General information for g12424.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Transient-receptor-potential-like protein.
Parent gene
- The parent gene g12424 is located on chr_1: 23507502..23515129 (- 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_1 | g12424 | g12424.t1 | isoform | g12424.t1 | 23507144 | 23515129 |
| chr_1 | g12424 | g12424.t1 | exon | g12424.t1.exon1 | 23507144 | 23507770 |
| chr_1 | g12424 | g12424.t1 | cds | g12424.t1.CDS1 | 23507144 | 23507770 |
| chr_1 | g12424 | g12424.t1 | exon | g12424.t1.exon2 | 23508190 | 23509142 |
| chr_1 | g12424 | g12424.t1 | cds | g12424.t1.CDS2 | 23508190 | 23509142 |
| chr_1 | g12424 | g12424.t1 | exon | g12424.t1.exon3 | 23509199 | 23509421 |
| chr_1 | g12424 | g12424.t1 | cds | g12424.t1.CDS3 | 23509199 | 23509421 |
| chr_1 | g12424 | g12424.t1 | exon | g12424.t1.exon4 | 23510648 | 23510842 |
| chr_1 | g12424 | g12424.t1 | cds | g12424.t1.CDS4 | 23510648 | 23510842 |
| chr_1 | g12424 | g12424.t1 | exon | g12424.t1.exon5 | 23510904 | 23511072 |
| chr_1 | g12424 | g12424.t1 | cds | g12424.t1.CDS5 | 23510904 | 23511072 |
| chr_1 | g12424 | g12424.t1 | exon | g12424.t1.exon6 | 23511279 | 23511347 |
| chr_1 | g12424 | g12424.t1 | cds | g12424.t1.CDS6 | 23511279 | 23511347 |
| chr_1 | g12424 | g12424.t1 | exon | g12424.t1.exon7 | 23511886 | 23511940 |
| chr_1 | g12424 | g12424.t1 | cds | g12424.t1.CDS7 | 23511886 | 23511940 |
| chr_1 | g12424 | g12424.t1 | exon | g12424.t1.exon8 | 23512025 | 23512093 |
| chr_1 | g12424 | g12424.t1 | cds | g12424.t1.CDS8 | 23512025 | 23512093 |
| chr_1 | g12424 | g12424.t1 | exon | g12424.t1.exon9 | 23512158 | 23512257 |
| chr_1 | g12424 | g12424.t1 | cds | g12424.t1.CDS9 | 23512158 | 23512257 |
| chr_1 | g12424 | g12424.t1 | exon | g12424.t1.exon10 | 23512991 | 23513364 |
| chr_1 | g12424 | g12424.t1 | cds | g12424.t1.CDS10 | 23512991 | 23513364 |
| chr_1 | g12424 | g12424.t1 | exon | g12424.t1.exon11 | 23513425 | 23513607 |
| chr_1 | g12424 | g12424.t1 | cds | g12424.t1.CDS11 | 23513425 | 23513607 |
| chr_1 | g12424 | g12424.t1 | exon | g12424.t1.exon12 | 23513744 | 23513795 |
| chr_1 | g12424 | g12424.t1 | cds | g12424.t1.CDS12 | 23513744 | 23513795 |
| chr_1 | g12424 | g12424.t1 | exon | g12424.t1.exon13 | 23514250 | 23514480 |
| chr_1 | g12424 | g12424.t1 | cds | g12424.t1.CDS13 | 23514250 | 23514480 |
| chr_1 | g12424 | g12424.t1 | exon | g12424.t1.exon14 | 23514586 | 23514735 |
| chr_1 | g12424 | g12424.t1 | cds | g12424.t1.CDS14 | 23514586 | 23514735 |
| chr_1 | g12424 | g12424.t1 | exon | g12424.t1.exon15 | 23515046 | 23515129 |
| chr_1 | g12424 | g12424.t1 | cds | g12424.t1.CDS15 | 23515046 | 23515129 |
| chr_1 | g12424 | g12424.t1 | TSS | g12424.t1 | NA | NA |
| chr_1 | g12424 | g12424.t1 | TTS | g12424.t1 | NA | NA |
Sequences
>g12424.t1 Gene=g12424 Length=3534
