General information for g9939.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-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.t1 | TTS | g9939.t1 | 6110297 | 6110297 |
| chr_1 | g9939 | g9939.t1 | isoform | g9939.t1 | 6110799 | 6116281 |
| chr_1 | g9939 | g9939.t1 | exon | g9939.t1.exon1 | 6110799 | 6111425 |
| chr_1 | g9939 | g9939.t1 | cds | g9939.t1.CDS1 | 6110799 | 6111425 |
| chr_1 | g9939 | g9939.t1 | exon | g9939.t1.exon2 | 6111483 | 6111987 |
| chr_1 | g9939 | g9939.t1 | cds | g9939.t1.CDS2 | 6111483 | 6111987 |
| chr_1 | g9939 | g9939.t1 | exon | g9939.t1.exon3 | 6112060 | 6112167 |
| chr_1 | g9939 | g9939.t1 | cds | g9939.t1.CDS3 | 6112060 | 6112167 |
| chr_1 | g9939 | g9939.t1 | exon | g9939.t1.exon4 | 6112524 | 6112662 |
| chr_1 | g9939 | g9939.t1 | cds | g9939.t1.CDS4 | 6112524 | 6112662 |
| chr_1 | g9939 | g9939.t1 | exon | g9939.t1.exon5 | 6112719 | 6112861 |
| chr_1 | g9939 | g9939.t1 | cds | g9939.t1.CDS5 | 6112719 | 6112861 |
| chr_1 | g9939 | g9939.t1 | exon | g9939.t1.exon6 | 6112921 | 6113123 |
| chr_1 | g9939 | g9939.t1 | cds | g9939.t1.CDS6 | 6112921 | 6113123 |
| chr_1 | g9939 | g9939.t1 | exon | g9939.t1.exon7 | 6113181 | 6113252 |
| chr_1 | g9939 | g9939.t1 | cds | g9939.t1.CDS7 | 6113181 | 6113252 |
| chr_1 | g9939 | g9939.t1 | exon | g9939.t1.exon8 | 6113312 | 6113419 |
| chr_1 | g9939 | g9939.t1 | cds | g9939.t1.CDS8 | 6113312 | 6113419 |
| chr_1 | g9939 | g9939.t1 | exon | g9939.t1.exon9 | 6113479 | 6113553 |
| chr_1 | g9939 | g9939.t1 | cds | g9939.t1.CDS9 | 6113479 | 6113553 |
| chr_1 | g9939 | g9939.t1 | exon | g9939.t1.exon10 | 6113621 | 6113701 |
| chr_1 | g9939 | g9939.t1 | cds | g9939.t1.CDS10 | 6113621 | 6113701 |
| chr_1 | g9939 | g9939.t1 | exon | g9939.t1.exon11 | 6114502 | 6114720 |
| chr_1 | g9939 | g9939.t1 | cds | g9939.t1.CDS11 | 6114502 | 6114720 |
| chr_1 | g9939 | g9939.t1 | exon | g9939.t1.exon12 | 6114776 | 6116025 |
| chr_1 | g9939 | g9939.t1 | cds | g9939.t1.CDS12 | 6114776 | 6116025 |
| chr_1 | g9939 | g9939.t1 | exon | g9939.t1.exon13 | 6116084 | 6116130 |
| chr_1 | g9939 | g9939.t1 | cds | g9939.t1.CDS13 | 6116084 | 6116130 |
| chr_1 | g9939 | g9939.t1 | exon | g9939.t1.exon14 | 6116187 | 6116281 |
| chr_1 | g9939 | g9939.t1 | cds | g9939.t1.CDS14 | 6116187 | 6116281 |
| chr_1 | g9939 | g9939.t1 | TSS | g9939.t1 | 6116430 | 6116430 |
Sequences
>g9939.t1 Gene=g9939 Length=3672
