General information for g1683.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Transient receptor potential cation channel subfamily V member 6.
Parent gene
- The parent gene g1683 is located on chr_3: 12500358..12518050 (+ 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 | g1683 | g1683.t1 | isoform | g1683.t1 | 12500358 | 12518050 |
| chr_3 | g1683 | g1683.t1 | exon | g1683.t1.exon1 | 12500358 | 12500502 |
| chr_3 | g1683 | g1683.t1 | cds | g1683.t1.CDS1 | 12500358 | 12500502 |
| chr_3 | g1683 | g1683.t1 | exon | g1683.t1.exon2 | 12501060 | 12501366 |
| chr_3 | g1683 | g1683.t1 | cds | g1683.t1.CDS2 | 12501060 | 12501366 |
| chr_3 | g1683 | g1683.t1 | exon | g1683.t1.exon3 | 12501425 | 12501693 |
| chr_3 | g1683 | g1683.t1 | cds | g1683.t1.CDS3 | 12501425 | 12501693 |
| chr_3 | g1683 | g1683.t1 | exon | g1683.t1.exon4 | 12501762 | 12501795 |
| chr_3 | g1683 | g1683.t1 | cds | g1683.t1.CDS4 | 12501762 | 12501795 |
| chr_3 | g1683 | g1683.t1 | exon | g1683.t1.exon5 | 12502681 | 12502785 |
| chr_3 | g1683 | g1683.t1 | cds | g1683.t1.CDS5 | 12502681 | 12502785 |
| chr_3 | g1683 | g1683.t1 | exon | g1683.t1.exon6 | 12502840 | 12503042 |
| chr_3 | g1683 | g1683.t1 | cds | g1683.t1.CDS6 | 12502840 | 12503042 |
| chr_3 | g1683 | g1683.t1 | exon | g1683.t1.exon7 | 12504930 | 12505509 |
| chr_3 | g1683 | g1683.t1 | cds | g1683.t1.CDS7 | 12504930 | 12505509 |
| chr_3 | g1683 | g1683.t1 | exon | g1683.t1.exon8 | 12506031 | 12506047 |
| chr_3 | g1683 | g1683.t1 | cds | g1683.t1.CDS8 | 12506031 | 12506047 |
| chr_3 | g1683 | g1683.t1 | exon | g1683.t1.exon9 | 12514230 | 12514254 |
| chr_3 | g1683 | g1683.t1 | cds | g1683.t1.CDS9 | 12514230 | 12514254 |
| chr_3 | g1683 | g1683.t1 | exon | g1683.t1.exon10 | 12514314 | 12514445 |
| chr_3 | g1683 | g1683.t1 | cds | g1683.t1.CDS10 | 12514314 | 12514445 |
| chr_3 | g1683 | g1683.t1 | exon | g1683.t1.exon11 | 12514509 | 12514551 |
| chr_3 | g1683 | g1683.t1 | cds | g1683.t1.CDS11 | 12514509 | 12514551 |
| chr_3 | g1683 | g1683.t1 | exon | g1683.t1.exon12 | 12514608 | 12514716 |
| chr_3 | g1683 | g1683.t1 | cds | g1683.t1.CDS12 | 12514608 | 12514716 |
| chr_3 | g1683 | g1683.t1 | exon | g1683.t1.exon13 | 12514777 | 12515134 |
| chr_3 | g1683 | g1683.t1 | cds | g1683.t1.CDS13 | 12514777 | 12515134 |
| chr_3 | g1683 | g1683.t1 | exon | g1683.t1.exon14 | 12515785 | 12516574 |
| chr_3 | g1683 | g1683.t1 | cds | g1683.t1.CDS14 | 12515785 | 12516574 |
| chr_3 | g1683 | g1683.t1 | exon | g1683.t1.exon15 | 12517464 | 12517591 |
| chr_3 | g1683 | g1683.t1 | cds | g1683.t1.CDS15 | 12517464 | 12517591 |
| chr_3 | g1683 | g1683.t1 | exon | g1683.t1.exon16 | 12517655 | 12517753 |
| chr_3 | g1683 | g1683.t1 | cds | g1683.t1.CDS16 | 12517655 | 12517753 |
| chr_3 | g1683 | g1683.t1 | exon | g1683.t1.exon17 | 12517834 | 12518050 |
