Gene loci information

Transcript annotation

  • This transcript has been annotated as Chloride channel protein 2.

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_3 g2744 g2744.t22 isoform g2744.t22 19951005 19952278
chr_3 g2744 g2744.t22 exon g2744.t22.exon1 19951005 19951865
chr_3 g2744 g2744.t22 cds g2744.t22.CDS1 19951005 19951865
chr_3 g2744 g2744.t22 exon g2744.t22.exon2 19951953 19952087
chr_3 g2744 g2744.t22 cds g2744.t22.CDS2 19951953 19952087
chr_3 g2744 g2744.t22 exon g2744.t22.exon3 19952146 19952214
chr_3 g2744 g2744.t22 cds g2744.t22.CDS3 19952146 19952214
chr_3 g2744 g2744.t22 exon g2744.t22.exon4 19952270 19952278
chr_3 g2744 g2744.t22 cds g2744.t22.CDS4 19952270 19952272
chr_3 g2744 g2744.t22 TSS g2744.t22 NA NA
chr_3 g2744 g2744.t22 TTS g2744.t22 NA NA

Sequences

>g2744.t22 Gene=g2744 Length=1074
GCTTTGATGGTTGCAACACTTTCCTATCCAAATGGATTGGGAAGATATATTGCAGGTGAA
CTTAGCACACATGAGCAGGTCTCAAATCTTTTTACTAATTTCACGTGGTCAGAGCCAAAC
TTGAACGTTGAACAATCTGCCATTGTGCGTTATTGGACAAACCCATATACAAATGAAATT
TTTAGTATATTAATTTTTTATTTATTATATACGTTTTTCGTTTCAATAGTTACATCGACA
ATACCAGTTCCGAGTGGAATCTTTATTCCTGTATTTAAAATTGGAGCTGCTTTAGGAAGA
ATTATTGGTGAATCGATGCATCTATGGTTTCCAACTGGAATAAGATATGGTGGTCATATC
AATCACATTATCCCTGGTGGATATGCAGTAGTTGGAGCCTCTGCTTTTGCTGGTGCTGTT
ACTCATACAGTCTCTGTTGGAGTAATTGTTTTTGAAATGACAGGACAAATCTCACATCTG
GTTCCTGTAATGATAGCTACTTTGATTTCTTGTGCCATAGCTACTATATTGCAACCATCA
ATGTACGACTCAATTATTCTCATAAAAAAATTGCCATATCTGCCCGATCTTTTACCTACA
TCGAGTGGAATGTATAATTTTACTGTCGAAGACTTTATGGTTCGAGATATTAAATACATT
TGGCAAAACATTACCTATCAAGAACTGAAAGAGATTTTAAAGAAAAATAAACAATTAAGA
AGCCTTCCACTAGTTGACAATCCTGATACCATGATTTTACTTGGATCAGTACAACGATTT
GACCTCATAAAAATGATTGACAAACATATTGGTCGTGAAAAACGTCTTGAAATGGCAGCT
AGACGTAAAAAAGAAGCTGAAGAGCGTGAAGAACAAGAAAGAATAAAGAAATTGCAAGAG
GGACCAAGACGTGCATCACGATTTGAAGTCGTTCCTGCACCTGATATTGTTAAGCTTCGA
CAAATTGCCAATAATGAAATGCTCACACCTCAAGCAAAGAAAGAGAGCAATCAATTTACT
CCAGTATTTGGAACGCAGCCGAAAAAATCAATTTTAAAAAAGACAAATTCATTT

>g2744.t22 Gene=g2744 Length=356
MVATLSYPNGLGRYIAGELSTHEQVSNLFTNFTWSEPNLNVEQSAIVRYWTNPYTNEIFS
ILIFYLLYTFFVSIVTSTIPVPSGIFIPVFKIGAALGRIIGESMHLWFPTGIRYGGHINH
IIPGGYAVVGASAFAGAVTHTVSVGVIVFEMTGQISHLVPVMIATLISCAIATILQPSMY
DSIILIKKLPYLPDLLPTSSGMYNFTVEDFMVRDIKYIWQNITYQELKEILKKNKQLRSL
PLVDNPDTMILLGSVQRFDLIKMIDKHIGREKRLEMAARRKKEAEEREEQERIKKLQEGP
RRASRFEVVPAPDIVKLRQIANNEMLTPQAKKESNQFTPVFGTQPKKSILKKTNSF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g2744.t22 Coils Coil Coil 271 299 -
10 g2744.t22 Gene3D G3DSA:1.10.3080.10 Clc chloride channel 1 193 4.4E-48
9 g2744.t22 Gene3D G3DSA:3.10.580.10 - 194 311 1.7E-32
24 g2744.t22 MobiDBLite mobidb-lite consensus disorder prediction 279 301 -
2 g2744.t22 PANTHER PTHR45720 CHLORIDE CHANNEL PROTEIN 2 2 316 1.7E-114
5 g2744.t22 PRINTS PR00762 Chloride channel signature 81 101 3.4E-36
6 g2744.t22 PRINTS PR00762 Chloride channel signature 124 140 3.4E-36
4 g2744.t22 PRINTS PR00762 Chloride channel signature 141 160 3.4E-36
3 g2744.t22 PRINTS PR00762 Chloride channel signature 179 193 3.4E-36
1 g2744.t22 Pfam PF00654 Voltage gated chloride channel 58 172 1.1E-29
14 g2744.t22 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 57 -
19 g2744.t22 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 58 79 -
16 g2744.t22 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 80 84 -
20 g2744.t22 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 85 101 -
13 g2744.t22 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 102 120 -
17 g2744.t22 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 121 149 -
15 g2744.t22 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 150 154 -
18 g2744.t22 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 155 175 -
12 g2744.t22 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 176 356 -
25 g2744.t22 ProSiteProfiles PS51371 CBS domain profile. 211 271 9.294
8 g2744.t22 SUPERFAMILY SSF81340 Clc chloride channel 26 193 2.75E-33
7 g2744.t22 SUPERFAMILY SSF54631 CBS-domain pair 201 274 4.19E-15
23 g2744.t22 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 58 80 -
21 g2744.t22 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 126 148 -
22 g2744.t22 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 155 177 -

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