General information for g6376.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Voltage-dependent calcium channel subunit alpha-2/delta-4.
Parent gene
- The parent gene g6376 is located on chr_2: 16718137..16723785 (- 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_2 | g6376 | g6376.t1 | isoform | g6376.t1 | 16718137 | 16723785 |
| chr_2 | g6376 | g6376.t1 | exon | g6376.t1.exon1 | 16718137 | 16718253 |
| chr_2 | g6376 | g6376.t1 | cds | g6376.t1.CDS1 | 16718137 | 16718253 |
| chr_2 | g6376 | g6376.t1 | exon | g6376.t1.exon2 | 16718315 | 16718841 |
| chr_2 | g6376 | g6376.t1 | cds | g6376.t1.CDS2 | 16718315 | 16718841 |
| chr_2 | g6376 | g6376.t1 | exon | g6376.t1.exon3 | 16719009 | 16719360 |
| chr_2 | g6376 | g6376.t1 | cds | g6376.t1.CDS3 | 16719009 | 16719360 |
| chr_2 | g6376 | g6376.t1 | exon | g6376.t1.exon4 | 16719547 | 16720368 |
| chr_2 | g6376 | g6376.t1 | cds | g6376.t1.CDS4 | 16719547 | 16720368 |
| chr_2 | g6376 | g6376.t1 | exon | g6376.t1.exon5 | 16720477 | 16720554 |
| chr_2 | g6376 | g6376.t1 | cds | g6376.t1.CDS5 | 16720477 | 16720554 |
| chr_2 | g6376 | g6376.t1 | exon | g6376.t1.exon6 | 16720831 | 16720938 |
| chr_2 | g6376 | g6376.t1 | cds | g6376.t1.CDS6 | 16720831 | 16720938 |
| chr_2 | g6376 | g6376.t1 | exon | g6376.t1.exon7 | 16721005 | 16721151 |
| chr_2 | g6376 | g6376.t1 | cds | g6376.t1.CDS7 | 16721005 | 16721151 |
| chr_2 | g6376 | g6376.t1 | exon | g6376.t1.exon8 | 16721211 | 16721411 |
| chr_2 | g6376 | g6376.t1 | cds | g6376.t1.CDS8 | 16721211 | 16721411 |
| chr_2 | g6376 | g6376.t1 | exon | g6376.t1.exon9 | 16721472 | 16722256 |
| chr_2 | g6376 | g6376.t1 | cds | g6376.t1.CDS9 | 16721472 | 16722256 |
| chr_2 | g6376 | g6376.t1 | exon | g6376.t1.exon10 | 16722677 | 16723040 |
| chr_2 | g6376 | g6376.t1 | cds | g6376.t1.CDS10 | 16722677 | 16723040 |
| chr_2 | g6376 | g6376.t1 | exon | g6376.t1.exon11 | 16723107 | 16723211 |
| chr_2 | g6376 | g6376.t1 | cds | g6376.t1.CDS11 | 16723107 | 16723211 |
| chr_2 | g6376 | g6376.t1 | exon | g6376.t1.exon12 | 16723465 | 16723546 |
| chr_2 | g6376 | g6376.t1 | cds | g6376.t1.CDS12 | 16723465 | 16723546 |
| chr_2 | g6376 | g6376.t1 | exon | g6376.t1.exon13 | 16723679 | 16723785 |
| chr_2 | g6376 | g6376.t1 | cds | g6376.t1.CDS13 | 16723679 | 16723785 |
| chr_2 | g6376 | g6376.t1 | TSS | g6376.t1 | NA | NA |
| chr_2 | g6376 | g6376.t1 | TTS | g6376.t1 | NA | NA |
Sequences