| chr_3 | g1683 | g1683.t1 | cds | g1683.t1.CDS17 | 12517834 | 12518050 |
| chr_3 | g1683 | g1683.t1 | TSS | g1683.t1 | NA | NA |
| chr_3 | g1683 | g1683.t1 | TTS | g1683.t1 | NA | NA |
Sequences
>g1683.t1 Gene=g1683 Length=3561
ATGAAATTTAATTTATTTAATTGCAAGGCATTTCGCAAGAAAAAACACATCGCTCAAGGT
GGTGCTATATTAGATCAAGTCATCTCTGAGTCATGTTCACCGAATAATAAAATTTTACTT
TACAAGTTGGCCAATTATAAGTTAGGTGGTGATTTAATTGACGCTTTCAATGTTGGTGGT
CAGTATGCCGTAGAGGAATTAATTCGTGAACAATTTGGTGTGTTTATGTATAAAGGCGGC
AAGGGACAGATAATTAATCGCGCTGAATATTTACGTTGGAAGTATATGGAAAATGCTGAA
GTATCAATTCCAATTGAAGCATCACTTTCATCTCATGATCCATTGGGAAAATGGGTCGAT
CATAAAGCATGCTGGCAAATGCAATATCGTGGACGACTGGGCGAAAGTCTTTTACATGTT
CTTATAATTTGCGATACAAAAGTTCATACCAAATTGGCACGTTTATTGATTCGAGTATTT
CCTGAGTTAGCAATTGATGTCATGGAGGGTGAAGAATATTTAGGAGCAAGTGGACTTCAT
TTAGCTATAGCTTATTCCAATGGTGAACTTGTGAGTGATTTAGTTGATGCTGGCGCCGAT
GTAAATCAGCGAGCAATCGGACGATTTTTCCTGCCACGTGATCAACAAAGCAACACACCA
TCAAATCAAACTGACTATGAAGGACTCGCTTATTTTGGAGAATTTCCACTCAGTTGGGCT
GCTTGCACAAACAATGAGTCTGCTTATAATTTACTGATGGAAGTTGGTGGGGATCCCGAC
GCACAAGATTCATTTGGAAATATGATTTTGCACATGGTTGTCGTTAACGATAAGCTCGAA
ATGTTTGGTTACGCTCTAAGACATCCAAAAAAACCGGCAAAGAATGGAATTGTAAATCGT
CAAGGTCTGACACCACTAACACTCGCTTGTAAGCTCGGTCGCAGTGAAGTGTTTCGTGAA
ATGTTGGAGTTGAGCTGTCGTGAATTTTGGCGCTACAGTAACATCACATGCTCTGCCTAT
CCATTAAACGCTTTAGACACAATACAGCCTGATGGCAGTACAAATTGGAACGCTGCGTTG
ATTTTAATTTTAAATGGAACAAAACCTGAACATTTAGATATGCTTGATGGTGGAATTATT
GAACGTTTGTTGGAAGAAAAATGGAAGACATTTGCACAACAGCAATTTTTAAAACGTCTT
CTTATTTTATTTATTCATCTTTTCTTTATGTCAATATCTGTTTATACACGACCAACTCGA
ATAAGTTCAAAAGAAAATAATGATGGAAATGATGGAAGTGGTAATGGTGCAACTGACAGT
GAACTTGTCTCGGAGGCATTAACAATGGAAGCTGGCCTAGACATAGATATGACCACAATT
GTACGGTATATCTGCGAGTGTGCAACCGTTGCGGGTGTTATCAGCTTTGTGGTTTTTCAG
CAAGGCGACGAACTGAAAAATCAGGGTCTAAAAGCGTTCATGAAACAATTAAAGCAAGCA
CCGGCCAAAGCAATTTTTCTCATCTCAAACTTCTTGATCCTATCATGCATTCCCTGTCGT
ATAATGGGCAACACAGAAATGGAAGAGAAATTACTGTGCTTTGCCGTGCCAGGCTCTTGG
TTTTTTATGATGTTCTTTGCCGGTGCTATACGATTGACAGGACCATTTGTGACAATGATC
TACAGCATGATTACTGGCGACATGTTCACTTTCTCCATCATTTATATGATATTTTTGTTT
GGATTTTCTCAAGCTTATTTTTTCCTTTACAAAGGTCATGAGAATGTCGATGACACTCCA
TATAACTCCTACATGAGTACTTGGATGGGACTTTTTCAGACGACACTTGGTGATTACGAT
TATGCACAACTCAATGAAGTTTCATATCCAAACTTGGCAAAGACAGTTTTCATAATATTT
ATGATTTTTGTTCCTATCTTGTTGCTTAACATGTTGATCGCTATGATGGGCAACACCTAC
GCTTATGTTATTGAGCAATCTGAAAAGGAATTTATGAAGCAATGGGCAAAAATTGTGGTC
ACACTCGAACGTGCTGTACCGGCAGCTGACGCACAAAAATATCTTGAAGAATATTCAATT
GGCCTTGGTCCAAGCGATGATCCACGCTATGAACAACGCGGTGTAATGGTAATAAAAACA
AAGAGTAAAACGCGAGCACGCCAACGTAAAGGTGCTGTCAGCAATTGGAAATATGTGTTG
AAAACTACACTAGGTGAATTAAAAAAGCGTGGCATGACTGGTGAAGAAATGAGGCGTCTT
ATGTGGGGAAGAATGAGCATAACAAGCCCGAAAAAGGTTTCTAAAAAGAAAAAGCGTGTC
GGTGTCGATATGGAGGATGAAGATCCTTTTGGTTTAACTGCAGCATTGGATCAAATGGCA
TTTGCTTCAGACATTGTAATGATTGATACGGATCCTGTGAAAGGCACAACTGTTGTTGAA
ATGACAACTGTGCCAATAACAACAACAACAACAACTACATCAACTATATCAACTGCTCCT
CCCGATTACGACACTGCCATCTCGACAGCCGCAGCAGTGACAACTGAAAGTATCACGCAA
