General information for g2388.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Voltage-dependent T-type calcium channel subunit alpha-1G.
Parent gene
- The parent gene g2388 is located on chr_3: 17534479..17562714 (+ 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 | g2388 | g2388.t1 | isoform | g2388.t1 | 17534479 | 17562714 |
| chr_3 | g2388 | g2388.t1 | exon | g2388.t1.exon1 | 17534479 | 17534571 |
| chr_3 | g2388 | g2388.t1 | cds | g2388.t1.CDS1 | 17534479 | 17534571 |
| chr_3 | g2388 | g2388.t1 | exon | g2388.t1.exon2 | 17535698 | 17535929 |
| chr_3 | g2388 | g2388.t1 | cds | g2388.t1.CDS2 | 17535698 | 17535929 |
| chr_3 | g2388 | g2388.t1 | exon | g2388.t1.exon3 | 17536259 | 17536375 |
| chr_3 | g2388 | g2388.t1 | cds | g2388.t1.CDS3 | 17536259 | 17536375 |
| chr_3 | g2388 | g2388.t1 | exon | g2388.t1.exon4 | 17536545 | 17536599 |
| chr_3 | g2388 | g2388.t1 | cds | g2388.t1.CDS4 | 17536545 | 17536599 |
| chr_3 | g2388 | g2388.t1 | exon | g2388.t1.exon5 | 17548439 | 17548560 |
| chr_3 | g2388 | g2388.t1 | cds | g2388.t1.CDS5 | 17548439 | 17548560 |
| chr_3 | g2388 | g2388.t1 | exon | g2388.t1.exon6 | 17550940 | 17551094 |
| chr_3 | g2388 | g2388.t1 | cds | g2388.t1.CDS6 | 17550940 | 17551094 |
| chr_3 | g2388 | g2388.t1 | exon | g2388.t1.exon7 | 17551485 | 17551577 |
| chr_3 | g2388 | g2388.t1 | cds | g2388.t1.CDS7 | 17551485 | 17551577 |
| chr_3 | g2388 | g2388.t1 | exon | g2388.t1.exon8 | 17553165 | 17553406 |
| chr_3 | g2388 | g2388.t1 | cds | g2388.t1.CDS8 | 17553165 | 17553406 |
| chr_3 | g2388 | g2388.t1 | exon | g2388.t1.exon9 | 17557977 | 17558355 |
| chr_3 | g2388 | g2388.t1 | cds | g2388.t1.CDS9 | 17557977 | 17558355 |
| chr_3 | g2388 | g2388.t1 | exon | g2388.t1.exon10 | 17558903 | 17559076 |
| chr_3 | g2388 | g2388.t1 | cds | g2388.t1.CDS10 | 17558903 | 17559076 |
| chr_3 | g2388 | g2388.t1 | exon | g2388.t1.exon11 | 17560150 | 17560796 |
| chr_3 | g2388 | g2388.t1 | cds | g2388.t1.CDS11 | 17560150 | 17560796 |
| chr_3 | g2388 | g2388.t1 | exon | g2388.t1.exon12 | 17561832 | 17562047 |
| chr_3 | g2388 | g2388.t1 | cds | g2388.t1.CDS12 | 17561832 | 17562047 |
| chr_3 | g2388 | g2388.t1 | exon | g2388.t1.exon13 | 17562564 | 17562714 |
| chr_3 | g2388 | g2388.t1 | cds | g2388.t1.CDS13 | 17562564 | 17562714 |
| chr_3 | g2388 | g2388.t1 | TSS | g2388.t1 | NA | NA |
| chr_3 | g2388 | g2388.t1 | TTS | g2388.t1 | NA | NA |
Sequences
>g2388.t1 Gene=g2388 Length=2676
ATGCTTGTTATCCTACTCAATTGCATAACACTTGGAATGTTTCAACCGTGCGTCGACGAC
AAATGTGAAAAAAATCGATGCAAAATTCTTCAGATATTTGACGACGTTATTTTCGTATTT
TTCTCACTAGAAATGACAATTAAAATGATTGCTATGGGAGCTTATGGCAGAGGAACTTAT
CTTGCTGACTCCTGGAACCGCTTGGACTTTTTCATCGTGATGTCTGGTGCTTTAGAATAC
