General information for g11943.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 g11943 is located on chr_1: 19540809..19545520 (+ 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 | g11943 | g11943.t1 | isoform | g11943.t1 | 19540809 | 19545520 |
| chr_1 | g11943 | g11943.t1 | exon | g11943.t1.exon1 | 19540809 | 19540964 |
| chr_1 | g11943 | g11943.t1 | cds | g11943.t1.CDS1 | 19540809 | 19540964 |
| chr_1 | g11943 | g11943.t1 | exon | g11943.t1.exon2 | 19541025 | 19541231 |
| chr_1 | g11943 | g11943.t1 | cds | g11943.t1.CDS2 | 19541025 | 19541231 |
| chr_1 | g11943 | g11943.t1 | exon | g11943.t1.exon3 | 19541299 | 19542877 |
| chr_1 | g11943 | g11943.t1 | cds | g11943.t1.CDS3 | 19541299 | 19542877 |
| chr_1 | g11943 | g11943.t1 | exon | g11943.t1.exon4 | 19542938 | 19543219 |
| chr_1 | g11943 | g11943.t1 | cds | g11943.t1.CDS4 | 19542938 | 19543219 |
| chr_1 | g11943 | g11943.t1 | exon | g11943.t1.exon5 | 19543301 | 19543809 |
| chr_1 | g11943 | g11943.t1 | cds | g11943.t1.CDS5 | 19543301 | 19543809 |
| chr_1 | g11943 | g11943.t1 | exon | g11943.t1.exon6 | 19543872 | 19544135 |
| chr_1 | g11943 | g11943.t1 | cds | g11943.t1.CDS6 | 19543872 | 19544135 |
| chr_1 | g11943 | g11943.t1 | exon | g11943.t1.exon7 | 19544618 | 19544967 |
| chr_1 | g11943 | g11943.t1 | cds | g11943.t1.CDS7 | 19544618 | 19544967 |
| chr_1 | g11943 | g11943.t1 | exon | g11943.t1.exon8 | 19545035 | 19545230 |
| chr_1 | g11943 | g11943.t1 | cds | g11943.t1.CDS8 | 19545035 | 19545230 |
| chr_1 | g11943 | g11943.t1 | exon | g11943.t1.exon9 | 19545401 | 19545520 |
| chr_1 | g11943 | g11943.t1 | cds | g11943.t1.CDS9 | 19545401 | 19545520 |
| chr_1 | g11943 | g11943.t1 | TSS | g11943.t1 | NA | NA |
| chr_1 | g11943 | g11943.t1 | TTS | g11943.t1 | NA | NA |
Sequences
>g11943.t1 Gene=g11943 Length=3663
ATGTCATATTGTTTATTGATAAAAAAAGAAAATTTTGAAATAAACATAGAAATTACTAAT
AAAAATTCATTCAGTATTGACAAGTGGGCAGAGCGATTTGGTAATGAACTTTGGGATTTA
GCGCAACGCATGACAAAGTCAAATGAGATCAAAGCGCGTTATAAAACATTAAATGCAAAA
GTCCAGGAAAAGAATGGAACACTATTGATTGCTGATATTGTTGCCTCAATAGGACGTATG
TTGAATAGAAAAATGGACGCAGTACAATGCATTGTTAACAAGTCAGAATCGGCATCAGAA