ATGTGTAGATTAAATTTTAACTCTTTTGTTTTATTATATCTGATACAGTCGACATTTATT
TGTGCAGATGAGTCAAAAGTCATCAAATATCAAACTGCTCAACAGTGGGCAGAGAAATTT
GGAGTTGACCTATGGAGTTTAGGTGAATTTATAACTAGAAAAAATGATGTGGTGCAAAGT
TTTAAGCAGGCACAAATTGTGAATCGATCTGGTTCAGTTATAGTGGAAGAGATAGCAAAA
GAGATTAAAAAGATGATGGATGCTCGAATAAGTGCCATCAAACGTATAGTTGACACAGCT
CAAGAAGTAGGATCAATATCAGCGAGTAATGACGAAGTGGTAGAAAAAAATTTTACATAT
TACAACTCAAAGCAAATGATAGAACCGAGTGAAGTGTCACTAAATGAGTCCCCAATAACA
TCTGATGGTGAAGAAAATTTAGATAAATTAGAATTGCCCAAACCTGTGATTTATTTAACC
GAAAGCGAAAAGTTTAGCGATTATGTGAATTTATCATTAAGTTCAGTTCACGTCCCTACA
AATGTATATGATAGAGCAAAAAATGTCATTAAAGCCATCAAGTGGTCTGAAGTGCTTGAT
AATATTTTCGATAGCAATTACAAACGTGATCCATCACTTTTTTGGCAATTTTTTTGTAGT
TCAACAGGTTTCATGCGTCAATTTCCAGCAACTAAATGGAAATTTGATCCCGTTGATCTT
TACGATTGCCGAATCAGACATTGGTATATTGCTGCAGCAAACAGTCCAAAAGATATGATA
ATTTTGATTGACAATTCTGGTTCAATGACCGGTCAGAAAAAGGATATTGCGAGACATATT
GTTGAAAACATTCTCGACACACTTACACCCAATGATTTTGTCAACATTTTTACATTTTCT
GACTTGATTCGTGATGTTGTCGACTGTTTTGGTGATACACTTGTTCAAGCTAATTCTGCC
AATATTCGAGCGATGAAAGAATCTTTGCACAATATTGAAACTAATGAGCTTGCAAATTTT
TCTGCAGCACTAACGAGAGCTTTTGATACACTCTCTAATTATCGTCATACTGGTGCAAAT
TGTAATCAGGCCATTATGTTGATTTCTGATGGACTTCCAATATCAGTCGATGATGTATTT
GAAATTTATAATTGGGGCGAGAAGCCAAATATTCCTGTTCGTGTCTTTACATATTTGATT
GGTCGTGAAGTCCCAGATGTGAAAAATATAAAAGATATGGCATGCAATAATCGGGGATTT
TATGTGCATATAAATACATTGGCTGAAGTTCGTGAACAAGTTTTAGAATATATTCCTGTC
ATGGCTCGACCTCTTGTACTTAATCGAACTCATCATCCTATAGTATGGTCACATATCTAT
GCAGACGTTGTGGATACACAATTGACTGATTATGAATGGGAGTGTCGTGAGCGAGCAAGT
CAACGTGATCGCTTCATGGCTTATAGAAAAACACGTACTTTTCAAGGCTTACCAGACGAT
CCATCGACATTGGGTTATGATTTTATTGAAAATGATGAATCTGAATTGACCAAGAAATTT
AATTTTATGACAACAGTCGCTATTCCAATATATGATAAACGTGAAAATGCTACACGAATT
GCAAACCTTCTTGGTGTCGCTGGCACTGACATACCCATTAATGACATTAAACGCATGATG
CAGCCATTTTTGTTGGGAGTAGGAGCATACGCATTTATTGTGGATAACAATGGCCATATT
CTTACACATCCAGACTTTCGTCCAGTGTTTTACAAAGATATTTTAAAACCAGCTTACGAT
TCAGTTGACATGATTGATGTAGAGCTTGTCGATGACGACAGAGAGCCAAGAGATTATGAT
CCGATTCTTATTGAGTTGCGTGAACAAATCATCAATCAATCAACTGGAAGTAAAACACTT
TTACAGAAATTTCATTTTGATAAAATGCGAAGAGTTTCACGAACGAAACGTCATTATTAT
TGGACAGGAATAAATGATACACCATTTACGTTGGTTATAACACTTCCTGAGGAATATGGA
AAATATCGTTTGCAAACACGCAGTGAAGATGAAATTCATCGTGACACTGCGAAAGGCACA
AATGTGCTAAACTTTTTCAATGGTTCAAACTGGAAAATTCATCCAGACTGGCTTTATTGC
AAACATAATAATGAATCATTCTCATCACCTGAGGCAGAGCTTATTTATTTTCTTGAAAGA
ATGAGACAGCCAGGCTGGCGATGGCCATTGAATAGAAGTCCACCAACACCTGAACATATG
AGCAACGTTTACACTAATATTACGGCAGGAAGATTTCTATCAGATAAAGATTCGTATTAT