>g6376.t1 Gene=g6376 Length=3795
ATGATGAAAGTGAATGTGATTTCAGTGTTGATAATGATAAATTTCTATCTAAATATTTCT
GGCGCCCAAAGTCTCGGTACTAATGCTGCTGCAATCGATTTTGGGATGGTTCAACAATTG
TCAAAACAAATTGGCGAGAAACTTTTGAATATTTCTGAAGCAGTGACGAAAAGAAACGAA
GTGCAAGATAGCTTTATGCATGCAAAAGTTGTAACTAAAAATGGAAGAAAAATTGTTGAA
GAAATCGCAAAAGATTTAGAAATGATGCTCGATATAAGAATAAAAGCTGTAAAGAAAATT
GTCCAATCAATTCAAAATCTTCCAAAAGTTCACGAAAATGACACATTTTTTACCAATTAT
ACATTTATAAATATACGAGAACGAGATAAACATGGAGCAGAAATTTTAGCTGAAAAAGAA
GAAGAAAATCTGAGAAAAGAAAAAGCATCTCAAGATCCAAATTATAAAAAGAAAAGAAAA
CCAAATAATGATGGTTCGATTTGTATTCCATCAGTATCAGTAGGTTCAAGTAAAAGCAAT
AATGACGATGATGAAGAAGATGGTGACGATGATGATACAATTTCATTTATTGATGAAGCT
GTCAATGTTAGATCAAAAGAAGCTGGTGTATTTCTTCCATTAGATGTTTATGATAAAGAA
GAGCCAACGATAGGATGGCAATATTTCTGCAATTCATCAGGTGTTTTTCGACATTTTCCA
GTAACAAATTGGACATTTTATCCAATGAATACTTTTGATTGTCGAATGCGGCCATGGTTT
ACAAATGCTGCTTCATCATCAAAAGATATTGTTGTACTGATAGAACAATCAGGTTCAATG
ACTGGTGAAAGACTTTCAATTGCAAAAGATGTTGTTCGAAATATTCTCAATACATTGACA
ATTAATGATTATGTCAATGTTTTTTCATTTAATGATGAATTTCGTCCAATAATTGATTGC
AAAGATGATTTTTGTAAAGATACTTTGATTCAAGCGACACCAGCAAATATATTTGAATTA
AAGCAAGCACTTGATAGTATAGAAGCAAAAGGTCAGACTGATTTGTTAGAAGCACTCAAT
CATACATTTCATTTATTACATTCAAAACGTGAAAGCAGCTCACATTGCAATAAAGTCATA
ATGCTCATTACTGATGGCATGGAATACAATACAACAATTAGGAAAGTATTTGAGGAAGAA
AATTGGGAAAAGAACAATGAAGTTCGTGTTTTTAGTTATTTAATTGGTGAAATGATTCCT
CAACATGACTTTAAGCAAGTCAAATCAATGGCTTGTGAAAATCGTGGCTATTATGTTCAA
ATTGATACAATCAAAGAGACACGTGAACAAGTGCTTCGATATATTCCAGTTATGGCTCGA
CCATTAGCTTTTAATAAAACTCAAAATCCAATTATTTTTACTAGTGTTTATGCTGATTTA
TTGGACACATATAGAGTGACAAATTATGATTGGAATTGCAAACAAAGAGCAACACAAAGA
CAACGTGTTGTTGATTATTTAAAAAAATACCAGAAATATTCATGTATCGCTGATAATGAA
GATGATGACGACAAGTCAGGTTTTCGTAAATATCTTTTTATGACGACAGTGGCAATGCCA
GCATTTGAGCAAGATAAAAACTCGTCACAACTGATGGGTGTTGCTGGTGTTGATGTGCCT
TTATATGAATTTGAAAGACTGTTTCAACAATTCCGTCTTGGAGTTCATTCGTATGCATTT
ATATTAGACGAAAATGGGAATATTTTAACACATCCGGATTTTCGACCATTTTTTCAAAAT
GAGCTTCTTAAGCCATCATATAATTCTATCGATATGGTTGAAGTTGAATTGATTGACGCC
GATAGATTTTGTAGAGATTTCCATCCAGAGCTTTTGAGTATGAGACGAGCAATGATTACA
AATGATAAAACAACGGGCTCAAAAGTGCTGCCAATTTTACAACATTTTGACGATTTGCGT
CGTGTAATGAAATTCAAGCGGCACTATTACTGGAAGAAAATCGACAAAACACCATTTACA
GTTGTCGTGACATTCTCCGACGACGCACCAAATCAAGTTCAAATACCCGAGCACGAAGTT
GATTCGATGACGACAAAGGGCAGTAAGAACCTTAAATACTTTCAAGGCAATTATCGTTTA
CATCCGAATTGGATTTACTGTCGTTCATTGAAGAAAAGTTTTGAAGATATGAAGCTTGGT
GAAATTGACCCAGACAATTGCGAAATGACACCCGAAGAAGAGCTCGAATATTTTCTAGAA
AAATTTGAAAAAAATGGTTGGAAATGGAGAACATCGAAAAATGATAAAGGAGCCTACAAA