TTTTTACAAGTTGAGAATTTAAATTTAACTGCTATCAGAACTATTAGAGTATTAAGGCCA
TTAAGGGCAATTAATAGAATTCCTAGTATGCGAATTTTAGTGATGTTGCTATTGGATACT
TTGCCAATGCTCGGCAACGTTCTTCTTCTATGTTTTTTCGTTTTCTTCATATTTGGAATC
ATTGGCGTACAGTTATGGGAAGGTATACTAAGGCAACGTTGCGTCTTGCAATTGCCCGAT
GGCGTACTTAAACCTGACATATCATTTTACTATGAATTTTCCAAAGAGCAGGATTACATC
TGCTCAAAACCAGAAGATTCTGGAATGCATTTATGTGCAAATTTACCACCATATCGAATA
GGACCGCTTATTTGTAACTCTTCTGCCGTGCCATATAGTTTAAATAAACCAACCGAGACA
TCGTGCGTCAATTGGAATCAATATTATACGAATTGTACTCAGCTTGGTGGCAATCCATTT
CAGGGGACGATATCATTTGACAATATTGGACTTGCATGGGTTGCAATTTTTCTTGTCATA
TCGCTGGAAGGCTGGACGGACATAATGTATTACGTTCAGGATGCCCACAGCTTCTGGGAC
TGGATATATTTTGTTTTATTGATTGTGATTGGCTCTTTCTTTATGATCAACTTGTGCTTG
GTCGTTATTGCTACGCAGTTTTCGGAGACAAAGAAGCGTGAGATGGAACGAATGCGACAA
GAAAGGGCACGTTTTACCTCGTCATCGACATTGGCATCGAGCACAAACAATTCTGAGCCA
ACGACCTGCTATGCTGAAATTGTTAAATACATCGCTCATCTTTATAGACGATTGAAACGC
CGTTTGATTAAGAAGTTACGATTGTATAAATATCAATATCAGCAGCGAAAAGAAGGCCTT
CTACCGCGTACACCTGACAATCTATTTTCACCACAAAAAATCCGCTGTCATCATCCAAAA
TGTCCGAAATTATTGAGCAATCATTGTGGTAGTGGCAGCAAACTAACGAACCTTCAAGAG
CAATCGAAGTCAAACAATCAATTGAACAGCATACAATCAGCACCATTAAACAATAGTAAC
AATAATCATGATGATATACTGTCAGACAACTCGGAAATACAATCGTTGAATAATACATTG
AGTGCGACAATGGATGAAAAGCAAAAAATGCTGCTTCTAAAAATAGCAAACAATTCTATC
GCCGCCGCTTCAGCTGTTGCTTCTGCAGCTGACAACGATTATGGAAACAATTCAGCAAGC
TCCAGCTTGTTGAGTCCACCAACATCGACCCGAAGACGTGGCTCGTCTGTTATGTTTAAT
GAATTCGTTATTCTTCACACTCCGCCCAAAATTGAACCGCAAAATGACAAGAATACGTTA
TCAGTGGAAAAAATGACACAGACTGGTGAAGGCATTTGGCAAGTCAATTTACCGCACAAC
ACCACCATCAACTCAGTCACCAACAACCTCAACGATTATTCGGATCTCAATCTAACTGAT
GCCATGACGTGTCAAGAATTGCTTGCACTCTCGGTCGCCTTCTCTGCCGCCCTTCCCACT
GGTCAAACAACACTCGATTCTTTTTATTCGACACTCACACGAAATAATAACAACAATAAT
GATTTTAACACACAAATTGAAGACTATGCATGCTGTTATGATCTTTATCAGCAAAATTTC
GATTATGCAGCACAAGAATATCATCAACATCAATTGCATCAATCGAGTGAAGATCTCGAA
GGGACAAAATCACGAACATATCATGCTTGTCTCACATGCTATAAAATTGTATCGAAAATA
TTCCATTTTATTCGCAAATACATCAAACGTCTCGTTGACCATAAGTACTTTCAGCAAGGC
ATTCTTTTGGCAATTCTCATCAACACACTCTCAATGGGCATTGAATATCACAATCAACCG
GAAGAATTGACGGCCATAGTTGAGACAAGCAATATTGTTTTCTCTGCCATATTTGCAGTT
GAAATGCTACTGAAAATCATTGCTGAGGGACCATTCAAATATATTTCGAATGGATTTAAT
GTTTTCGATGGAATAATCGTGGTATTGAGTGCTGTCGAACTATGTCAAGCATTTATGCGA
GATGGGACGTCTGTGAATTCTGGAAATTCAGGATTGTCGGTATTAAGGACATTTCGTTTG
CTTCGTATACTTAAATTGGTTCGATTTATGCCAAACCTCAGGCGACAACTTTTTGTTATG
CTTCGCACCATGGACAATGTTGCCATCTTCTTCTCGCTATTGATTTTATTCATTTTCATA
TTCAGTCTTGTGATAAGAACACAAGAAAATTTTCATATCGTGATTTATGACTCTCATCAA
CTCTTGACCCTTTTCATTATGATTTTCTATCCACCATTGCTGCCATCATCATCATCATCC
ACTTACAATTTTCCTATCATCATCTATACAAATTAA
>g2388.t1 Gene=g2388 Length=891
MLVILLNCITLGMFQPCVDDKCEKNRCKILQIFDDVIFVFFSLEMTIKMIAMGAYGRGTY
LADSWNRLDFFIVMSGALEYFLQVENLNLTAIRTIRVLRPLRAINRIPSMRILVMLLLDT