TGTGATAGAAACTTAATGCAATCATTAGTATACGATGCTAAAGTAACTGAATGGTTTAGT
CGAAATACTAGTTCAGGATTGAATGATAATGGGAGCGAGTTTAAGCAGCGTTTTGGCGTG
AGTGTGTCATTTTTAGCCACGCACAGTGGCCTCCTGAGATGGCAAGACTACAACCAAATG
GGTGAAGAAATACGACCAGAAAATGAGTTTAGTGAGACGAATAAGAGAGCAATTGATGAA
ACGTGGTATAAGAGAGCCGTTGAGCAACATTTTATTGAACCGAATAGTTTTGTTTATTCA
GTGCCGTTTGATGCTGCTAATAAAAACGATACTTTAGTAACTGCAACACATGCAGTTTTC
CATAGAGATAATACACGTTTTGCACCGGCAGCAGTTGTTGGTTTTCAATTTCAACTTACT
GCCATGCAAGGTCTCTTTAAGAACATCACCAATGGCTGCACTGAACCATCTTGCGTCTCA
TGCATGCATGATAGCTTTGAATGTTTTTTATTGGATGATAATGGCTATGTAATTGTTTCA
AATATCGATTTTGCTGATACTGGAAGATTTTTCGGAGAAGTTCGTGGCTCTGCAATGAGA
CGTATGATTGATGAAGGAATTTATCAAGCCGTTACAGTTTATGACTATCAAGCCATTTGC
TTTATTAATAAGGACTCATCAAGTTTAGCTAGCAAACTCATTACGCCATTTATATACATT
TGGAAACTTTTCAAGATTATTGCAAGTCATATGATTTGGTTATATGTTAGTCTCTTAGTT
GAAAATGTTAGTGGATATGGATCTTACTCATATGATGGAGCCAATTATGATAATGTCGAC
TATTATCCACCAGATCCTACAGAACGTGAACCAGTTTCAAAAACCAAAGAACAAGAATTT
GATAGAAGAGTTCTCATCAATCGAACACGACCAGAACGATGTGATAAGGTTTTCACACTT
TATCAAATGCTTCGACCAAAAGAAAAAGAAAAGTCACCATTTGATCTTCCTATGAGTCAA
TGCAACAGGCCATACATTGCTATACCAATACCGAATAGTAATATGCTCCTTTATGTAGGT
GATGCAATGTGTTTTAGACATGAAGAAAATATTCCACTATTAAATCAACCTGTTGAGAAG
GACTATAATGAAACGTTGCATTGTATGAAATCACGCAAGGCGCCACAATATAGGAGACAA
TTGAAACACTGCTTTAGTAACAATTCAAACGAAGCCCAAATAGAGATTTGCGGAAAAGCC
AATAAATTCCACTTAAGTTTGTACACTTTGATTTTAGCCGTATTTGTTGCGATTAAGAGT
TTCATATATTAG
>g9939.t1 Gene=g9939 Length=1223
MCRLNFNSFVLLYLIQSTFICADESKVIKYQTAQQWAEKFGVDLWSLGEFITRKNDVVQS
FKQAQIVNRSGSVIVEEIAKEIKKMMDARISAIKRIVDTAQEVGSISASNDEVVEKNFTY
YNSKQMIEPSEVSLNESPITSDGEENLDKLELPKPVIYLTESEKFSDYVNLSLSSVHVPT
NVYDRAKNVIKAIKWSEVLDNIFDSNYKRDPSLFWQFFCSSTGFMRQFPATKWKFDPVDL
YDCRIRHWYIAAANSPKDMIILIDNSGSMTGQKKDIARHIVENILDTLTPNDFVNIFTFS
DLIRDVVDCFGDTLVQANSANIRAMKESLHNIETNELANFSAALTRAFDTLSNYRHTGAN
CNQAIMLISDGLPISVDDVFEIYNWGEKPNIPVRVFTYLIGREVPDVKNIKDMACNNRGF
YVHINTLAEVREQVLEYIPVMARPLVLNRTHHPIVWSHIYADVVDTQLTDYEWECRERAS
QRDRFMAYRKTRTFQGLPDDPSTLGYDFIENDESELTKKFNFMTTVAIPIYDKRENATRI
ANLLGVAGTDIPINDIKRMMQPFLLGVGAYAFIVDNNGHILTHPDFRPVFYKDILKPAYD
SVDMIDVELVDDDREPRDYDPILIELREQIINQSTGSKTLLQKFHFDKMRRVSRTKRHYY
WTGINDTPFTLVITLPEEYGKYRLQTRSEDEIHRDTAKGTNVLNFFNGSNWKIHPDWLYC
KHNNESFSSPEAELIYFLERMRQPGWRWPLNRSPPTPEHMSNVYTNITAGRFLSDKDSYY
CDRNLMQSLVYDAKVTEWFSRNTSSGLNDNGSEFKQRFGVSVSFLATHSGLLRWQDYNQM
GEEIRPENEFSETNKRAIDETWYKRAVEQHFIEPNSFVYSVPFDAANKNDTLVTATHAVF
HRDNTRFAPAAVVGFQFQLTAMQGLFKNITNGCTEPSCVSCMHDSFECFLLDDNGYVIVS
NIDFADTGRFFGEVRGSAMRRMIDEGIYQAVTVYDYQAICFINKDSSSLASKLITPFIYI
