGRLLGVITKKDVLRHVKQMDNEDPTTILF
N

Protein features from InterProScan

Transcript Database ID Name Start End E.value
42 g11830.t7 CDD cd03684 ClC_3_like 41 487 0.0
41 g11830.t7 CDD cd04591 CBS_pair_voltage-gated_CLC_euk_bac 498 646 1.73152E-46
16 g11830.t7 Gene3D G3DSA:1.10.3080.10 Clc chloride channel 31 489 8.9E-144
17 g11830.t7 Gene3D G3DSA:3.90.1280.20 - 495 650 3.0E-70
15 g11830.t7 Gene3D G3DSA:3.10.580.20 - 512 602 3.0E-70
4 g11830.t7 PANTHER PTHR45711 CHLORIDE CHANNEL PROTEIN 1 655 0.0
5 g11830.t7 PANTHER PTHR45711:SF8 H(+)/CL(-) EXCHANGE TRANSPORTER 3 1 655 0.0
7 g11830.t7 PRINTS PR00762 Chloride channel signature 81 98 2.4E-75
11 g11830.t7 PRINTS PR00762 Chloride channel signature 112 131 2.4E-75
9 g11830.t7 PRINTS PR00762 Chloride channel signature 166 185 2.4E-75
12 g11830.t7 PRINTS PR00762 Chloride channel signature 367 387 2.4E-75
10 g11830.t7 PRINTS PR00762 Chloride channel signature 417 433 2.4E-75
8 g11830.t7 PRINTS PR00762 Chloride channel signature 435 454 2.4E-75
6 g11830.t7 PRINTS PR00762 Chloride channel signature 474 488 2.4E-75
3 g11830.t7 Pfam PF00654 Voltage gated chloride channel 68 467 1.2E-99
2 g11830.t7 Pfam PF00571 CBS domain 512 560 0.0012
1 g11830.t7 Pfam PF00571 CBS domain 601 647 6.6E-7
24 g11830.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 50 -
31 g11830.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 51 76 -
20 g11830.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 77 108 -
40 g11830.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 109 126 -
29 g11830.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 127 131 -
32 g11830.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 132 148 -
23 g11830.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 149 159 -
36 g11830.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 160 184 -
27 g11830.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 185 195 -
30 g11830.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 196 213 -
21 g11830.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 214 232 -
34 g11830.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 233 255 -
26 g11830.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 256 274 -
33 g11830.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 275 294 -
18 g11830.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 295 343 -
35 g11830.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 344 365 -
25 g11830.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 366 370 -
39 g11830.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 371 390 -
22 g11830.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 391 417 -
37 g11830.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 418 443 -
28 g11830.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 444 448 -
38 g11830.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 449 466 -
19 g11830.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 467 661 -
55 g11830.t7 ProSiteProfiles PS51371 CBS domain profile. 503 569 8.529
56 g11830.t7 ProSiteProfiles PS51371 CBS domain profile. 598 656 10.748
54 g11830.t7 SMART SM00116 cbs_1 511 561 0.011
53 g11830.t7 SMART SM00116 cbs_1 601 648 9.8E-9
14 g11830.t7 SUPERFAMILY SSF81340 Clc chloride channel 51 490 2.49E-116
13 g11830.t7 SUPERFAMILY SSF54631 CBS-domain pair 490 647 3.41E-28
51 g11830.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 54 76 -
49 g11830.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 103 125 -
50 g11830.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 130 147 -
44 g11830.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 160 182 -
46 g11830.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 232 254 -
43 g11830.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 275 297 -
47 g11830.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 344 365 -
52 g11830.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 372 394 -
48 g11830.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 414 431 -
45 g11830.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 438 460 -

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

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