General information for g12965.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Calmodulin.
Parent gene
- The parent gene g12965 is located on chr_1: 27184934..27195957 (- 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 | g12965 | g12965.t3 | TTS | g12965.t3 | 27184680 | 27184680 |
| chr_1 | g12965 | g12965.t3 | isoform | g12965.t3 | 27184934 | 27195957 |
| chr_1 | g12965 | g12965.t3 | exon | g12965.t3.exon1 | 27184934 | 27184965 |
| chr_1 | g12965 | g12965.t3 | cds | g12965.t3.CDS1 | 27184934 | 27184965 |
| chr_1 | g12965 | g12965.t3 | exon | g12965.t3.exon2 | 27185033 | 27185181 |
| chr_1 | g12965 | g12965.t3 | cds | g12965.t3.CDS2 | 27185033 | 27185181 |
| chr_1 | g12965 | g12965.t3 | exon | g12965.t3.exon3 | 27186891 | 27187026 |
| chr_1 | g12965 | g12965.t3 | cds | g12965.t3.CDS3 | 27186891 | 27187026 |
| chr_1 | g12965 | g12965.t3 | exon | g12965.t3.exon4 | 27187083 | 27187184 |
| chr_1 | g12965 | g12965.t3 | cds | g12965.t3.CDS4 | 27187083 | 27187184 |
| chr_1 | g12965 | g12965.t3 | exon | g12965.t3.exon5 | 27187878 | 27187911 |
| chr_1 | g12965 | g12965.t3 | cds | g12965.t3.CDS5 | 27187878 | 27187911 |
| chr_1 | g12965 | g12965.t3 | exon | g12965.t3.exon6 | 27188262 | 27188387 |
| chr_1 | g12965 | g12965.t3 | cds | g12965.t3.CDS6 | 27188262 | 27188357 |
| chr_1 | g12965 | g12965.t3 | exon | g12965.t3.exon7 | 27195890 | 27195957 |
| chr_1 | g12965 | g12965.t3 | TSS | g12965.t3 | NA | NA |
Sequences
>g12965.t3 Gene=g12965 Length=647
TTTATTTTACAATTTTTTCAGTCAACTGAAAAAAAATTCTGAAAAATAAATTTTTTTACA
ATAAATCATGAAAGTGTATGAATAAATTTTAATCAAAAATGGCAACACAAAGTTCAAATA
ATGAAGATCCTTATAAACGTGAATACACTAGAGTAAAATCTCTAATAGAGAGCAATTATG
TTCGACAAACATCTTCTGAATATGGATTAACTGAAGAACAAGTTGCAGAATTCAAGGAAG
TTTTCATGTTATTCGATAAGGATGAGGATGGATCGATAACTATGGCTGAATTAGCAGTCG
TAATGCGTTCAATGGGCCAGCGTCCGACAGAAACTGAATTGCGAAACATGGTTAATGATG
TTGATCAAAATGATAATGGAATGATTGAGTTTAATGAGTTCCTTCAAATGATGTCGAAAA
AGATGCGCGAAGGTGACAGCGAAGACGAGCTAAAAGAAGCTTTCAAATGTTTTGATAAAA
ATAATGATGGATTAATATCATCATCTGAGCTTCGACGCGTGATGACCAATTTGGGTGAAA
AATTGTCAGAAGAAGAAGTCGATGATATGATAAAAGAAGCAGACATGGATGGTGATGGTC
AAGTTAATTACAATGAATTTGTAATGATATTGATGGCGCGCAACTAG
>g12965.t3 Gene=g12965 Length=182
MATQSSNNEDPYKREYTRVKSLIESNYVRQTSSEYGLTEEQVAEFKEVFMLFDKDEDGSI
TMAELAVVMRSMGQRPTETELRNMVNDVDQNDNGMIEFNEFLQMMSKKMREGDSEDELKE
AFKCFDKNNDGLISSSELRRVMTNLGEKLSEEEVDDMIKEADMDGDGQVNYNEFVMILMA
RN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g12965.t3 | CDD | cd00051 | EFh | 44 | 106 | 1.04311E-15 |
| 10 | g12965.t3 | CDD | cd00051 | EFh | 117 | 179 | 5.15393E-20 |
| 8 | g12965.t3 | Gene3D | G3DSA:1.10.238.10 | - | 13 | 70 | 2.8E-8 |
| 7 | g12965.t3 | Gene3D | G3DSA:1.10.238.10 | - | 71 | 101 | 5.8E-14 |
| 6 | g12965.t3 | Gene3D | G3DSA:1.10.238.10 | - | 102 | 182 | 2.1E-32 |
| 3 | g12965.t3 | PANTHER | PTHR23050 | CALCIUM BINDING PROTEIN | 36 | 180 | 5.6E-62 |
| 4 | g12965.t3 | PANTHER | PTHR23050:SF427 | CALMODULIN-1 | 36 | 180 | 5.6E-62 |
| 2 | g12965.t3 | Pfam | PF13499 | EF-hand domain pair | 45 | 106 | 8.0E-14 |
| 1 | g12965.t3 | Pfam | PF13499 | EF-hand domain pair | 116 | 175 | 7.3E-15 |
| 13 | g12965.t3 | ProSitePatterns | PS00018 | EF-hand calcium-binding domain. | 53 | 65 | - |
| 12 | g12965.t3 | ProSitePatterns | PS00018 | EF-hand calcium-binding domain. | 89 | 101 | - |
| 14 | g12965.t3 | ProSitePatterns | PS00018 | EF-hand calcium-binding domain. | 126 | 138 | - |
| 11 | g12965.t3 | ProSitePatterns | PS00018 | EF-hand calcium-binding domain. | 162 | 174 | - |
| 20 | g12965.t3 | ProSiteProfiles | PS50222 | EF-hand calcium-binding domain profile. | 40 | 75 | 15.016 |
| 19 | g12965.t3 | ProSiteProfiles | PS50222 | EF-hand calcium-binding domain profile. | 76 | 111 | 13.23 |
| 22 | g12965.t3 | ProSiteProfiles | PS50222 | EF-hand calcium-binding domain profile. | 113 | 148 | 16.689 |
| 21 | g12965.t3 | ProSiteProfiles | PS50222 | EF-hand calcium-binding domain profile. | 149 | 182 | 13.537 |
| 18 | g12965.t3 | SMART | SM00054 | efh_1 | 44 | 72 | 2.5E-5 |
| 17 | g12965.t3 | SMART | SM00054 | efh_1 | 80 | 108 | 9.9E-4 |
| 15 | g12965.t3 | SMART | SM00054 | efh_1 | 117 | 145 | 2.4E-7 |
| 16 | g12965.t3 | SMART | SM00054 | efh_1 | 153 | 181 | 3.3E-6 |
| 5 | g12965.t3 | SUPERFAMILY | SSF47473 | EF-hand | 32 | 179 | 1.38E-51 |
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:0005509 | calcium ion binding | MF |
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. There were no conditions that were differentially expressed