General information for g3059.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Calcium-transporting ATPase sarcoplasmic/endoplasmic reticulum type.
Parent gene
- The parent gene g3059 is located on chr_3: 22373974..22380788 (- 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_3 | g3059 | g3059.t2 | isoform | g3059.t2 | 22370258 | 22372058 |
| chr_3 | g3059 | g3059.t2 | exon | g3059.t2.exon1 | 22370258 | 22371646 |
| chr_3 | g3059 | g3059.t2 | cds | g3059.t2.CDS1 | 22371494 | 22371646 |
| chr_3 | g3059 | g3059.t2 | exon | g3059.t2.exon2 | 22371704 | 22372058 |
| chr_3 | g3059 | g3059.t2 | cds | g3059.t2.CDS2 | 22371704 | 22372015 |
| chr_3 | g3059 | g3059.t2 | TSS | g3059.t2 | NA | NA |
| chr_3 | g3059 | g3059.t2 | TTS | g3059.t2 | NA | NA |
Sequences
>g3059.t2 Gene=g3059 Length=1744
AGAGCCAGCTCACAAGTCAAAGATTGTCGAATATTTGCAAAGCATGAATGAAATCTCAGC
TATGACAGGTGATGGTGTCAATGACGCTCCTGCTTTGAAAAAGGCTGAAATTGGTATTGC
TATGGGTTCTGGTACTGCTGTCGCTAAATCTGCTTCAGAAATGGTTCTCGCTGACGATAA
CTTCTCATCAATTGTCGCTGCCGTTGAAGAAGGTCGTGCCATTTACAACAACATGAAACA
ATTCATTCGTTATCTCATTTCATCAAACATTGGTGAGGTTGTCTCAATTTTCTTGACTGC
TGCTCTTGGCTTACCAGAAGCTCTCATTCCCGTTCAATTGTTGTGGGTCAACTTGGTTAC
TGATGGTCTCCCAGCTACAGCTCTTGGTTTTAATCCACCTGATTTAGATATTATGACTAA
GCCACCACGTAAAGCCGATGAAGGTCTTATTTCAGGATGGTTGTTCTTCCGTTACATGGC
TATTGGTGGTTATGTTGGTGAGTTTTAAAAATTCTTATATAATTAAATTAATTTGTTTAA
CTGAAGAAAGAGAGAGAGATTTAATCATTCTTTGCCTTCATTTATCAAAATGAAGTTGCC
CAAAATTCACCGCGTGGAGGTGATGGTTAACGAATTTCTCTGAATGTTTGTTAACGCAGT
TATTCAGTGCCTCTGCGAAGCATAACTTTTGATAAAGCAGACATGCTTGCGTACTGCTTT
GGGATGTTTTTTTACGTAGTTACCCCATGCCTCTACGATGCACAACTTTTGATAAGGCAG
GTGTGCATGCGTACTGCCATCTTAAAAACTAATAATTCATAAATACAACTTAATTCTATA
TATCTGAATGTTTTTTAACGCAGTTACTCAGTGCCTCTGCGAAGTATAACTTTTGATAAA
GCAGGCATGCTTGCGTACTGCTTTGGGATGTTTTTTTACGTAGTTACCCCATGCCTCTAC
GATGCACAACTTTTGTTAAGGCAGGCGTGCATGCGTACTGCCGTAAGCATTTGAAGGAGC
TCTACTTGTTATTTGATTTTGATGTCGATGGCTGTTGATGAATTTTAATGTGCTTGCGCA
TTCTGTCAGCAGAGTACTCTTTTCCACAAAACTTGCATTTTTGTCGTGGCAAGTGAGTTT
TTTTATGCGAATAGAGCCAAGTTTTTGTGCCCATCTTTCCACAAGTTTCGCAAGCAACCT
TTGGCTCCACTTTTTTTGGTTCATTTTTCTTTGTGTGCGTCTTAATGTGTGCTTTTATGG
ATTGTTTTGTAAAATATTTCAAACATGTTGGGCACTGCTCTTTCTCATGCATTTTCATGT
GAGTGCCGAGGTTTGTAGCAAGTTTTCCACAAACAGGACATGCTTTTTTCGGTCGTGTCT
CTTCAGTGTGCTGGTATTTTTTGTGTTCATCAATTTTTTTATAATTGATCATCTTGTGGC
AGATATTGCATTCAATTTTATGCTGTCCAACATGCACTTTCACGTGATACACCATTCCCT
CACGAGTTAATATTTTGCCACAATAATCACATTCTAGACAGTCTGCATTATTGTGAAGAT
TGGCAATGTGTCGCCGCATATCAATAGGGCAGACCATAGCACCACAAAGGTCGCAAGGTT
CTTTCTCTCGGCGGTTGATGTTTTGCTCACAGTGATGTCTGTAGTGAACTCCTGTTTCAG
CTCGTGTCTCAAAGTGCTTTCCGCAAGCAGGACAATTAGTACTAAGTGTACTTTCATAAG
ACCA
>g3059.t2 Gene=g3059 Length=154
MNEISAMTGDGVNDAPALKKAEIGIAMGSGTAVAKSASEMVLADDNFSSIVAAVEEGRAI
YNNMKQFIRYLISSNIGEVVSIFLTAALGLPEALIPVQLLWVNLVTDGLPATALGFNPPD
LDIMTKPPRKADEGLISGWLFFRYMAIGGYVGEF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g3059.t2 | Gene3D | G3DSA:1.20.1110.10 | - | 20 | 154 | 1.1E-55 |
| 3 | g3059.t2 | PANTHER | PTHR42861:SF6 | SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 3 | 2 | 152 | 9.0E-99 |
| 4 | g3059.t2 | PANTHER | PTHR42861 | CALCIUM-TRANSPORTING ATPASE | 2 | 152 | 9.0E-99 |
| 5 | g3059.t2 | PRINTS | PR00119 | P-type cation-transporting ATPase superfamily signature | 8 | 27 | 8.5E-15 |
| 8 | g3059.t2 | PRINTS | PR00120 | H+-transporting ATPase (proton pump) signature | 8 | 24 | 1.8E-13 |
| 6 | g3059.t2 | PRINTS | PR00119 | P-type cation-transporting ATPase superfamily signature | 31 | 43 | 8.5E-15 |
| 7 | g3059.t2 | PRINTS | PR00120 | H+-transporting ATPase (proton pump) signature | 39 | 64 | 1.8E-13 |
| 2 | g3059.t2 | Pfam | PF08282 | haloacid dehalogenase-like hydrolase | 8 | 51 | 1.3E-5 |
| 1 | g3059.t2 | Pfam | PF00689 | Cation transporting ATPase, C-terminus | 91 | 149 | 3.5E-19 |
| 11 | g3059.t2 | SUPERFAMILY | SSF56784 | HAD-like | 5 | 65 | 3.85E-20 |
| 10 | g3059.t2 | SUPERFAMILY | SSF81665 | Calcium ATPase, transmembrane domain M | 53 | 152 | 4.71E-35 |
| 13 | g3059.t2 | TIGRFAM | TIGR01494 | ATPase_P-type: HAD ATPase, P-type, family IC | 3 | 94 | 2.6E-26 |
| 9 | g3059.t2 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 67 | 89 | - |
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:0016021 | integral component of membrane | CC |
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.
