General information for g2744.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Chloride channel protein 2.
Parent gene
- The parent gene g2744 is located on chr_3: 19951005..19955422 (- strand)
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.t1 | TTS | g2744.t1 | 19949722 | 19949722 |
| chr_3 | g2744 | g2744.t1 | isoform | g2744.t1 | 19950191 | 19955422 |
| chr_3 | g2744 | g2744.t1 | exon | g2744.t1.exon1 | 19950191 | 19950457 |
| chr_3 | g2744 | g2744.t1 | cds | g2744.t1.CDS1 | 19950191 | 19950457 |
| chr_3 | g2744 | g2744.t1 | exon | g2744.t1.exon2 | 19950534 | 19951865 |
| chr_3 | g2744 | g2744.t1 | cds | g2744.t1.CDS2 | 19950534 | 19951865 |
| chr_3 | g2744 | g2744.t1 | exon | g2744.t1.exon3 | 19951953 | 19952087 |
| chr_3 | g2744 | g2744.t1 | cds | g2744.t1.CDS3 | 19951953 | 19952087 |
| chr_3 | g2744 | g2744.t1 | exon | g2744.t1.exon4 | 19952146 | 19952214 |
| chr_3 | g2744 | g2744.t1 | cds | g2744.t1.CDS4 | 19952146 | 19952214 |
| chr_3 | g2744 | g2744.t1 | exon | g2744.t1.exon5 | 19952270 | 19952638 |
| chr_3 | g2744 | g2744.t1 | cds | g2744.t1.CDS5 | 19952270 | 19952638 |
| chr_3 | g2744 | g2744.t1 | exon | g2744.t1.exon6 | 19952707 | 19952715 |
| chr_3 | g2744 | g2744.t1 | cds | g2744.t1.CDS6 | 19952707 | 19952715 |
| chr_3 | g2744 | g2744.t1 | exon | g2744.t1.exon7 | 19952793 | 19953052 |
| chr_3 | g2744 | g2744.t1 | cds | g2744.t1.CDS7 | 19952793 | 19953052 |
| chr_3 | g2744 | g2744.t1 | exon | g2744.t1.exon8 | 19953136 | 19953324 |
| chr_3 | g2744 | g2744.t1 | cds | g2744.t1.CDS8 | 19953136 | 19953324 |
| chr_3 | g2744 | g2744.t1 | exon | g2744.t1.exon9 | 19953381 | 19953486 |
| chr_3 | g2744 | g2744.t1 | cds | g2744.t1.CDS9 | 19953381 | 19953486 |
| chr_3 | g2744 | g2744.t1 | exon | g2744.t1.exon10 | 19953608 | 19953715 |
| chr_3 | g2744 | g2744.t1 | cds | g2744.t1.CDS10 | 19953608 | 19953715 |
| chr_3 | g2744 | g2744.t1 | exon | g2744.t1.exon11 | 19955186 | 19955422 |
| chr_3 | g2744 | g2744.t1 | cds | g2744.t1.CDS11 | 19955186 | 19955422 |
| chr_3 | g2744 | g2744.t1 | TSS | g2744.t1 | NA | NA |
Sequences
>g2744.t1 Gene=g2744 Length=3081
ATGGACATTGAAGATGAATACACTCGAGATTTTTCATTTGAACCGGAATTTATTACTCGA
AAAGATTCACTTCAAATGCATCGATCGCGTTTAGAGCGAACAAGAAAGCATAATAAAATT
TTTAAAATAAAGACAATATCATTGGATATTATTTTGGAGAAAGCACTTGTTAATGAACAA
CAAACCACATTGAGCACACAAAATATTGTCGAAGCTGAAGTTGAAGCATTTCGCACGATG
TATGGTCGCTATACAAAAGATTTAAGTGAATATGCCAAGGACGAAGCCAGAAGACTTAAG
CAGTTGGAAAGACAACGAAAAAAGGACGATAGAGCTAGAAATAAGGAACTTCTCGGTAAA
AAGGAGGGAAAATTTTTACGTGCATTCCGATGGTTTTGGAAACGTACATTTGCTAGAATG
GGAGAGGATTGGATTTTCTTAGCACTTTTAGGCATAATTATGGCTATAATTTCATATTGT
ATGGATAAGGGTATATCTATGTGCACAAATGCAAGAGTTTGGCTTTATAGAGATTTAGCT
GATCATCCAGTTACACAATATTTCGCATGGATCACATTACCAGTATGTCTGATATTATTT
TCAGCAGGTTTTGTACATCTATTAGCACCGCAATCAATTGGCTCTGGAATTCCCGAAATG
AAAACAATTTTGCGTGGTGTTCAATTAAAAGAATATTTGACATTCAAGACGTTGGTAGCA
