General information for g12938.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Voltage-dependent L-type calcium channel subunit beta-2.
Parent gene
- The parent gene g12938 is located on chr_1: 27014728..27022494 (- 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 | g12938 | g12938.t1 | isoform | g12938.t1 | 27014728 | 27022494 |
| chr_1 | g12938 | g12938.t1 | exon | g12938.t1.exon1 | 27014728 | 27015227 |
| chr_1 | g12938 | g12938.t1 | cds | g12938.t1.CDS1 | 27014728 | 27015227 |
| chr_1 | g12938 | g12938.t1 | exon | g12938.t1.exon2 | 27016532 | 27016628 |
| chr_1 | g12938 | g12938.t1 | cds | g12938.t1.CDS2 | 27016532 | 27016628 |
| chr_1 | g12938 | g12938.t1 | exon | g12938.t1.exon3 | 27016691 | 27016858 |
| chr_1 | g12938 | g12938.t1 | cds | g12938.t1.CDS3 | 27016691 | 27016858 |
| chr_1 | g12938 | g12938.t1 | exon | g12938.t1.exon4 | 27017355 | 27017523 |
| chr_1 | g12938 | g12938.t1 | cds | g12938.t1.CDS4 | 27017355 | 27017523 |
| chr_1 | g12938 | g12938.t1 | exon | g12938.t1.exon5 | 27017586 | 27017681 |
| chr_1 | g12938 | g12938.t1 | cds | g12938.t1.CDS5 | 27017586 | 27017681 |
| chr_1 | g12938 | g12938.t1 | exon | g12938.t1.exon6 | 27017760 | 27018451 |
| chr_1 | g12938 | g12938.t1 | cds | g12938.t1.CDS6 | 27017760 | 27018451 |
| chr_1 | g12938 | g12938.t1 | exon | g12938.t1.exon7 | 27022423 | 27022494 |
| chr_1 | g12938 | g12938.t1 | cds | g12938.t1.CDS7 | 27022423 | 27022494 |
| chr_1 | g12938 | g12938.t1 | TSS | g12938.t1 | 27022856 | 27022856 |
| chr_1 | g12938 | g12938.t1 | TTS | g12938.t1 | NA | NA |
Sequences
>g12938.t1 Gene=g12938 Length=1794
ATGAACAGAAGACATCACCATCATCATCATCGTTCGACATATAAGCCTCCATTTCGGCTG
AAAAACAGACGGGGTTCTGCTGATTCCAATTATTCACAACCATCTTCCGATCTGTCGCTG
GACGAGGAAAAAGAGTCTCTTCGGAGAGAAAAAGAGCGTCAAGCTCTTGGTCAGCTGGAA
AAGGCGAGAACAAAGCCAGTTGCATTTGCCGTTCGTACGAATGTTTCATACGATGGTAGC
GTCGATGATGACTCGCCGGTACACGGCAGTGCGGTGTCGTTTGAAATTGGAGACTTTTTA
CATATTAAGGAAAAATATGACAATAACTGGTGGATCGGAAGACTCGTGAAAGAGGGGTGT
GAAGTCGGCTTCATCCCGAGTCCGGTTAAGCTTGAACACATTCGCATTCAGGCGACTGCT
GTGCGATCGTCAAAGCTTTATGCATCCAAAGCCTCGTCGAGCGGGAATTTGGGTACGGCG
ACCGCCCCCGGTGCAGAAGCATCGAGAGGCAGTACTCCTCCAACTCCCGGCGACGAGAGT
GACTCGATGGGTGCATCACGCCATCCAAAGACACCCCTCGCTACACCACCTACAAAAGAG
AAGCGAAAACCTTTCTTTAAGAAGCAAGAAACGTCCTCGCCGTATGATGTCGTTCCATCA
ATGCGTCCAGTCGTGCTGGTGGGACCGAGTCTTAAAGGTTACGAAGTGACCGATATGATG
CAAAAAGCTTTATTTGATTTCCTCAAACATCGGTTTGAATCAAGGATAATTATAACTCGT
GTTCAAGCAGATATATCATTAGCTAAACGATCCCTGATGAATAATCCTTCAAAGCGAGCA
ATCATGGAACGATCAAATAGTCGTTCCACATGTCTGGCTGAAGTGCAAGCTGAAATTGAA
