General information for g9939.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t3 | isoform | g9939.t3 | 6114776 | 6116025 |
| chr_1 | g9939 | g9939.t3 | exon | g9939.t3.exon1 | 6114776 | 6116025 |
| chr_1 | g9939 | g9939.t3 | cds | g9939.t3.CDS1 | 6114776 | 6115915 |
| chr_1 | g9939 | g9939.t3 | TSS | g9939.t3 | 6116430 | 6116430 |
| chr_1 | g9939 | g9939.t3 | TTS | g9939.t3 | NA | NA |
Sequences
>g9939.t3 Gene=g9939 Length=1250
GTGAATTTATAACTAGAAAAAATGATGTGGTGCAAAGTTTTAAGCAGGCACAAATTGTGA
ATCGATCTGGTTCAGTTATAGTGGAAGAGATAGCAAAAGAGATTAAAAAGATGATGGATG
CTCGAATAAGTGCCATCAAACGTATAGTTGACACAGCTCAAGAAGTAGGATCAATATCAG
CGAGTAATGACGAAGTGGTAGAAAAAAATTTTACATATTACAACTCAAAGCAAATGATAG
AACCGAGTGAAGTGTCACTAAATGAGTCCCCAATAACATCTGATGGTGAAGAAAATTTAG
ATAAATTAGAATTGCCCAAACCTGTGATTTATTTAACCGAAAGCGAAAAGTTTAGCGATT
ATGTGAATTTATCATTAAGTTCAGTTCACGTCCCTACAAATGTATATGATAGAGCAAAAA
ATGTCATTAAAGCCATCAAGTGGTCTGAAGTGCTTGATAATATTTTCGATAGCAATTACA
AACGTGATCCATCACTTTTTTGGCAATTTTTTTGTAGTTCAACAGGTTTCATGCGTCAAT
TTCCAGCAACTAAATGGAAATTTGATCCCGTTGATCTTTACGATTGCCGAATCAGACATT
GGTATATTGCTGCAGCAAACAGTCCAAAAGATATGATAATTTTGATTGACAATTCTGGTT
CAATGACCGGTCAGAAAAAGGATATTGCGAGACATATTGTTGAAAACATTCTCGACACAC
TTACACCCAATGATTTTGTCAACATTTTTACATTTTCTGACTTGATTCGTGATGTTGTCG
ACTGTTTTGGTGATACACTTGTTCAAGCTAATTCTGCCAATATTCGAGCGATGAAAGAAT
CTTTGCACAATATTGAAACTAATGAGCTTGCAAATTTTTCTGCAGCACTAACGAGAGCTT
TTGATACACTCTCTAATTATCGTCATACTGGTGCAAATTGTAATCAGGCCATTATGTTGA
TTTCTGATGGACTTCCAATATCAGTCGATGATGTATTTGAAATTTATAATTGGGGCGAGA
AGCCAAATATTCCTGTTCGTGTCTTTACATATTTGATTGGTCGTGAAGTCCCAGATGTGA
AAAATATAAAAGATATGGCATGCAATAATCGGGGATTTTATGTGCATATAAATACATTGG
CTGAAGTTCGTGAACAAGTTTTAGAATATATTCCTGTCATGGCTCGACCTCTTGTACTTA
ATCGAACTCATCATCCTATAGTATGGTCACATATCTATGCAGACGTTGTG
>g9939.t3 Gene=g9939 Length=380
MMDARISAIKRIVDTAQEVGSISASNDEVVEKNFTYYNSKQMIEPSEVSLNESPITSDGE
ENLDKLELPKPVIYLTESEKFSDYVNLSLSSVHVPTNVYDRAKNVIKAIKWSEVLDNIFD
SNYKRDPSLFWQFFCSSTGFMRQFPATKWKFDPVDLYDCRIRHWYIAAANSPKDMIILID
NSGSMTGQKKDIARHIVENILDTLTPNDFVNIFTFSDLIRDVVDCFGDTLVQANSANIRA
MKESLHNIETNELANFSAALTRAFDTLSNYRHTGANCNQAIMLISDGLPISVDDVFEIYN
WGEKPNIPVRVFTYLIGREVPDVKNIKDMACNNRGFYVHINTLAEVREQVLEYIPVMARP
LVLNRTHHPIVWSHIYADVV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g9939.t3 | Gene3D | G3DSA:3.40.50.410 | - | 173 | 354 | 0.000 |
| 3 | g9939.t3 | PANTHER | PTHR10166:SF31 | RE14947P | 1 | 379 | 0.000 |
| 4 | g9939.t3 | PANTHER | PTHR10166 | VOLTAGE-DEPENDENT CALCIUM CHANNEL SUBUNIT ALPHA-2/DELTA-RELATED | 1 | 379 | 0.000 |
| 1 | g9939.t3 | Pfam | PF08399 | VWA N-terminal | 24 | 149 | 0.000 |
| 2 | g9939.t3 | Pfam | PF13519 | von Willebrand factor type A domain | 175 | 287 | 0.000 |
| 8 | g9939.t3 | ProSiteProfiles | PS50234 | VWFA domain profile. | 174 | 361 | 15.976 |
| 6 | g9939.t3 | SMART | SM00327 | VWA_4 | 172 | 351 | 0.000 |
| 5 | g9939.t3 | SUPERFAMILY | SSF53300 | vWA-like | 172 | 353 | 0.000 |
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.
