General information for g9939.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Voltage-dependent calcium channel subunit alpha-2/delta-3.
Parent gene
- The parent gene g9939 is located on chr_1: 6114776..6116281 (- 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 | g9939 | g9939.t2 | isoform | g9939.t2 | 6111152 | 6111987 |
| chr_1 | g9939 | g9939.t2 | exon | g9939.t2.exon1 | 6111152 | 6111425 |
| chr_1 | g9939 | g9939.t2 | cds | g9939.t2.CDS1 | 6111153 | 6111425 |
| chr_1 | g9939 | g9939.t2 | TTS | g9939.t2 | 6111154 | 6111154 |
| chr_1 | g9939 | g9939.t2 | exon | g9939.t2.exon2 | 6111483 | 6111987 |
| chr_1 | g9939 | g9939.t2 | cds | g9939.t2.CDS2 | 6111483 | 6111764 |
| chr_1 | g9939 | g9939.t2 | TSS | g9939.t2 | NA | NA |
Sequences
>g9939.t2 Gene=g9939 Length=779
AAATGAGTTTAGTGAGACGAATAAGAGAGCAATTGATGAAACGTGGTATAAGAGAGCCGT
TGAGCAACATTTTATTGAACCGAATAGTTTTGTTTATTCAGTGCCGTTTGATGCTGCTAA
TAAAAACGATACTTTAGTAACTGCAACACATGCAGTTTTCCATAGAGATAATACACGTTT
TGCACCGGCAGCAGTTGTTGGTTTTCAATTTCAACTTACTGCCATGCAAGGTCTCTTTAA
GAACATCACCAATGGCTGCACTGAACCATCTTGCGTCTCATGCATGCATGATAGCTTTGA
ATGTTTTTTATTGGATGATAATGGCTATGTAATTGTTTCAAATATCGATTTTGCTGATAC
TGGAAGATTTTTCGGAGAAGTTCGTGGCTCTGCAATGAGACGTATGATTGATGAAGGAAT
TTATCAAGCCGTTACAGTTTATGACTATCAAGCCATTTGCTTTATTAATAAGGACTCATC
AAGTTTAGCTAGCAAACTCATTACGCCATTTATATACATTTGGAAACTTTTCAAGATTAT
TGCAAGTCATATGATTTGGTTATATGTTAGTCTCTTAGTTGAAAATGTTAGTGGATATGG
ATCTTACTCATATGATGGAGCCAATTATGATAATGTCGACTATTATCCACCAGATCCTAC
AGAACGTGAACCAGTTTCAAAAACCAAAGAACAAGAATTTGATAGAAGAGTTCTCATCAA
TCGAACACGACCAGAACGATGTGATAAGGTTTTCACACTTTATCAAATGCTTCGACCAA
>g9939.t2 Gene=g9939 Length=185
MQGLFKNITNGCTEPSCVSCMHDSFECFLLDDNGYVIVSNIDFADTGRFFGEVRGSAMRR
MIDEGIYQAVTVYDYQAICFINKDSSSLASKLITPFIYIWKLFKIIASHMIWLYVSLLVE
NVSGYGSYSYDGANYDNVDYYPPDPTEREPVSKTKEQEFDRRVLINRTRPERCDKVFTLY
QMLRP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g9939.t2 | PANTHER | PTHR10166:SF31 | RE14947P | 4 | 183 | 0 |
| 3 | g9939.t2 | PANTHER | PTHR10166 | VOLTAGE-DEPENDENT CALCIUM CHANNEL SUBUNIT ALPHA-2/DELTA-RELATED | 4 | 183 | 0 |
| 1 | g9939.t2 | Pfam | PF08473 | Neuronal voltage-dependent calcium channel alpha 2acd | 9 | 90 | 0 |
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.