ATGACTGTGAAACTTTTAGTGCTGCACCAGAATTATATTTACATTAGAAGGTTTTCATTA
TTGTCATTTTGTTTCTGCTTATTCGACGTAAAATGTCCATGTGATGAGTGTATTAGAAAA
TCAACAGAAGATTCATTGCGCCATTCATTATCGAGAGTTAGTGAATATCGTGCTCTTGCA
AGTCCATCATTGATTGCTTTAAGCTCAGTTGATCCATTGAGCACAGCATTTCAGCTGTCA
TGGGAGCTACGTAATTTGGCGTTTGCCGAGCAAGAGTCGAAGGCGGAATATTTAGAGTTA
CGACGTCAATGTCAACAATTTGCTGTCGATTTATTAGATCAAACACGTTCATCACAAGAA
TTGGCAATCATTTTAAATTACGACCCAGAAAGTGATCCTTATGTAGATGGAGAACATATG
AAATTGAAGAGACTTGAAATGGCAATCGATTATAAGCAAAAGAAGTTTGTAGCACATCCA
AATATCCAACAGTTACTTGCTTCACTGTGGTATGAAGGCGTCCCAGGCTTTCGTAGAAAA
ACGGCAATACAAAAAATGTTGATCATCTCAAAAGTGGCTTTGTTATTTCCCTTTTATTGT
CTATTGTACATGTTTTTACCATACTGTCATTCAGCAAAAATTATGCGAAAACCATTTATG
AAATTTTTGATTCACGCCTCGTCTTATTTATTTTTTCTATTCATTTTAATTTTGGTAAGT
CAACGGGCTGAAGTTCAAGTTATTTTGATATTAGGAACAGAAAAAATGAAGGAGGCAATG
AGAGAATCATTAAAAAGGCAACGCGGAAATCCACCAACGCCTTTGGAATTTCTTGTCGTC
ATTTATGTCCTTGGTTTTATATGGGAAGAAACACAAGAAATTTTTGGTGAAGGGATTCGC
AGTTACCTACGCAATATGTGGAATTTTATTGACTTCAGTCGAAATTCACTTTATGTGCTT
GTGTTTTTGTTGCGTGGTTTCGCCTACTTCCAACAAATGAATCAAATCAATCATGATCCA
AAAACTGCTTACATCCCACGAGAACATTGGGATGATTTCGATCCTCAACTAATTGCTGAA
GGTCTTTTTGCAGCTGCCAATATATTCTCTGCTCTCAAACTTATTCATCTTTTCTCAATC
AATCCACATTTGGGACCATTGCAGATTTCACTTGGTCGAATGGTCATTGATATTGTGAAA
TTCTTGATTATCTACACCTTAGTTCTATTTGCTTTTGCTTGCGGCTTGAATCAACTTCTG
TGGTATTATGCCGATTTAGAGAAAGCCAAATGTTATAGTCTGCCAGGTGGTTTACCAGAT
TGGGACAATCAAGGCGATGCTTGCATGAAATGGCGTCGATTTGGAAATTTGTTTGAATCA
TCGCAGTCGTTGTTTTGGGCATCATTCGGCACAGTTGGACTTGAAAACTTTGAATTACTT
GGCATTAAGTCTTATACTCGCTTCTGGGGTTTATTGATGTTTGGTTCTTACAGTGTTATC
AATGTTATTGTCTTACTCAACTTGCTTATTGCCATGATGTCAAATTCTTATGCTATGATT
GAAGAACATTCAGATACAGAATGGAAATTTGCTCGAACTAAATTATGGATGTCATATTTT
GACGAATCTGCAACTTTGCCACCGCCATTTAACATTTTTCCAAATGTCAAGCATTTTACA
AAATGCTGTCGCAGCAGTAAGAAACGCGATATCAACCGAGAATCAACTATTCGTCGAAAA
GAAGAAAAAGAGCGAGACAATCGTTATACAGCTGTTATGAGATCGCTTGTATGGCGTTAT
GTTTCAGCAATGCATCGTCGTGAAGAAGAAAGTGCAGTGACTGAAGATGATATCAACGAA
GTAAAAGGTGAAGTCTCAGCAATGCGATACGAGCTAATTGAGATTTTTGAGAAGAATGGC
ATGGACATTTCGAGTGTTGATAGAAAGGAAAAAACTGTCTTGGCAAAGAAAATGAAAGTT
TGGGAGCGAAGATTAATGAAAGATTTCCAAGTTGCACCAGTTGAAGTTCAAGAAGCAGGT
GAAGGTGAAGAAAATGCAACTGAAGAAAATAATGAAACACCATTGGAAAGATTTAAAAGA
GTTTCCAAGCAAGTCGCATCACAATCGACAACTGCAAAATGGAGTGAAGTCATTCGAAGT
GCAACAATTGAGGCAAACAGTCAAATTGGTCGATGTAGAAATCGTGAAAGTTTCAGAAAT
CAACAAAATTTACTTAAAGCAATGGAACAAGCTAGAAAACTTATTGAGCGTGGACCAATT
CCACCATCACCAAGTCATAGTGATTCTTATAGTGTCGTTTGTGATCAAACCAATGAAACT
TTGGTTCAATTGTTGAAAAATATTTCTGAAGAAATCAATGAACTTTCACCACACAGTACT
TTGGCTGTTACACCAAGATCACGTCGTTCTGCAACACCGTTACATTCATTGAATGTTCAA
TTGCAATCACTTATTACTAAATCACCATCACCTTATGCAACTAAAGTTAAATCTCGAGGA
CATTCACCAAAACCAACAATACTTGACTTACGCAAGCCATCAATGCCTGAAATTGAAAGA
TACATGTCACCACCACCAAAATGTGACACACCAAAATCACCAAAATCAAAATCTGAAACA
CCAAAATCTTCACGTCCATCAACACCAAAATCACCTGGCAGATTTGAACTTTCTAAATCG
CCATTGTCAAAACCACCGCAATCAATTTTGAAAAATGGTCGATCACCAACTCCAGACAGT
TGCAAATCTTTAGATGATACAAAATCAGTTGATAGTTTCAAATTGACACAAGAAAATGTA