GAATTTCACCGCAATGGCGTAATAGAAGAGGATTTTCAATATTATTCGAGCAAATATTCA
TTGGTGAATCTCTATAACGTGACTGATGAATTTATGAATTTAACTAACCGTAAATATACA
GATTTTGAAACAGAAAGTGTAGCTGATGGAAGATTTTTGAATATGACACTTGATCGAGAT
TCCCATTTCTTTGATTTGTACGTCAATACTAGCTATAGTTCAGTTCATGTGCCAACAAAT
GTTTACGATAAAGGACCTGAAGCTGCTGAATTTATTCAATGGTCTGAAGCACTCAATGAA
GTTTTTGATCAAAATTATAAATCAGATCCTGCTCTATCATGGCAATATTTTGGATCGAAT
CTTGGTGTAATGCGGCATTTTCCTGCTATGACTTGGGTACGAAATAGAACTGACACTTAT
AATTGTCGGAAACGTTCATGGTATATTGAGACAGCAACATGTTCAAAAGATGTTGTTATT
CTGCTAGATAATTCTGGCTCTATGACTGGATATAGAAGCTATATTGCAGAATATACAATT
CGCAGTTTGCTTGACACGTTTTCCAACAGCGATTTTATCAACATTTACAAATATTCAAAA
CACACCGAAGAATTAATTCCATGCTTTGCTGATAGTCTTGTACAAGCCACACCCGAGAAT
ATTGCTGTATTTAATAAGGCTGTGGCAGAATTACAACCTGATGGTTATGCCAACGTTATG
CTAGCATTAGAAAAAGCTTTTCAACTTTTAGCCAAATACCGTGATATTCGCAAATGTAAT
GAGTCCATCACTGGGTGCAATCAAGCAATTATGTTAGTGACTGATGGTGTGCCTGGTAAT
GCAACTGAAATTTTTCAAAAATACAATTGGTTTGCTAATGACACAAAAGCTTATCCTGTG
CGAATATTTACATATTTGCTCGGGAAAGAAGTGACTAAAGTAAAGGAAATTCAACTTTAT
GCATGTTTAAATCGTGGATTTTATTCTCATATTCAATCACTTGATGAAGTTGCTGAAGAA
GTTCTTAAATATGTTAATGTCATTGCTGCACCTTTAGTGCTACAAAAAGAGGAACATCCT
CCTACTTGGACTCATGCATACATTGATGAAACATTTGAAACTGAATTTGATGAGAAACGA
CTGAGTATAGAGCACAAATCTCGAATGATGATTGCAGTTGGTTCACCAGCTTACAATTTA
TCTTCATATGGCGAGGCAAATTCAACTGGGCGACCAACATTACTTGGAGTTGCAGGTACT
GATATTCCACTCGATGATATCAATCGTCTTGCATTACCATACAAACTTGGCGTCAATGGA
TATGCATTTATCGTCTCAAACAATGGCTATGTTCTTCTCCATCCAGACTTGCGACCGTTA
GATAAAAATCACGATGATGAAATCAAGAAAAATTATAATAGCATTGATTTGACTGAAGTT
GAACAATTTGGTGATGATATATTGCCTAGATATCCCAGTGAAAAACTTCAAGAATTGAGA
AAGGCAATGGTTGATCATAAATTTGGAAAAATTATAGGAGTTCCTGTGAAATTTCATTAT
GATCAAATGAGAAGAGTAGAGCATAGCATGCAAGACTTTTATTTTGCTCCAATTCCACAT
ACTCCTTTTTCTTTAGGAATTGCACTTCCTCATTCATATGGAAATACATGGATCAAAGTT
GGTGATGAAATCCAACGCAATACGTATACGAAAGTAAATATTTCTGATTTTTTTGTTGGT
GAAAATTGGAAAATTCATCCTGATTGGGTTTATTGTAAATATCATTATTTTGAAGACCAT
GAGTTTGCATCACCAGAAGCAGAATTGCGTCATTTTTTAAAGAAAATTGTTGAGCCAAAT
TGGAAATGGTCACAACAGTATGAACCTGATCCAGAAGCTGACAAAGTGAAAGATTCAAAA
GAGGTAAATTGCGGTCGAAAGTCGTTGGAAAAAGATGACTACTATTGCAATAAAGAACTC
GTTGAGTTGTTAGTGTTTGATGCAAAAGTGACAAACGACAGCTATCAATCATGGACTTTT
