General information for g12004.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Transient receptor potential cation channel subfamily V member 5.
Parent gene
- The parent gene g12004 is located on chr_1: 20288252..20291555 (- 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 | g12004 | g12004.t1 | isoform | g12004.t1 | 20287993 | 20291555 |
| chr_1 | g12004 | g12004.t1 | exon | g12004.t1.exon1 | 20287993 | 20288160 |
| chr_1 | g12004 | g12004.t1 | cds | g12004.t1.CDS1 | 20287993 | 20288160 |
| chr_1 | g12004 | g12004.t1 | exon | g12004.t1.exon2 | 20288324 | 20288566 |
| chr_1 | g12004 | g12004.t1 | cds | g12004.t1.CDS2 | 20288324 | 20288566 |
| chr_1 | g12004 | g12004.t1 | exon | g12004.t1.exon3 | 20288636 | 20288921 |
| chr_1 | g12004 | g12004.t1 | cds | g12004.t1.CDS3 | 20288636 | 20288921 |
| chr_1 | g12004 | g12004.t1 | exon | g12004.t1.exon4 | 20288978 | 20289129 |
| chr_1 | g12004 | g12004.t1 | cds | g12004.t1.CDS4 | 20288978 | 20289129 |
| chr_1 | g12004 | g12004.t1 | exon | g12004.t1.exon5 | 20289194 | 20289301 |
| chr_1 | g12004 | g12004.t1 | cds | g12004.t1.CDS5 | 20289194 | 20289301 |
| chr_1 | g12004 | g12004.t1 | exon | g12004.t1.exon6 | 20289360 | 20289797 |
| chr_1 | g12004 | g12004.t1 | cds | g12004.t1.CDS6 | 20289360 | 20289797 |
| chr_1 | g12004 | g12004.t1 | exon | g12004.t1.exon7 | 20289865 | 20290602 |
| chr_1 | g12004 | g12004.t1 | cds | g12004.t1.CDS7 | 20289865 | 20290602 |
| chr_1 | g12004 | g12004.t1 | exon | g12004.t1.exon8 | 20290825 | 20290887 |
| chr_1 | g12004 | g12004.t1 | cds | g12004.t1.CDS8 | 20290825 | 20290887 |
| chr_1 | g12004 | g12004.t1 | exon | g12004.t1.exon9 | 20291119 | 20291280 |
| chr_1 | g12004 | g12004.t1 | cds | g12004.t1.CDS9 | 20291119 | 20291280 |
| chr_1 | g12004 | g12004.t1 | exon | g12004.t1.exon10 | 20291382 | 20291555 |
| chr_1 | g12004 | g12004.t1 | cds | g12004.t1.CDS10 | 20291382 | 20291555 |
| chr_1 | g12004 | g12004.t1 | TSS | g12004.t1 | NA | NA |
| chr_1 | g12004 | g12004.t1 | TTS | g12004.t1 | NA | NA |
Sequences
>g12004.t1 Gene=g12004 Length=2532
ATGGGTAATACTGAGAGTAATGTGACATCTGGGGTCAAAAAACAGGCAGGAGTTTCAACA
CAGAAGCTTTATAAACTTGTGAACTTGAAGGGTGGTGGACTTCTTGTAGATATGATGAAA
CGAGCCATAAATAATAAGCAATTCGCTGAAATTGATCATGCCATAAAGACTAAGGTTGAA
CCATTTCTTTACAACAAGGGTCGTGGTCGCTATATTCCAATTGCACAAATTGTTAAAATG
AGAAACTGTGAACGACCAAAGCACAAACAATTGCCAGATATACGAATTTTAGAAAATCCA
GAAGAGGATTATGACATTCATGCTGATTGTCCGGAAGTGAGCGAAGCAGATTATTTAATT
AACCCATCAGGATACAGAGAGGTCTGTTGGGATTTGAAGGAACGTGGTGCTGTAGGTGAA
ACGATTCTTCACTTGTGCTTTCTAAATGCTACGTCACTTCATGCTGACTTGGCAAAAAGG
CTATTGCGATTCTATCCAAAATTGATTAATGATATTTATATGTGTGACGAGTACTATGGT
GAAAATGTGTTGCATATTGCAATTGTCAATGAGGATCCAGCTGCAGTAAAATTTCTATTA
GACAGTGGTGCTGATATTCACGAGAGATGTTTTGGAACATTTATGTCACCTGAAGATCAA
AAAGGAACGCGATATGATGTTATTGAACATGAGGCTATCTGTGTAAATCCGATTACAAAT
TATGAAGGCTATGTATACTGGGGTGAATATCCGCTTTCATTTGCCGCATGCCTTTGTCAA
GAGGAATGTTATCGTTTAGTGTTGGCAAAGAAAGCTGATCCAGATAATCAAGATATAAAT