AAGGTCATTGGCCTCACTGCGACTTTAGGAAGTGGTATGCCTTTAGGAAAAGAAGGCCCA
TTTGTACACATTGCTTCAATTGTAGCACAACTCTTGAGCAAATTAGTCACATCATTTCAG
GGTATTTTTGAAAATGAATCGAGAAACACAGAAATGCTTGCTGCAGCTTGTGCTGTCGGT
GTGGGCTCGTGCTTTGCAGCGCCTGTTGGTGGTGTTTTGTTTAGCATTGAAGTAACTACA
ACGTATTTTGCTGTTCGTAATTATTGGCGTGGTTTCTTTGGTGCTGTATGTGGTGCTACT
TTCTTTCGCTTGTTAGCTGTATGGTTTCAAAAAGCTGATACACTCACAGCACTTTTCCTT
ACTAGCTTCCACATGGATTTTCCCTATGATCCACAAGAACTTATAGCTTTTGCTATGATT
GGGGTTATAAGTGGACTTGGTGGTGCAGCATATGTGTGGATTCATCGTCAGTACGTTTTG
TTTATGCGATCGAGCAAACGAATGAATAACTTTTTACAAAAGAATAGATTTCTTTATCCA
GGAATATTGGCTTTGATGGTTGCAACACTTTCCTATCCAAATGGATTGGGAAGATATATT
GCAGGTGAACTTAGCACACATGAGCAGGTCTCAAATCTTTTTACTAATTTCACGTGGTCA
GAGCCAAACTTGAACGTTGAACAATCTGCCATTGTGCGTTATTGGACAAACCCATATACA
AATGAAATTTTTAGTATATTAATTTTTTATTTATTATATACGTTTTTCGTTTCAATAGTT
ACATCGACAATACCAGTTCCGAGTGGAATCTTTATTCCTGTATTTAAAATTGGAGCTGCT
TTAGGAAGAATTATTGGTGAATCGATGCATCTATGGTTTCCAACTGGAATAAGATATGGT
GGTCATATCAATCACATTATCCCTGGTGGATATGCAGTAGTTGGAGCCTCTGCTTTTGCT
GGTGCTGTTACTCATACAGTCTCTGTTGGAGTAATTGTTTTTGAAATGACAGGACAAATC
TCACATCTGGTTCCTGTAATGATAGCTACTTTGATTTCTTGTGCCATAGCTACTATATTG
CAACCATCAATGTACGACTCAATTATTCTCATAAAAAAATTGCCATATCTGCCCGATCTT
TTACCTACATCGAGTGGAATGTATAATTTTACTGTCGAAGACTTTATGGTTCGAGATATT
AAATACATTTGGCAAAACATTACCTATCAAGAACTGAAAGAGATTTTAAAGAAAAATAAA
CAATTAAGAAGCCTTCCACTAGTTGACAATCCTGATACCATGATTTTACTTGGATCAGTA
CAACGATTTGACCTCATAAAAATGATTGACAAACATATTGGTCGTGAAAAACGTCTTGAA
ATGGCAGCTAGACGTAAAAAAGAAGCTGAAGAGCGTGAAGAACAAGAAAGAATAAAGAAA
TTGCAAGAGGGACCAAGACGTGCATCACGATTTGAAGTCGTTCCTGCACCTGATATTGTT
AAGCTTCGACAAATTGCCAATAATGAAATGCTCACACCTCAAGCAAAGAAAGAGAGCAAT
CAATTTACTCCAGTATTTGGAACGCAGCCGAAAAAATCAATTTTAAAAAAGACAAATTCA
TTTACTATGAAAGGCTTCAGTCCATTATCACCTCATTCACCAGTAAATACGCCTTATTCA
ACAATCACCGGTGCAGAATCACGTTTACGTTCTGCGTTTGACATTATCTTTAGAAAATCA
GCTACACTACAAGATGTCCAAAATAACGATCCTGAGCTCGGTTCAAAATCATCAATTCAA
ACACCCAGTATCGATGGAACTCCATATCCTTCATCTCACATTTCTAAAAAAGTTCAATTG
CCACGCGAACGTGTCATAGACATGTCGGCTGAAGAACAAAAAATGTGGGAAATGGAAGAA
ATGTCGAAACCAATTGATTTGGATGCAGCCAATGTGAACATTGACCCATCTCCCTTCCAA
CTTGTACGTACAACTTCATTACTCAAAGTTCATTCACTGTTTTCGATGATTGGTATTAAT
CATGCATACGTCACACATGTTGGTCGTTTGGTCGGTGTTGTAGCTTTGAAAGAGCTTCGT
AAAGCAATTGAAGATGTAAACAGCGGAAATTTAGTGCCAAAAGAGAAACAACAAGAGACA
AAAATACCAGAAACACCAATTTCACCGTGTGCTGAGCCACTTCTCAATAAAGAGCTTATG
AAAAATGAAAAAGAAGTAAATAATTTAAGCAACACAGTCAATTCAGTTGATTCGTTGTTT
CAAACAAATTCCAATTCAGAGAACTGTTCAACAACAGATATAGAGCTTGACAATATTCGA
AATAATTTAAGATTAAAATGA
>g2744.t1 Gene=g2744 Length=1026
MDIEDEYTRDFSFEPEFITRKDSLQMHRSRLERTRKHNKIFKIKTISLDIILEKALVNEQ
QTTLSTQNIVEAEVEAFRTMYGRYTKDLSEYAKDEARRLKQLERQRKKDDRARNKELLGK
KEGKFLRAFRWFWKRTFARMGEDWIFLALLGIIMAIISYCMDKGISMCTNARVWLYRDLA
DHPVTQYFAWITLPVCLILFSAGFVHLLAPQSIGSGIPEMKTILRGVQLKEYLTFKTLVA
KVIGLTATLGSGMPLGKEGPFVHIASIVAQLLSKLVTSFQGIFENESRNTEMLAAACAVG
VGSCFAAPVGGVLFSIEVTTTYFAVRNYWRGFFGAVCGATFFRLLAVWFQKADTLTALFL