LPMLGNVLLLCFFVFFIFGIIGVQLWEGILRQRCVLQLPDGVLKPDISFYYEFSKEQDYI
CSKPEDSGMHLCANLPPYRIGPLICNSSAVPYSLNKPTETSCVNWNQYYTNCTQLGGNPF
QGTISFDNIGLAWVAIFLVISLEGWTDIMYYVQDAHSFWDWIYFVLLIVIGSFFMINLCL
VVIATQFSETKKREMERMRQERARFTSSSTLASSTNNSEPTTCYAEIVKYIAHLYRRLKR
RLIKKLRLYKYQYQQRKEGLLPRTPDNLFSPQKIRCHHPKCPKLLSNHCGSGSKLTNLQE
QSKSNNQLNSIQSAPLNNSNNNHDDILSDNSEIQSLNNTLSATMDEKQKMLLLKIANNSI
AAASAVASAADNDYGNNSASSSLLSPPTSTRRRGSSVMFNEFVILHTPPKIEPQNDKNTL
SVEKMTQTGEGIWQVNLPHNTTINSVTNNLNDYSDLNLTDAMTCQELLALSVAFSAALPT
GQTTLDSFYSTLTRNNNNNNDFNTQIEDYACCYDLYQQNFDYAAQEYHQHQLHQSSEDLE
GTKSRTYHACLTCYKIVSKIFHFIRKYIKRLVDHKYFQQGILLAILINTLSMGIEYHNQP
EELTAIVETSNIVFSAIFAVEMLLKIIAEGPFKYISNGFNVFDGIIVVLSAVELCQAFMR
DGTSVNSGNSGLSVLRTFRLLRILKLVRFMPNLRRQLFVMLRTMDNVAIFFSLLILFIFI
FSLVIRTQENFHIVIYDSHQLLTLFIMIFYPPLLPSSSSSTYNFPIIIYTN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g2388.t1 | Gene3D | G3DSA:1.20.120.350 | - | 1 | 108 | 2.9E-21 |
| 11 | g2388.t1 | Gene3D | G3DSA:1.10.287.70 | - | 228 | 313 | 1.9E-15 |
| 12 | g2388.t1 | Gene3D | G3DSA:1.20.120.350 | - | 686 | 817 | 1.1E-34 |
| 3 | g2388.t1 | PANTHER | PTHR10037:SF137 | VOLTAGE-DEPENDENT T-TYPE CALCIUM CHANNEL SUBUNIT ALPHA-1G | 1 | 843 | 1.9E-237 |
| 4 | g2388.t1 | PANTHER | PTHR10037 | VOLTAGE-GATED CATION CHANNEL CALCIUM AND SODIUM | 1 | 843 | 1.9E-237 |
| 7 | g2388.t1 | PRINTS | PR01629 | T-type voltage-dependent calcium channel alpha-1 subunit signature | 16 | 32 | 1.6E-11 |
| 5 | g2388.t1 | PRINTS | PR01629 | T-type voltage-dependent calcium channel alpha-1 subunit signature | 339 | 353 | 1.6E-11 |
| 6 | g2388.t1 | PRINTS | PR01629 | T-type voltage-dependent calcium channel alpha-1 subunit signature | 713 | 726 | 1.6E-11 |
| 2 | g2388.t1 | Pfam | PF00520 | Ion transport protein | 1 | 314 | 6.9E-70 |
| 1 | g2388.t1 | Pfam | PF00520 | Ion transport protein | 694 | 845 | 3.5E-30 |
| 19 | g2388.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 35 | - |
| 35 | g2388.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 36 | 58 | - |
| 23 | g2388.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 59 | 63 | - |
| 37 | g2388.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 64 | 82 | - |
| 14 | g2388.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 83 | 102 | - |
| 29 | g2388.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 103 | 121 | - |
| 21 | g2388.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 122 | 126 | - |
| 28 | g2388.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 127 | 146 | - |
| 18 | g2388.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 147 | 243 | - |
| 31 | g2388.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 244 | 262 | - |
| 26 | g2388.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 263 | 281 | - |