GGGAATACTGTTCTTCATTTGCTAGTAATTCATGAGAAGCTTAGTACATTTGATATGGCA
TATGAGACAGGCGCAAATTTATATATCAAAAATAATTTGAATTTGACACCTTTAACACTT
GCCGCGAAGCTAGCAAGAGTTGAAATGTTTTTTCATATTTTAAACATTGATCGTGAAATT
TATTGGCAATTAGGATCAATTACTTGCGCCGCATATCCATTAGAGCAACTCGATACGATT
AATACAAAGACCGGAAATATCAACAAGGATTCGGTTTTAAATTTAGTTGTTTTCGGAGAT
AAAGACGAACATTTAGATTTACTAGAGGGCGTTCTTATTGACTTGTTAAAAACTAAATGG
AATACATTTGTTAAAGCAAAATTTTATCAGCAATTTTATTTGTTCACAATTTACTTTTTC
ATTTCACTTTTTGCATTTCTATTGAGACCTAAAGCGTTTAGCGATGACAAAGCAACGAAA
AATGGAAATAGCACTCAAACGGATATGAATGTCAATGACACAATAAATGCACCTGTTAAA
TCTCTTTTCATTCATAATTTGACAGAGATTTTCTGCAATTATTCAGCTGCGTATGCTGAT
ATTGTCATGCAATCGGATATGAGCATGAATAATTTATCGATCATAGATAACAATTCGACG
TTGCCAATGGATGATGATGAGTGGTCACCAATTTCTGAATGTCCACTTTTAGACATAAGT
ACACTTGAGAGTCGAATAAAACTAAGCGCTGAAGCTCTCATGACAGTTGGTGCATTACTT
TATATTCTAACAGCTTTACGCGAGGCACGTTTTCTTGGTGCAAAAATGTTTTTCGAAAAC
TTGAGCACGGCACCATCGCGTGTTATGTTTTTATTTTCATGCATATTAATGCTGACAATA
CCATTTATAAAGTTTTTCTGTTTACCGAAGCTGGAGGATCATGTTGCTGTGGCAATTATG
CTGACAACAGGACCTTATTTTTTATTCTTTTGCAGAGGATTTAAAACAGTTGGACCTTTC
GTAGTCATGATATATCGCATGGTAGTGGGAGATCTTTTACGTTTCGTTACAATTTATATG
GTGTTTGTTATGGGTTTTTCACAAGCATATTATATCATATTTTTAACTTTTGATAACTCG
GAGGAAGAGGAGCCTGATCCCGAATTTAATCCCATAGCATCGCCAATGGAAAGTTTTATA
TCAATGTTTTTAATGTCGCTTGGTAATTTTGGTGATTATTATGGAGGAATGGAATATACT
GCGCATGAAATGCAAGCAAAAACACTCTTTGTATTGTTTATGGCAATTGTTGCAGTTCTT
CTTATCAACATGTTGATCGCTATGATGGGCAACACTTATACAAAAATTGCAGAAACAAAA
AATGAATGGCAACGTCAGTGGGCTCGCATTGTACTTGTTGTAGAGCGAAGTGTTCCACCG
CATGATCGTTTAAAAAATTTTAATCATTATAGTCAAATTATGGCAGATGGGCGAACTGCA
TTAATTTTACGATTAAACATGACAGATGAAGAGAAAGCAGAAATGAAAGATATTCTAGAA
ATGAAATGTGTTCATACAAAACTTGCAAAGAAACGTCATGATGAACGTCAAGCACGCCTA
CAAAAGATTGAACTAGATCGTCAACGTGGTTATGAATTGAAAGCAAAAGCAAATCGTTAT
GCGAACCAATAA
>g12004.t1 Gene=g12004 Length=843
MGNTESNVTSGVKKQAGVSTQKLYKLVNLKGGGLLVDMMKRAINNKQFAEIDHAIKTKVE
PFLYNKGRGRYIPIAQIVKMRNCERPKHKQLPDIRILENPEEDYDIHADCPEVSEADYLI
NPSGYREVCWDLKERGAVGETILHLCFLNATSLHADLAKRLLRFYPKLINDIYMCDEYYG
ENVLHIAIVNEDPAAVKFLLDSGADIHERCFGTFMSPEDQKGTRYDVIEHEAICVNPITN
YEGYVYWGEYPLSFAACLCQEECYRLVLAKKADPDNQDINGNTVLHLLVIHEKLSTFDMA
YETGANLYIKNNLNLTPLTLAAKLARVEMFFHILNIDREIYWQLGSITCAAYPLEQLDTI
NTKTGNINKDSVLNLVVFGDKDEHLDLLEGVLIDLLKTKWNTFVKAKFYQQFYLFTIYFF
ISLFAFLLRPKAFSDDKATKNGNSTQTDMNVNDTINAPVKSLFIHNLTEIFCNYSAAYAD
IVMQSDMSMNNLSIIDNNSTLPMDDDEWSPISECPLLDISTLESRIKLSAEALMTVGALL
YILTALREARFLGAKMFFENLSTAPSRVMFLFSCILMLTIPFIKFFCLPKLEDHVAVAIM
LTTGPYFLFFCRGFKTVGPFVVMIYRMVVGDLLRFVTIYMVFVMGFSQAYYIIFLTFDNS
EEEEPDPEFNPIASPMESFISMFLMSLGNFGDYYGGMEYTAHEMQAKTLFVLFMAIVAVL
LINMLIAMMGNTYTKIAETKNEWQRQWARIVLVVERSVPPHDRLKNFNHYSQIMADGRTA
LILRLNMTDEEKAEMKDILEMKCVHTKLAKKRHDERQARLQKIELDRQRGYELKAKANRY
ANQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g12004.t1 | Gene3D | G3DSA:1.25.40.20 | - | 113 | 389 | 1.1E-68 |
| 7 | g12004.t1 | Gene3D | G3DSA:1.10.287.70 | - | 618 | 738 | 1.4E-5 |
| 3 | g12004.t1 | PANTHER | PTHR10582:SF28 | NANCHUNG, ISOFORM B | 1 | 800 | 0.0 |