CAGAAAAACGCTGCTCCAAAAGTTTTCTCAACACCATCAGTTGAAATCACTTGTGAAGAC
GAATTTGATAAGCCAGCAACACCAGAGACAAAACCACCAACACCAGTTGAAAGATCAATT
ACACCACCAGCATTGAAAATAAAAACTCCCTCACCAGAGCCTGAAAAGACAATCATTCAA
GAAAAGCCAGCAAAACTTCTTATCGATTTTACCAATGATGAAAAAATTCCAGAAGGCCCA
CCCAAAGTTATTAAAAGAAAAGCTCCAGTTCCAATTTCGACTGAACAGTCTCAAGATATT
GCAATATCACGACCACAAGCACCAAAAGTGCCAATCAATCAAGGCATGATTCCACCACCA
CCTAAAAAAGAAGAAAGCAAGCCACCAGTTCAAATTCCAATTTTATCAACAACACCAGCA
ACGCCTTTACCTTTGCAAAAGCATTTTGTTGAACCAACACCGCCTTCACCTATAAATGAA
GTAAAAAATCAAGCATCAGAACAACCTCAAGTCATTAAATGTGAAACGCCACCACCTTCT
GCTATTGCAATCGATTCTGCTGCCTCATTTAGCAGCACTGAAAAACTTGTCACATCAACC
GATCCTGGTAAAGAAGCAAATTTTGCTGCATCATCGCCACCAATGTTGCGACCCGTAAAT
AAAATTGAGGATGTAAAAACAATAAAAAGGCAAATGAAGACTGGTTGGCTATAA
>g12424.t1 Gene=g12424 Length=1177
MTVKLLVLHQNYIYIRRFSLLSFCFCLFDVKCPCDECIRKSTEDSLRHSLSRVSEYRALA
SPSLIALSSVDPLSTAFQLSWELRNLAFAEQESKAEYLELRRQCQQFAVDLLDQTRSSQE
LAIILNYDPESDPYVDGEHMKLKRLEMAIDYKQKKFVAHPNIQQLLASLWYEGVPGFRRK
TAIQKMLIISKVALLFPFYCLLYMFLPYCHSAKIMRKPFMKFLIHASSYLFFLFILILVS
QRAEVQVILILGTEKMKEAMRESLKRQRGNPPTPLEFLVVIYVLGFIWEETQEIFGEGIR
SYLRNMWNFIDFSRNSLYVLVFLLRGFAYFQQMNQINHDPKTAYIPREHWDDFDPQLIAE
GLFAAANIFSALKLIHLFSINPHLGPLQISLGRMVIDIVKFLIIYTLVLFAFACGLNQLL
WYYADLEKAKCYSLPGGLPDWDNQGDACMKWRRFGNLFESSQSLFWASFGTVGLENFELL
GIKSYTRFWGLLMFGSYSVINVIVLLNLLIAMMSNSYAMIEEHSDTEWKFARTKLWMSYF
DESATLPPPFNIFPNVKHFTKCCRSSKKRDINRESTIRRKEEKERDNRYTAVMRSLVWRY
VSAMHRREEESAVTEDDINEVKGEVSAMRYELIEIFEKNGMDISSVDRKEKTVLAKKMKV
WERRLMKDFQVAPVEVQEAGEGEENATEENNETPLERFKRVSKQVASQSTTAKWSEVIRS
ATIEANSQIGRCRNRESFRNQQNLLKAMEQARKLIERGPIPPSPSHSDSYSVVCDQTNET
LVQLLKNISEEINELSPHSTLAVTPRSRRSATPLHSLNVQLQSLITKSPSPYATKVKSRG
HSPKPTILDLRKPSMPEIERYMSPPPKCDTPKSPKSKSETPKSSRPSTPKSPGRFELSKS
PLSKPPQSILKNGRSPTPDSCKSLDDTKSVDSFKLTQENVQKNAAPKVFSTPSVEITCED
EFDKPATPETKPPTPVERSITPPALKIKTPSPEPEKTIIQEKPAKLLIDFTNDEKIPEGP
PKVIKRKAPVPISTEQSQDIAISRPQAPKVPINQGMIPPPPKKEESKPPVQIPILSTTPA
TPLPLQKHFVEPTPPSPINEVKNQASEQPQVIKCETPPPSAIAIDSAASFSSTEKLVTST
DPGKEANFAASSPPMLRPVNKIEDVKTIKRQMKTGWL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g12424.t1 | Coils | Coil | Coil | 774 | 794 | - |
| 34 | g12424.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 830 | 1052 | - |
| 32 | g12424.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 880 | 894 | - |
| 35 | g12424.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 901 | 923 | - |
| 31 | g12424.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 933 | 950 | - |
| 33 | g12424.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 998 | 1022 | - |
| 3 | g12424.t1 | PANTHER | PTHR10117:SF47 | TRANSIENT-RECEPTOR-POTENTIAL-LIKE PROTEIN | 27 | 864 | 0.0 |
| 4 | g12424.t1 | PANTHER | PTHR10117 | TRANSIENT RECEPTOR POTENTIAL CHANNEL | 27 | 864 | 0.0 |
| 6 | g12424.t1 | PRINTS | PR01097 | Transient receptor potential family signature | 495 | 516 | 1.2E-19 |