GCAATAGCAAGTAACAGTGCTGCTCCCACACCACCATCAACTGTTCATTCTCGTGTGACT
ACAGCAACAACAACACCAGCGAGAATTCCTGAAAAAACATTTTCGGATCCACTTCGCGAC
TTGATATTGCTATCAGAAGTCATTTTGATTGATGACGAGGAAGATTTTTTACGGAATGTA
AAGTCATTAGCTGAAGATAGCTCATGTTTGGATTACGTGCTTGAAGTAAAAAGCACGGAT
AGCTATAATCAGTTACAACAACAAAAACAAGACTTAATGAATTCAAATAAAGTTGAACAA
GGAATTGCACTGTTTCAAAATCCTAAAGAAATTATTGATCCAGTCAAAGAGGCAGAGTTT
TTAAAAACATTAGAAGCACTAGAGGATACAGATGATAGTGATGCAGTTGAAAAACCAGTA
CTTGGTAAAATATCATTAGTTAGACGAGCAAAATCGGCTGCAACACGAACGTCATCTGAT
AATAAAAGGAAAAGCGATGAAAATCCATTATATAATGTGGCATGGGAAGAGATTGAGAAT
GGTGATGAAAACAGCATAATTAATTGGATCTACGATGGCGACAGATTGAAGACAGGCGAT
GATGACGAAGAAATTGTGACTGTTGAAGATGTTAAGCGTAAAATGGAAATGTTTCATTTA
AATCGAAAAAGCTCAGCCGATAGCGAATCAACTTCAGAGCATACAAAATCAAAGAAAAAG
ACAAAGAAGAATGGAGTTGGCGGCTATCGAGGCAGAAATAACAAAATTTCACCAGAAGAA
TCACGAGATGAGTCAACAACATCAAAGAGAAGAGGTAAATCTGCACCAAGTGCAGGAATA
GAAATATCACGTCATATCATGGAGAAAGTTGCACCCGATGGCGGTGTTATTAGTGGACCC
GAGCCTGACCCACTAGAACCGTGGAGCACAAGAAACATTAAAAGCATCAACAACATACTT
GATAACTCTGACCGAGAATAA
>g1683.t1 Gene=g1683 Length=1186
MKFNLFNCKAFRKKKHIAQGGAILDQVISESCSPNNKILLYKLANYKLGGDLIDAFNVGG
QYAVEELIREQFGVFMYKGGKGQIINRAEYLRWKYMENAEVSIPIEASLSSHDPLGKWVD
HKACWQMQYRGRLGESLLHVLIICDTKVHTKLARLLIRVFPELAIDVMEGEEYLGASGLH
LAIAYSNGELVSDLVDAGADVNQRAIGRFFLPRDQQSNTPSNQTDYEGLAYFGEFPLSWA
ACTNNESAYNLLMEVGGDPDAQDSFGNMILHMVVVNDKLEMFGYALRHPKKPAKNGIVNR
QGLTPLTLACKLGRSEVFREMLELSCREFWRYSNITCSAYPLNALDTIQPDGSTNWNAAL
ILILNGTKPEHLDMLDGGIIERLLEEKWKTFAQQQFLKRLLILFIHLFFMSISVYTRPTR
ISSKENNDGNDGSGNGATDSELVSEALTMEAGLDIDMTTIVRYICECATVAGVISFVVFQ
QGDELKNQGLKAFMKQLKQAPAKAIFLISNFLILSCIPCRIMGNTEMEEKLLCFAVPGSW
FFMMFFAGAIRLTGPFVTMIYSMITGDMFTFSIIYMIFLFGFSQAYFFLYKGHENVDDTP
YNSYMSTWMGLFQTTLGDYDYAQLNEVSYPNLAKTVFIIFMIFVPILLLNMLIAMMGNTY
AYVIEQSEKEFMKQWAKIVVTLERAVPAADAQKYLEEYSIGLGPSDDPRYEQRGVMVIKT
KSKTRARQRKGAVSNWKYVLKTTLGELKKRGMTGEEMRRLMWGRMSITSPKKVSKKKKRV
GVDMEDEDPFGLTAALDQMAFASDIVMIDTDPVKGTTVVEMTTVPITTTTTTTSTISTAP
PDYDTAISTAAAVTTESITQAIASNSAAPTPPSTVHSRVTTATTTPARIPEKTFSDPLRD
LILLSEVILIDDEEDFLRNVKSLAEDSSCLDYVLEVKSTDSYNQLQQQKQDLMNSNKVEQ
GIALFQNPKEIIDPVKEAEFLKTLEALEDTDDSDAVEKPVLGKISLVRRAKSAATRTSSD
NKRKSDENPLYNVAWEEIENGDENSIINWIYDGDRLKTGDDDEEIVTVEDVKRKMEMFHL
NRKSSADSESTSEHTKSKKKTKKNGVGGYRGRNNKISPEESRDESTTSKRRGKSAPSAGI
EISRHIMEKVAPDGGVISGPEPDPLEPWSTRNIKSINNILDNSDRE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g1683.t1 | Coils | Coil | Coil | 1180 | 1186 | - |
| 5 | g1683.t1 | Gene3D | G3DSA:1.25.40.20 | - | 121 | 376 | 2.5E-59 |
| 31 | g1683.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1079 | 1170 | - |
| 33 | g1683.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1079 | 1096 | - |
| 32 | g1683.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1115 | 1130 | - |
| 3 | g1683.t1 | PANTHER | PTHR10582 | TRANSIENT RECEPTOR POTENTIAL ION CHANNEL PROTEIN | 16 | 764 | 1.0E-186 |