AAAAACGACGCAGAGCGAGAGGTTATTGAACGTTATAATGCAACGGTGCGCTTCGTTTCG
ACAATGAGTGGCTTGACACGATGGCAATTTATCTTTGGTGAGGTGGAGGTCGATTATGAT
AAGGAATTTGGTGACATTTATTCAACATCGCTTAATGAACCATGGTATAAGAGTGCTGTA
CTCCAACATAATATCAGCAAGGAAAGCTTTGTTTATTCAGTGCCACACTATGATGATGAA
AAGATTGAAGGTGATAGTTATCTCAAAGTAACAGCTTCCATGGCTATTTTTCCTCGTGAT
GGTGGAAAAGAAGCACCATCAGCTGTTGTTGGTTTTCAATTTTCACATCAACCAATGTAC
GATAGATTTATGGAAATCACTTCAACTGTCAATTGTGATGATTGCATCAAATCTTGTGGT
TCAGATGAACAAGATTGCTATGTGATTGATAGCAATGGTTACATTATCATTTCTGAAGCA
AATACTAACAACACAGGCCGTTTCTTTGGTGAAATAGAAGGTGCTATTATGGAAGTAATG
GTTGAAAATAACATTTTTTCAAGAATTACGGTGTACGATTATCAGGGCTTATGTAAAAAC
GTGACACGAGGAAACGAGACAAGTGATGAAGAGAGTCATGCAAATGGACTGATAACGCCA
TTCAAATTTTTACTACTCGGACTGGAATGGATTCTTACTGAAATGATAATTGAACTGTCA
CGGATTCGAATATGGGCAGCGAGTGTTCCCTTGTCTGATTATGAGGAACATGATTATCAA
GACGAACATACAACTCCAAAGCCAAAAACCAAACCAATTCATCGTGGTAAAGGTGCAGAG
GGTTATGAAGCAGAAGAATATTTCCGTGCATTGAACGAGGAAAAGGCAAACAAAATAACA
ACTACTTATTATCCATGTGACAAGCGAGCTGATTTGTATGTAATGAACAAAACTTTCATA
AAAGAAGAACATGCAAAAAGTCCGAGATCGAATATCATTGAACATCGAGACTTTTTTGTG
AGTCCAATTCGATATTCAAATTTGATGTTGATTGTTATAAATCAAATGACCGGTAGTAGT
GCATCAATTGAACTCTCAACAAAGTTGAAAGAAGTCAATCCATGGTGGACATACAATCAG
TCGCATCCTTGTTATAAAAACTACATGAATAATTTACCACGTCGTCGTTTGGATGAATGC
TTTACTGAACACCCAGAGGAAGCGGAAATGGCATATTGTGGCTCCGCATCGCGCATTAAA
TCTACATTGTTGTTACTTTCACTGCTGTTGTCGCCAATGTTTTATCTCATGAGATTCAAA
TGA
>g11943.t1 Gene=g11943 Length=1220
MSYCLLIKKENFEINIEITNKNSFSIDKWAERFGNELWDLAQRMTKSNEIKARYKTLNAK
VQEKNGTLLIADIVASIGRMLNRKMDAVQCIVNKSESASEEFHRNGVIEEDFQYYSSKYS
LVNLYNVTDEFMNLTNRKYTDFETESVADGRFLNMTLDRDSHFFDLYVNTSYSSVHVPTN
VYDKGPEAAEFIQWSEALNEVFDQNYKSDPALSWQYFGSNLGVMRHFPAMTWVRNRTDTY
NCRKRSWYIETATCSKDVVILLDNSGSMTGYRSYIAEYTIRSLLDTFSNSDFINIYKYSK
HTEELIPCFADSLVQATPENIAVFNKAVAELQPDGYANVMLALEKAFQLLAKYRDIRKCN
ESITGCNQAIMLVTDGVPGNATEIFQKYNWFANDTKAYPVRIFTYLLGKEVTKVKEIQLY
ACLNRGFYSHIQSLDEVAEEVLKYVNVIAAPLVLQKEEHPPTWTHAYIDETFETEFDEKR
LSIEHKSRMMIAVGSPAYNLSSYGEANSTGRPTLLGVAGTDIPLDDINRLALPYKLGVNG
YAFIVSNNGYVLLHPDLRPLDKNHDDEIKKNYNSIDLTEVEQFGDDILPRYPSEKLQELR
KAMVDHKFGKIIGVPVKFHYDQMRRVEHSMQDFYFAPIPHTPFSLGIALPHSYGNTWIKV