AGAATATTCGAATTGGCTCGAACGCTTCAGTTAGTAGTTCTTGACTGTGATACTATCAAC
CATCCGTCACAGTTGGCAAAGACATCATTAGCACCAACTATAGTTTATTTGAAAATAGCT
AGCAGTAAAGTTTTGCAAAGATTAATCAAATCACGTGGTAAAGCTCAAGCGAAAAATTTA
TCAGTGCAAATGGTGGCAGCAGAAAAATTAAGTCAATGTCCACCCGAGATGTTTGACGTT
ATTTTAGATGAAAATCAACTTGAAGAGGCGTGTAATCATTTAGCGGAATATTTAGAAACT
TATTGGAGAGCAACACATCCGCCTGTTAGATCAACACCAATGCAAAGACAATTGCCGCCA
GAAACTTCAACACCGGTTGATCGTACTCCTCCTGGATCATCAACCTATCATAATCAACAA
AATAGAAGATCAACACGTTATCCAGATCGCGAAAAAGACAGATTAGATCGATTGGAACGC
GAGAGAGAGAGAATACATGCACGTGAACGTGACATGATGAGCTACAATTTGAATGAAGAT
GAGATGATAAACGATAGACATTATAATCGAGATAGAGAGCGAGAACGAGAAAGAGATCGA
GATATGGGTGGCGCGAGTAGTGGCAGTGAATATCCAATGCACAGAGAAGAACGGCGTGTT
ATAGATAGAGACTTGCGTGAACGTGATCCGCGTGATGTTCGAATGGATGCGCGTGATAGA
CGCGAACATTATGTAGGCAGTAATAGTAGACACTTAATGAATAATAGTTACGATAACGAT
AATGTGGATCTAATACGCGAAAAAGAAAAAGAGCGCTATGCACATCGTCGTGATGAATAT
AGCTATAGTCCTCATAGAGGTAACAGAAGAGTCTTAAATATGAACGCCATGTAG
>g12938.t1 Gene=g12938 Length=597
MNRRHHHHHHRSTYKPPFRLKNRRGSADSNYSQPSSDLSLDEEKESLRREKERQALGQLE
KARTKPVAFAVRTNVSYDGSVDDDSPVHGSAVSFEIGDFLHIKEKYDNNWWIGRLVKEGC
EVGFIPSPVKLEHIRIQATAVRSSKLYASKASSSGNLGTATAPGAEASRGSTPPTPGDES
DSMGASRHPKTPLATPPTKEKRKPFFKKQETSSPYDVVPSMRPVVLVGPSLKGYEVTDMM
QKALFDFLKHRFESRIIITRVQADISLAKRSLMNNPSKRAIMERSNSRSTCLAEVQAEIE
RIFELARTLQLVVLDCDTINHPSQLAKTSLAPTIVYLKIASSKVLQRLIKSRGKAQAKNL
SVQMVAAEKLSQCPPEMFDVILDENQLEEACNHLAEYLETYWRATHPPVRSTPMQRQLPP
ETSTPVDRTPPGSSTYHNQQNRRSTRYPDREKDRLDRLERERERIHARERDMMSYNLNED
EMINDRHYNRDRERERERDRDMGGASSGSEYPMHREERRVIDRDLRERDPRDVRMDARDR
REHYVGSNSRHLMNNSYDNDNVDLIREKEKERYAHRRDEYSYSPHRGNRRVLNMNAM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g12938.t1 | CDD | cd11863 | SH3_CACNB | 69 | 130 | 8.03647E-41 |
| 17 | g12938.t1 | Gene3D | G3DSA:2.30.30.40 | SH3 Domains | 32 | 149 | 2.3E-46 |
| 16 | g12938.t1 | Gene3D | G3DSA:3.40.50.300 | - | 197 | 418 | 1.2E-110 |
| 22 | g12938.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 54 | - |
| 25 | g12938.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 18 | - |
| 29 | g12938.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 38 | 54 | - |
| 21 | g12938.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 152 | 179 | - |
| 23 | g12938.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 152 | 211 | - |
| 28 | g12938.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 194 | 209 | - |
| 26 | g12938.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 408 | 460 | - |
| 27 | g12938.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 410 | 442 | - |