TSFHMDFPYDPQELIAFAMIGVISGLGGAAYVWIHRQYVLFMRSSKRMNNFLQKNRFLYP
GILALMVATLSYPNGLGRYIAGELSTHEQVSNLFTNFTWSEPNLNVEQSAIVRYWTNPYT
NEIFSILIFYLLYTFFVSIVTSTIPVPSGIFIPVFKIGAALGRIIGESMHLWFPTGIRYG
GHINHIIPGGYAVVGASAFAGAVTHTVSVGVIVFEMTGQISHLVPVMIATLISCAIATIL
QPSMYDSIILIKKLPYLPDLLPTSSGMYNFTVEDFMVRDIKYIWQNITYQELKEILKKNK
QLRSLPLVDNPDTMILLGSVQRFDLIKMIDKHIGREKRLEMAARRKKEAEEREEQERIKK
LQEGPRRASRFEVVPAPDIVKLRQIANNEMLTPQAKKESNQFTPVFGTQPKKSILKKTNS
FTMKGFSPLSPHSPVNTPYSTITGAESRLRSAFDIIFRKSATLQDVQNNDPELGSKSSIQ
TPSIDGTPYPSSHISKKVQLPRERVIDMSAEEQKMWEMEEMSKPIDLDAANVNIDPSPFQ
LVRTTSLLKVHSLFSMIGINHAYVTHVGRLVGVVALKELRKAIEDVNSGNLVPKEKQQET
KIPETPISPCAEPLLNKELMKNEKEVNNLSNTVNSVDSLFQTNSNSENCSTTDIELDNIR
NNLRLK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 40 | g2744.t1 | CDD | cd03683 | ClC_1_like | 143 | 619 | 0.0 |
| 41 | g2744.t1 | CDD | cd04591 | CBS_pair_voltage-gated_CLC_euk_bac | 894 | 942 | 2.01731E-16 |
| 17 | g2744.t1 | Coils | Coil | Coil | 85 | 112 | - |
| 18 | g2744.t1 | Coils | Coil | Coil | 696 | 724 | - |
| 16 | g2744.t1 | Gene3D | G3DSA:1.10.3080.10 | Clc chloride channel | 136 | 618 | 3.4E-148 |
| 15 | g2744.t1 | Gene3D | G3DSA:3.10.580.10 | - | 619 | 735 | 9.6E-32 |
| 14 | g2744.t1 | Gene3D | G3DSA:3.10.580.10 | - | 848 | 948 | 6.3E-34 |
| 54 | g2744.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 704 | 725 | - |
| 55 | g2744.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 827 | 856 | - |
| 56 | g2744.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 827 | 854 | - |
| 3 | g2744.t1 | PANTHER | PTHR45720:SF10 | CHLORIDE CHANNEL PROTEIN 2 | 80 | 953 | 0.0 |
| 4 | g2744.t1 | PANTHER | PTHR45720 | CHLORIDE CHANNEL PROTEIN 2 | 80 | 953 | 0.0 |
| 11 | g2744.t1 | PRINTS | PR00762 | Chloride channel signature | 210 | 227 | 2.2E-69 |
| 5 | g2744.t1 | PRINTS | PR00762 | Chloride channel signature | 241 | 260 | 2.2E-69 |
| 10 | g2744.t1 | PRINTS | PR00762 | Chloride channel signature | 298 | 317 | 2.2E-69 |
| 9 | g2744.t1 | PRINTS | PR00762 | Chloride channel signature | 506 | 526 | 2.2E-69 |
| 8 | g2744.t1 | PRINTS | PR00762 | Chloride channel signature | 549 | 565 | 2.2E-69 |
| 6 | g2744.t1 | PRINTS | PR00762 | Chloride channel signature | 566 | 585 | 2.2E-69 |
| 7 | g2744.t1 | PRINTS | PR00762 | Chloride channel signature | 604 | 618 | 2.2E-69 |
| 2 | g2744.t1 | Pfam | PF00654 | Voltage gated chloride channel | 197 | 597 | 9.3E-84 |
| 1 | g2744.t1 | Pfam | PF00571 | CBS domain | 632 | 689 | 0.0027 |
| 20 | g2744.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 143 | - |
| 32 | g2744.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 144 | 167 | - |
| 26 | g2744.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 168 | 186 | - |
| 39 | g2744.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 187 | 209 | - |
| 24 | g2744.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 210 | 260 | - |