| 1 | g1683.t1 | Pfam | PF12796 | Ankyrin repeats (3 copies) | 237 | 323 | 1.2E-6 |
| 2 | g1683.t1 | Pfam | PF00520 | Ion transport protein | 498 | 667 | 2.0E-12 |
| 10 | g1683.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 395 | - |
| 18 | g1683.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 396 | 415 | - |
| 12 | g1683.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 416 | 459 | - |
| 15 | g1683.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 460 | 479 | - |
| 7 | g1683.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 480 | 499 | - |
| 16 | g1683.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 500 | 521 | - |
| 13 | g1683.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 522 | 540 | - |
| 19 | g1683.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 541 | 561 | - |
| 8 | g1683.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 562 | 567 | - |
| 14 | g1683.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 568 | 589 | - |
| 11 | g1683.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 590 | 635 | - |
| 17 | g1683.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 636 | 663 | - |
| 9 | g1683.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 664 | 1186 | - |
| 34 | g1683.t1 | ProSiteProfiles | PS50297 | Ankyrin repeat region circular profile. | 174 | 323 | 17.184 |
| 35 | g1683.t1 | ProSiteProfiles | PS50088 | Ankyrin repeat profile. | 174 | 206 | 10.606 |
| 36 | g1683.t1 | ProSiteProfiles | PS50088 | Ankyrin repeat profile. | 232 | 264 | 8.977 |
| 28 | g1683.t1 | SMART | SM00248 | ANK_2a | 133 | 165 | 820.0 |
| 26 | g1683.t1 | SMART | SM00248 | ANK_2a | 174 | 203 | 1.8 |
| 29 | g1683.t1 | SMART | SM00248 | ANK_2a | 232 | 261 | 230.0 |
| 27 | g1683.t1 | SMART | SM00248 | ANK_2a | 265 | 294 | 640.0 |
| 30 | g1683.t1 | SMART | SM00248 | ANK_2a | 301 | 337 | 160.0 |
| 4 | g1683.t1 | SUPERFAMILY | SSF48403 | Ankyrin repeat | 125 | 323 | 1.57E-21 |
| 23 | g1683.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 400 | 417 | - |
| 22 | g1683.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 460 | 482 | - |
| 20 | g1683.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 502 | 524 | - |
| 21 | g1683.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 531 | 553 | - |
| 25 | g1683.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 568 | 590 | - |
| 24 | g1683.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 635 | 657 | - |
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:0005515 | protein binding | MF |
| GO:0005216 | ion channel activity | MF |
| GO:0016021 | integral component of membrane | CC |
| GO:0006811 | ion transport | BP |
KEGG
Orthology
- This transcript has been annotated with K04975 (transient receptor potential cation channel subfamily V member 6)
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.