WKLFKIIASHMIWLYVSLLVENVSGYGSYSYDGANYDNVDYYPPDPTEREPVSKTKEQEF
DRRVLINRTRPERCDKVFTLYQMLRPKEKEKSPFDLPMSQCNRPYIAIPIPNSNMLLYVG
DAMCFRHEENIPLLNQPVEKDYNETLHCMKSRKAPQYRRQLKHCFSNNSNEAQIEICGKA
NKFHLSLYTLILAVFVAIKSFIY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g9939.t1 | CDD | cd01463 | vWA_VGCC_like | 244 | 428 | 4.61935E-77 |
| 20 | g9939.t1 | CDD | cd18774 | PDC2_HK_sensor | 555 | 677 | 5.39321E-7 |
| 10 | g9939.t1 | Gene3D | G3DSA:3.40.50.410 | - | 257 | 438 | 9.2E-26 |
| 11 | g9939.t1 | Gene3D | G3DSA:3.30.450.20 | - | 532 | 678 | 4.8E-20 |
| 4 | g9939.t1 | PANTHER | PTHR10166:SF31 | RE14947P | 9 | 473 | 4.0E-299 |
| 6 | g9939.t1 | PANTHER | PTHR10166 | VOLTAGE-DEPENDENT CALCIUM CHANNEL SUBUNIT ALPHA-2/DELTA-RELATED | 9 | 473 | 4.0E-299 |
| 5 | g9939.t1 | PANTHER | PTHR10166:SF31 | RE14947P | 507 | 1216 | 4.0E-299 |
| 7 | g9939.t1 | PANTHER | PTHR10166 | VOLTAGE-DEPENDENT CALCIUM CHANNEL SUBUNIT ALPHA-2/DELTA-RELATED | 507 | 1216 | 4.0E-299 |
| 2 | g9939.t1 | Pfam | PF08399 | VWA N-terminal | 108 | 233 | 1.3E-34 |
| 3 | g9939.t1 | Pfam | PF13519 | von Willebrand factor type A domain | 259 | 371 | 2.2E-13 |
| 1 | g9939.t1 | Pfam | PF08473 | Neuronal voltage-dependent calcium channel alpha 2acd | 777 | 1011 | 1.9E-19 |
| 14 | g9939.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 22 | - |
| 15 | g9939.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 7 | - |
| 16 | g9939.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 8 | 15 | - |
| 18 | g9939.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 22 | - |
| 13 | g9939.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 23 | 1202 | - |
| 17 | g9939.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 1203 | 1222 | - |
| 12 | g9939.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1223 | 1223 | - |
| 23 | g9939.t1 | ProSiteProfiles | PS50234 | VWFA domain profile. | 258 | 445 | 15.976 |
| 22 | g9939.t1 | SMART | SM00327 | VWA_4 | 256 | 435 | 2.2E-16 |
| 8 | g9939.t1 | SUPERFAMILY | SSF53300 | vWA-like | 256 | 437 | 2.08E-23 |
| 9 | g9939.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 22 | - |
| 21 | g9939.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 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 transcript has been annotated with K04860 (voltage-dependent calcium channel alpha-2/delta-3)
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.