| 31 | g12938.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 443 | 460 | - |
| 24 | g12938.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 476 | 504 | - |
| 30 | g12938.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 476 | 523 | - |
| 3 | g12938.t1 | PANTHER | PTHR11824 | VOLTAGE-DEPENDENT CALCIUM CHANNEL BETA SUBUNIT | 21 | 497 | 1.9E-227 |
| 4 | g12938.t1 | PANTHER | PTHR11824:SF5 | CA2+-CHANNEL-PROTEIN-BETA-SUBUNIT, ISOFORM L | 21 | 497 | 1.9E-227 |
| 6 | g12938.t1 | PRINTS | PR01626 | L-type calcium channel beta subunit signature | 214 | 228 | 2.3E-73 |
| 9 | g12938.t1 | PRINTS | PR01626 | L-type calcium channel beta subunit signature | 229 | 243 | 2.3E-73 |
| 12 | g12938.t1 | PRINTS | PR01626 | L-type calcium channel beta subunit signature | 244 | 259 | 2.3E-73 |
| 8 | g12938.t1 | PRINTS | PR01626 | L-type calcium channel beta subunit signature | 260 | 274 | 2.3E-73 |
| 13 | g12938.t1 | PRINTS | PR01626 | L-type calcium channel beta subunit signature | 294 | 308 | 2.3E-73 |
| 11 | g12938.t1 | PRINTS | PR01626 | L-type calcium channel beta subunit signature | 309 | 324 | 2.3E-73 |
| 5 | g12938.t1 | PRINTS | PR01626 | L-type calcium channel beta subunit signature | 327 | 343 | 2.3E-73 |
| 7 | g12938.t1 | PRINTS | PR01626 | L-type calcium channel beta subunit signature | 348 | 363 | 2.3E-73 |
| 10 | g12938.t1 | PRINTS | PR01626 | L-type calcium channel beta subunit signature | 364 | 375 | 2.3E-73 |
| 1 | g12938.t1 | Pfam | PF12052 | Voltage gated calcium channel subunit beta domain 4Aa N terminal | 25 | 65 | 9.7E-21 |
| 2 | g12938.t1 | Pfam | PF00625 | Guanylate kinase | 220 | 400 | 2.0E-46 |
| 32 | g12938.t1 | ProSiteProfiles | PS50002 | Src homology 3 (SH3) domain profile. | 66 | 135 | 15.268 |
| 19 | g12938.t1 | SMART | SM00326 | SH3_2 | 69 | 133 | 1.5E-4 |
| 20 | g12938.t1 | SMART | SM00072 | gk_7 | 220 | 402 | 2.6E-28 |
| 15 | g12938.t1 | SUPERFAMILY | SSF50044 | SH3-domain | 47 | 218 | 4.73E-38 |
| 14 | g12938.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 219 | 405 | 9.03E-43 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0070588 | calcium ion transmembrane transport | BP |
| GO:0005515 | protein binding | MF |
| GO:0005245 | voltage-gated calcium channel activity | MF |
| GO:0005891 | voltage-gated calcium channel complex | CC |
KEGG
Orthology
- This transcript has been annotated with K04863 (voltage-dependent calcium channel beta-2)
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.