| 7 | g12424.t1 | PRINTS | PR01097 | Transient receptor potential family signature | 517 | 530 | 1.2E-19 |
| 5 | g12424.t1 | PRINTS | PR01097 | Transient receptor potential family signature | 545 | 558 | 1.2E-19 |
| 2 | g12424.t1 | Pfam | PF08344 | Transient receptor ion channel II | 32 | 94 | 2.8E-24 |
| 1 | g12424.t1 | Pfam | PF00520 | Ion transport protein | 232 | 524 | 1.4E-34 |
| 13 | g12424.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 11 | - |
| 19 | g12424.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 30 | - |
| 9 | g12424.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 31 | 185 | - |
| 23 | g12424.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 186 | 206 | - |
| 15 | g12424.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 207 | 225 | - |
| 21 | g12424.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 226 | 251 | - |
| 12 | g12424.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 252 | 271 | - |
| 17 | g12424.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 272 | 288 | - |
| 14 | g12424.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 289 | 311 | - |
| 22 | g12424.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 312 | 330 | - |
| 11 | g12424.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 331 | 401 | - |
| 20 | g12424.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 402 | 424 | - |
| 16 | g12424.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 425 | 487 | - |
| 18 | g12424.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 488 | 510 | - |
| 10 | g12424.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 511 | 1177 | - |
| 36 | g12424.t1 | TIGRFAM | TIGR00870 | trp: transient-receptor-potential calcium channel protein | 14 | 631 | 1.0E-177 |
| 30 | g12424.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 187 | 209 | - |
| 28 | g12424.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 229 | 251 | - |
| 26 | g12424.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 312 | 329 | - |
| 24 | g12424.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 358 | 380 | - |
| 29 | g12424.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 401 | 423 | - |
| 25 | g12424.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 464 | 481 | - |
| 27 | g12424.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 488 | 510 | - |
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:0070588 | calcium ion transmembrane transport | BP |
| GO:0016020 | membrane | CC |
| GO:0055085 | transmembrane transport | BP |
| GO:0005216 | ion channel activity | MF |
| GO:0005262 | calcium channel activity | MF |
| GO:0006811 | ion transport | BP |
KEGG
Orthology
- This transcript has been annotated with K13803 (transient-receptor-potential-like protein)
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. There were no conditions that were differentially expressed