TGTGATCAAAAACTGATGCAAGCTTTACTATATGATGCAAAAGTAACACAAAATTATCCA
CATGAACCGACAAAATCAAATAATAAAAAAGATAAAAATTCAAATATTTTTGAAGAGTAT
GAAATCAGTACATCTTTCATTGCAACTCACAGTGGTCTATTACGTTATAAAATTTTCTCT
AAAGATGAAGACGATGACGAAATTAACCAAAGAAGCGACGAATTTGGTGATGAGTTTAAA
AAATCAATTGATGAAGACTGGTACAAGCACACGACATATTTCAATAAACATGAACCAAAG
AGCTTCATTTATAAATTACCATTTAACGCTAACAAGGAATCATTAATAACAGCAACAACA
ACAATCTATGCTCGCGATGGTACTGAACGTGCTCCAGTTGCTGTTTTGGGATATCAATTT
CCACATGCAAAATTTGCTAAATTATTAGATAGCGATTTGTGTGCAATGAATGCCGAACAA
GTTTGCTTCATTCTTGATGATTATGCTTATGTAATTGCCGATTCAAGAGAAGAACAAGAA
GGAAAATTTTTTGGTGATGTCGACAAAAAATTAATGAAAATTTTAATTCATGATAATATT
TATGAGAAAAAGCAAATTTACGATTTTCAAGGAGTTTGTTATCAAGATAGAGAAATTGAA
TATGAATATATTATGGAAATTGTCTCAAATGCTGGATCAATTTTGTTATGGAATCCATTG
AAAAATTTATGGATGGCTTTGATAGCTTTATTTACGACTATTGGAAAGTTTTTTGAAACT
GAAGCAGTAGCGAAGAAATTTGTTCCAAATTTGATGTATCCAGATCCAGATTATTATTAT
GAAGATGACAGTACAGCATATTGTCCATATGCAGATGATGGTTCATTTGATAAATGTCTC
AAAGAAAATGACGTAAAAAAGTCAGATAAGGAAAATGAAAAATATATACAATGTGAAAAA
AATTACACACAAGCTTATAAAGTTTGTCATAATAGCTTACAATGGTCGACAAATCTCCTT
AAACGTCATACAAATAAAACTCGACCAATAAAATGTGATAAAAATAATTTTGTTTATGTG
TTGAATTTAGATGAAAGCAATTTGCGTAAGCCTTATAACAAGTGTGAGCGACCATTCATT
GTTCAACGAATACCAAATAGCAATTTAATTTTACTTGTGACAAAGAGTGATTGTGACAAA
AATGTAAATGTTGAACCATTCAATATTCAACCAAAAACTATTGGAATTGAAGATTATCAA
ATGTCATTGTTTTGTTATAAGCTGCGCAATCCACTATATAGACGTCATTCTAAATCGTGT
ATTAATTACCATGCAAATGAACCTATTGAACGTGGAAAAAATACATCACTTTGTGGACGA
GGAAATCGATTAGAAATGAAATTTAAATTTCTTCTAATATCGCCAGTAATTTTAATAATG
CTCAAATTTTTATGA
>g6376.t1 Gene=g6376 Length=1264
MMKVNVISVLIMINFYLNISGAQSLGTNAAAIDFGMVQQLSKQIGEKLLNISEAVTKRNE
VQDSFMHAKVVTKNGRKIVEEIAKDLEMMLDIRIKAVKKIVQSIQNLPKVHENDTFFTNY
TFINIRERDKHGAEILAEKEEENLRKEKASQDPNYKKKRKPNNDGSICIPSVSVGSSKSN
NDDDEEDGDDDDTISFIDEAVNVRSKEAGVFLPLDVYDKEEPTIGWQYFCNSSGVFRHFP
VTNWTFYPMNTFDCRMRPWFTNAASSSKDIVVLIEQSGSMTGERLSIAKDVVRNILNTLT
INDYVNVFSFNDEFRPIIDCKDDFCKDTLIQATPANIFELKQALDSIEAKGQTDLLEALN
HTFHLLHSKRESSSHCNKVIMLITDGMEYNTTIRKVFEEENWEKNNEVRVFSYLIGEMIP
QHDFKQVKSMACENRGYYVQIDTIKETREQVLRYIPVMARPLAFNKTQNPIIFTSVYADL
LDTYRVTNYDWNCKQRATQRQRVVDYLKKYQKYSCIADNEDDDDKSGFRKYLFMTTVAMP
AFEQDKNSSQLMGVAGVDVPLYEFERLFQQFRLGVHSYAFILDENGNILTHPDFRPFFQN
ELLKPSYNSIDMVEVELIDADRFCRDFHPELLSMRRAMITNDKTTGSKVLPILQHFDDLR
RVMKFKRHYYWKKIDKTPFTVVVTFSDDAPNQVQIPEHEVDSMTTKGSKNLKYFQGNYRL
HPNWIYCRSLKKSFEDMKLGEIDPDNCEMTPEEELEYFLEKFEKNGWKWRTSKNDKGAYK
CDQKLMQALLYDAKVTQNYPHEPTKSNNKKDKNSNIFEEYEISTSFIATHSGLLRYKIFS
KDEDDDEINQRSDEFGDEFKKSIDEDWYKHTTYFNKHEPKSFIYKLPFNANKESLITATT