| 36 | g2744.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 261 | 280 | - |
| 27 | g2744.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 281 | 291 | - |
| 37 | g2744.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 292 | 316 | - |
| 22 | g2744.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 317 | 327 | - |
| 30 | g2744.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 328 | 349 | - |
| 25 | g2744.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 350 | 373 | - |
| 33 | g2744.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 374 | 394 | - |
| 19 | g2744.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 395 | 414 | - |
| 35 | g2744.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 415 | 432 | - |
| 28 | g2744.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 433 | 482 | - |
| 38 | g2744.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 483 | 506 | - |
| 21 | g2744.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 507 | 550 | - |
| 34 | g2744.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 551 | 574 | - |
| 29 | g2744.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 575 | 579 | - |
| 31 | g2744.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 580 | 600 | - |
| 23 | g2744.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 601 | 1026 | - |
| 58 | g2744.t1 | ProSiteProfiles | PS51371 | CBS domain profile. | 636 | 696 | 9.294 |
| 57 | g2744.t1 | ProSiteProfiles | PS51371 | CBS domain profile. | 894 | 952 | 7.581 |
| 52 | g2744.t1 | SMART | SM00116 | cbs_1 | 639 | 690 | 1.7 |
| 53 | g2744.t1 | SMART | SM00116 | cbs_1 | 897 | 944 | 3.0 |
| 13 | g2744.t1 | SUPERFAMILY | SSF81340 | Clc chloride channel | 126 | 618 | 6.67E-101 |
| 12 | g2744.t1 | SUPERFAMILY | SSF54631 | CBS-domain pair | 626 | 944 | 5.67E-28 |
| 50 | g2744.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 144 | 166 | - |
| 49 | g2744.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 187 | 209 | - |
| 43 | g2744.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 292 | 314 | - |
| 47 | g2744.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 327 | 349 | - |
| 51 | g2744.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 374 | 396 | - |
| 42 | g2744.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 417 | 436 | - |
| 48 | g2744.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 483 | 500 | - |
| 44 | g2744.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 507 | 526 | - |
| 45 | g2744.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 551 | 573 | - |
| 46 | g2744.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 580 | 602 | - |
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 transcript has been annotated with K05011 (chloride channel 2)
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.
