General information for g3059.t17
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.t17 | isoform | g3059.t17 | 22373308 | 22380788 |
| chr_3 | g3059 | g3059.t17 | exon | g3059.t17.exon1 | 22373308 | 22373836 |
| chr_3 | g3059 | g3059.t17 | cds | g3059.t17.CDS1 | 22373309 | 22373836 |
| chr_3 | g3059 | g3059.t17 | exon | g3059.t17.exon2 | 22373935 | 22374029 |
| chr_3 | g3059 | g3059.t17 | cds | g3059.t17.CDS2 | 22373935 | 22374029 |
| chr_3 | g3059 | g3059.t17 | exon | g3059.t17.exon3 | 22375067 | 22375162 |
| chr_3 | g3059 | g3059.t17 | cds | g3059.t17.CDS3 | 22375067 | 22375162 |
| chr_3 | g3059 | g3059.t17 | exon | g3059.t17.exon4 | 22377283 | 22377454 |
| chr_3 | g3059 | g3059.t17 | cds | g3059.t17.CDS4 | 22377283 | 22377400 |
| chr_3 | g3059 | g3059.t17 | exon | g3059.t17.exon5 | 22380704 | 22380788 |
| chr_3 | g3059 | g3059.t17 | TSS | g3059.t17 | 22380898 | 22380898 |
| chr_3 | g3059 | g3059.t17 | TTS | g3059.t17 | NA | NA |
Sequences
>g3059.t17 Gene=g3059 Length=977
TTTTTTCTCCTCGTGAAGTGTGTAGTTTATTTAATGTCAATCGATAATAAGTGAGAAATA
AAAAATTATTTAAAGTCAGATAATTAATAATTGAATCTTAGATTATACGACACAATAAAT
TAATAATCAAGTCTCAATAATGGAGGACGCCCATTGCAAGACATCCGACGAGGTGTTAAA
GTACTTCGGCACAAATGAAGAATTAGGATTAACGCCAGATCAAGTCAAACAATATCAGGC
TAAATACGGACCTAATGCCGAGGAAGGCAAAACAATATGGCAATTAGTACTTGAACAGTT
TGACGATCTTTTAGTTAAAATTTTGTTATTGGCTGCTATTATTTCATTTGTAACTCTTTT
TGAAGAACATGAGGGTATTGAAGCATTCGTAGAACCATTTGTAATTTTACTTATTTTAAT
TGCTAATGCTGTTGTTGGTGTTTGGCAAGAACGAAATGCAGAGTCAGCAATTGAAGCCCT
CAAAGAATATGAACCCGAAATGGGTAAAGTCGTTCGTCAGGATAAGTCCGGAGTACAAAA
ACTCCGTGCCAAAGAGATTGTACCAGGTGATATCGTTGAAGTGTCAGTCGGTGACAAAAT
TCCAGCTGATATTCGTTTAATTAAGATCTACTCAACGACAATTCGTATTGATCAATCTAT
CTTGACTGGTGAATCAGTTTCAGTCATTAAACACACTGATGCTGTCCCAGATCCACGCGC
TGTCAACCAAGATAAGAAAAATATTTTGTTCTCAGGAACTAATGTTGCCGCTGGTAAGGC
ACGTGGTATCGTTATTGGAACTGGCCTTAACACTGCTATCGGTAAAATTCGTACTGAAAT
GTCAGAAACTGAAGAAATTAAGACACCATTGCAACAAAAATTGGATGAATTCGGTGAACA
ATTGTCAAAGGTCATTTCAATCATTTGCGTTGCTGTCTGGGCTATCAACATTGGTCACTT
TAACGATCCAGCTCATG
>g3059.t17 Gene=g3059 Length=279
MEDAHCKTSDEVLKYFGTNEELGLTPDQVKQYQAKYGPNAEEGKTIWQLVLEQFDDLLVK
ILLLAAIISFVTLFEEHEGIEAFVEPFVILLILIANAVVGVWQERNAESAIEALKEYEPE
MGKVVRQDKSGVQKLRAKEIVPGDIVEVSVGDKIPADIRLIKIYSTTIRIDQSILTGESV
SVIKHTDAVPDPRAVNQDKKNILFSGTNVAAGKARGIVIGTGLNTAIGKIRTEMSETEEI
KTPLQQKLDEFGEQLSKVISIICVAVWAINIGHFNDPAH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g3059.t17 | Gene3D | G3DSA:2.70.150.10 | - | 1 | 61 | 4.4E-8 |
| 8 | g3059.t17 | Gene3D | G3DSA:2.70.150.10 | - | 93 | 215 | 4.1E-42 |
| 9 | g3059.t17 | Gene3D | G3DSA:1.20.1110.10 | - | 216 | 279 | 2.9E-11 |
| 3 | g3059.t17 | PANTHER | PTHR42861:SF18 | SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 2 | 2 | 279 | 9.8E-132 |
| 4 | g3059.t17 | PANTHER | PTHR42861 | CALCIUM-TRANSPORTING ATPASE | 2 | 279 | 9.8E-132 |
| 2 | g3059.t17 | Pfam | PF00690 | Cation transporter/ATPase, N-terminus | 6 | 69 | 5.1E-15 |
| 1 | g3059.t17 | Pfam | PF00122 | E1-E2 ATPase | 118 | 277 | 2.9E-39 |
| 12 | g3059.t17 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 56 | - |
| 14 | g3059.t17 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 57 | 75 | - |
| 10 | g3059.t17 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 76 | 81 | - |
| 13 | g3059.t17 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 82 | 102 | - |
| 11 | g3059.t17 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 103 | 279 | - |
| 17 | g3059.t17 | SMART | SM00831 | Cation_ATPase_N_a_2 | 3 | 74 | 2.6E-11 |
| 5 | g3059.t17 | SUPERFAMILY | SSF81665 | Calcium ATPase, transmembrane domain M | 1 | 275 | 2.22E-38 |
| 6 | g3059.t17 | SUPERFAMILY | SSF81653 | Calcium ATPase, transduction domain A | 127 | 231 | 5.36E-28 |
| 18 | g3059.t17 | TIGRFAM | TIGR01494 | ATPase_P-type: HAD ATPase, P-type, family IC | 88 | 199 | 3.0E-19 |
| 16 | g3059.t17 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 57 | 74 | - |
| 15 | g3059.t17 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 79 | 101 | - |
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. There were no conditions that were differentially expressed