TIYARDGTERAPVAVLGYQFPHAKFAKLLDSDLCAMNAEQVCFILDDYAYVIADSREEQE
GKFFGDVDKKLMKILIHDNIYEKKQIYDFQGVCYQDREIEYEYIMEIVSNAGSILLWNPL
KNLWMALIALFTTIGKFFETEAVAKKFVPNLMYPDPDYYYEDDSTAYCPYADDGSFDKCL
KENDVKKSDKENEKYIQCEKNYTQAYKVCHNSLQWSTNLLKRHTNKTRPIKCDKNNFVYV
LNLDESNLRKPYNKCERPFIVQRIPNSNLILLVTKSDCDKNVNVEPFNIQPKTIGIEDYQ
MSLFCYKLRNPLYRRHSKSCINYHANEPIERGKNTSLCGRGNRLEMKFKFLLISPVILIM
LKFL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g6376.t1 | CDD | cd18774 | PDC2_HK_sensor | 563 | 686 | 1.16096E-6 |
| 10 | g6376.t1 | Gene3D | G3DSA:3.40.50.410 | - | 267 | 455 | 5.5E-29 |
| 11 | g6376.t1 | Gene3D | G3DSA:3.30.450.20 | - | 539 | 692 | 1.2E-16 |
| 21 | g6376.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 141 | 190 | - |
| 22 | g6376.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 141 | 163 | - |
| 4 | g6376.t1 | PANTHER | PTHR10166:SF31 | RE14947P | 28 | 483 | 2.8E-181 |
| 6 | g6376.t1 | PANTHER | PTHR10166 | VOLTAGE-DEPENDENT CALCIUM CHANNEL SUBUNIT ALPHA-2/DELTA-RELATED | 28 | 483 | 2.8E-181 |
| 3 | g6376.t1 | PANTHER | PTHR10166:SF31 | RE14947P | 517 | 1260 | 2.8E-181 |
| 5 | g6376.t1 | PANTHER | PTHR10166 | VOLTAGE-DEPENDENT CALCIUM CHANNEL SUBUNIT ALPHA-2/DELTA-RELATED | 517 | 1260 | 2.8E-181 |
| 2 | g6376.t1 | Pfam | PF00092 | von Willebrand factor type A domain | 269 | 446 | 4.9E-15 |
| 1 | g6376.t1 | Pfam | PF08473 | Neuronal voltage-dependent calcium channel alpha 2acd | 753 | 999 | 1.5E-11 |
| 14 | g6376.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 31 | - |
| 15 | g6376.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 5 | - |
| 16 | g6376.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 6 | 13 | - |
| 18 | g6376.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 31 | - |
| 13 | g6376.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 32 | 1245 | - |
| 17 | g6376.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 1246 | 1263 | - |
| 12 | g6376.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1264 | 1264 | - |
| 23 | g6376.t1 | ProSiteProfiles | PS50234 | VWFA domain profile. | 269 | 455 | 18.16 |
| 20 | g6376.t1 | SMART | SM00327 | VWA_4 | 267 | 452 | 1.7E-15 |
| 7 | g6376.t1 | SUPERFAMILY | SSF53300 | vWA-like | 268 | 453 | 3.18E-26 |
| 9 | g6376.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 22 | - |
| 8 | g6376.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 22 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