GDEIQRNTYTKVNISDFFVGENWKIHPDWVYCKYHYFEDHEFASPEAELRHFLKKIVEPN
WKWSQQYEPDPEADKVKDSKEVNCGRKSLEKDDYYCNKELVELLVFDAKVTNDSYQSWTF
KNDAEREVIERYNATVRFVSTMSGLTRWQFIFGEVEVDYDKEFGDIYSTSLNEPWYKSAV
LQHNISKESFVYSVPHYDDEKIEGDSYLKVTASMAIFPRDGGKEAPSAVVGFQFSHQPMY
DRFMEITSTVNCDDCIKSCGSDEQDCYVIDSNGYIIISEANTNNTGRFFGEIEGAIMEVM
VENNIFSRITVYDYQGLCKNVTRGNETSDEESHANGLITPFKFLLLGLEWILTEMIIELS
RIRIWAASVPLSDYEEHDYQDEHTTPKPKTKPIHRGKGAEGYEAEEYFRALNEEKANKIT
TTYYPCDKRADLYVMNKTFIKEEHAKSPRSNIIEHRDFFVSPIRYSNLMLIVINQMTGSS
ASIELSTKLKEVNPWWTYNQSHPCYKNYMNNLPRRRLDECFTEHPEEAEMAYCGSASRIK
STLLLLSLLLSPMFYLMRFK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g11943.t1 | CDD | cd01463 | vWA_VGCC_like | 243 | 435 | 2.08634E-84 |
| 7 | g11943.t1 | Gene3D | G3DSA:3.40.50.410 | - | 255 | 446 | 7.8E-24 |
| 8 | g11943.t1 | Gene3D | G3DSA:3.30.450.20 | - | 508 | 655 | 4.1E-22 |
| 14 | g11943.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1037 | 1056 | - |
| 4 | g11943.t1 | PANTHER | PTHR10166:SF31 | RE14947P | 15 | 1210 | 0.0 |
| 5 | g11943.t1 | PANTHER | PTHR10166 | VOLTAGE-DEPENDENT CALCIUM CHANNEL SUBUNIT ALPHA-2/DELTA-RELATED | 15 | 1210 | 0.0 |
| 2 | g11943.t1 | Pfam | PF08399 | VWA N-terminal | 96 | 232 | 7.1E-36 |
| 3 | g11943.t1 | Pfam | PF13519 | von Willebrand factor type A domain | 258 | 376 | 6.9E-10 |
| 1 | g11943.t1 | Pfam | PF08473 | Neuronal voltage-dependent calcium channel alpha 2acd | 752 | 1012 | 2.1E-22 |
| 10 | g11943.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 1198 | - |
| 11 | g11943.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 1199 | 1217 | - |
| 9 | g11943.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1218 | 1220 | - |
| 15 | g11943.t1 | ProSiteProfiles | PS50234 | VWFA domain profile. | 257 | 448 | 14.092 |
| 13 | g11943.t1 | SMART | SM00327 | VWA_4 | 255 | 449 | 3.6E-8 |
| 6 | g11943.t1 | SUPERFAMILY | SSF53300 | vWA-like | 254 | 443 | 2.86E-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 K04861 (voltage-dependent calcium channel alpha-2/delta-4)
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. There were no conditions that were differentially expressed