| 33 | g2388.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 282 | 307 | - |
| 20 | g2388.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 308 | 695 | - |
| 27 | g2388.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 696 | 714 | - |
| 24 | g2388.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 715 | 725 | - |
| 34 | g2388.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 726 | 747 | - |
| 17 | g2388.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 748 | 758 | - |
| 30 | g2388.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 759 | 779 | - |
| 22 | g2388.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 780 | 790 | - |
| 36 | g2388.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 791 | 807 | - |
| 16 | g2388.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 808 | 826 | - |
| 32 | g2388.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 827 | 845 | - |
| 25 | g2388.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 846 | 850 | - |
| 38 | g2388.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 851 | 870 | - |
| 15 | g2388.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 871 | 891 | - |
| 9 | g2388.t1 | SUPERFAMILY | SSF81324 | Voltage-gated potassium channels | 1 | 310 | 1.28E-31 |
| 8 | g2388.t1 | SUPERFAMILY | SSF81324 | Voltage-gated potassium channels | 694 | 851 | 3.41E-27 |
| 10 | g2388.t1 | SignalP_EUK | SignalP-TM | SignalP-TM | 1 | 19 | - |
| 45 | g2388.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 36 | 55 | - |
| 43 | g2388.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 70 | 92 | - |
| 44 | g2388.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 112 | 143 | - |
| 42 | g2388.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 249 | 271 | - |
| 39 | g2388.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 283 | 305 | - |
| 40 | g2388.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 823 | 845 | - |
| 41 | g2388.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 852 | 874 | - |
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:0005245 | voltage-gated calcium channel activity | MF |
| GO:0006811 | ion transport | BP |
| GO:0005261 | cation channel activity | MF |
| GO:0008332 | low voltage-gated calcium channel activity | MF |
| GO:0070509 | calcium ion import | BP |
| GO:0005216 | ion channel activity | MF |
| GO:0005886 | plasma membrane | CC |
| GO:0005891 | voltage-gated calcium channel complex | CC |
KEGG
Orthology
- This transcript has been annotated with K21864 (voltage-dependent calcium channel)
Pathway
This gene does not belong to any 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