| 4 | g12004.t1 | PANTHER | PTHR10582 | TRANSIENT RECEPTOR POTENTIAL ION CHANNEL PROTEIN | 1 | 800 | 0.0 |
| 1 | g12004.t1 | Pfam | PF12796 | Ankyrin repeats (3 copies) | 138 | 208 | 7.6E-7 |
| 2 | g12004.t1 | Pfam | PF00520 | Ion transport protein | 531 | 739 | 4.1E-14 |
| 12 | g12004.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 407 | - |
| 22 | g12004.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 408 | 428 | - |
| 11 | g12004.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 429 | 527 | - |
| 19 | g12004.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 528 | 546 | - |
| 13 | g12004.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 547 | 565 | - |
| 17 | g12004.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 566 | 588 | - |
| 9 | g12004.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 589 | 594 | - |
| 21 | g12004.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 595 | 615 | - |
| 15 | g12004.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 616 | 634 | - |
| 18 | g12004.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 635 | 657 | - |
| 8 | g12004.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 658 | 668 | - |
| 20 | g12004.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 669 | 688 | - |
| 14 | g12004.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 689 | 707 | - |
| 16 | g12004.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 708 | 730 | - |
| 10 | g12004.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 731 | 843 | - |
| 34 | g12004.t1 | ProSiteProfiles | PS50297 | Ankyrin repeat region circular profile. | 179 | 334 | 17.343 |
| 36 | g12004.t1 | ProSiteProfiles | PS50088 | Ankyrin repeat profile. | 179 | 211 | 10.045 |
| 35 | g12004.t1 | ProSiteProfiles | PS50088 | Ankyrin repeat profile. | 280 | 312 | 8.576 |
| 33 | g12004.t1 | SMART | SM00248 | ANK_2a | 138 | 171 | 190.0 |
| 32 | g12004.t1 | SMART | SM00248 | ANK_2a | 179 | 208 | 0.0011 |
| 31 | g12004.t1 | SMART | SM00248 | ANK_2a | 247 | 276 | 690.0 |
| 30 | g12004.t1 | SMART | SM00248 | ANK_2a | 280 | 309 | 31.0 |
| 29 | g12004.t1 | SMART | SM00248 | ANK_2a | 313 | 342 | 410.0 |
| 5 | g12004.t1 | SUPERFAMILY | SSF48403 | Ankyrin repeat | 130 | 336 | 4.5E-24 |
| 25 | g12004.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 409 | 428 | - |
| 28 | g12004.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 568 | 585 | - |
| 24 | g12004.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 595 | 614 | - |
| 27 | g12004.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 635 | 657 | - |
| 26 | g12004.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 672 | 691 | - |
| 23 | g12004.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 708 | 730 | - |
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 K04974 (transient receptor potential cation channel subfamily V member 5)
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.
