General information for g3059.t16
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.t16 | isoform | g3059.t16 | 22373308 | 22380788 |
| chr_3 | g3059 | g3059.t16 | exon | g3059.t16.exon1 | 22373308 | 22373836 |
| chr_3 | g3059 | g3059.t16 | cds | g3059.t16.CDS1 | 22373309 | 22373836 |
| chr_3 | g3059 | g3059.t16 | exon | g3059.t16.exon2 | 22373935 | 22374036 |
| chr_3 | g3059 | g3059.t16 | cds | g3059.t16.CDS2 | 22373935 | 22374036 |
| chr_3 | g3059 | g3059.t16 | exon | g3059.t16.exon3 | 22375071 | 22375171 |
| chr_3 | g3059 | g3059.t16 | cds | g3059.t16.CDS3 | 22375071 | 22375171 |
| chr_3 | g3059 | g3059.t16 | exon | g3059.t16.exon4 | 22377283 | 22377523 |
| chr_3 | g3059 | g3059.t16 | cds | g3059.t16.CDS4 | 22377283 | 22377400 |
| chr_3 | g3059 | g3059.t16 | exon | g3059.t16.exon5 | 22380704 | 22380788 |
| chr_3 | g3059 | g3059.t16 | TSS | g3059.t16 | 22380898 | 22380898 |
| chr_3 | g3059 | g3059.t16 | TTS | g3059.t16 | NA | NA |
Sequences
>g3059.t16 Gene=g3059 Length=1058
TTTTTTCTCCTCGTGAAGTGTGTAGTTTATTTAATGTCAATCGATAATAAGTGAGAAATA
AAAAATTATTTAAAGTCAGATAATTGAAGGAAAACATTTTAACGCGAGCATTATTCTTTG
TTTTCGTGCTTTGTCACGGTTTTATCGATTGCAGAATAATTGAATCTTAGATTATACGAC
ACAATAAATTAATAATCAAGTCTCAATAATGGAGGACGCCCATTGCAAGACATCCGACGA
GGTGTTAAAGTACTTCGGCACAAATGAAGAATTAGGATTAACGCCAGATCAAGTCAAACA
ATATCAGGCTAAATACGGACCTAATGAACTTCCAGCCGAGGAAGGCAAAACAATATGGCA
ATTAGTACTTGAACAGTTTGACGATCTTTTAGTTAAAATTTTGTTATTGGCTGCTATTAT
TTCATTTGTATTAGCTCTTTTTGAAGAACATGAGGGTATTGAAGCATTCGTAGAACCATT
TGTAATTTTACTTATTTTAATTGCTAATGCTGTTGTTGGTGTTTGGCAAGAACGAAATGC
AGAGTCAGCAATTGAAGCCCTCAAAGAATATGAACCCGAAATGGGTAAAGTCGTTCGTCA
GGATAAGTCCGGAGTACAAAAACTCCGTGCCAAAGAGATTGTACCAGGTGATATCGTTGA
AGTGTCAGTCGGTGACAAAATTCCAGCTGATATTCGTTTAATTAAGATCTACTCAACGAC
AATTCGTATTGATCAATCTATCTTGACTGGTGAATCAGTTTCAGTCATTAAACACACTGA
TGCTGTCCCAGATCCACGCGCTGTCAACCAAGATAAGAAAAATATTTTGTTCTCAGGAAC
TAATGTTGCCGCTGGTAAGGCACGTGGTATCGTTATTGGAACTGGCCTTAACACTGCTAT
CGGTAAAATTCGTACTGAAATGTCAGAAACTGAAGAAATTAAGACACCATTGCAACAAAA
ATTGGATGAATTCGGTGAACAATTGTCAAAGGTCATTTCAATCATTTGCGTTGCTGTCTG
GGCTATCAACATTGGTCACTTTAACGATCCAGCTCATG
>g3059.t16 Gene=g3059 Length=283
MEDAHCKTSDEVLKYFGTNEELGLTPDQVKQYQAKYGPNELPAEEGKTIWQLVLEQFDDL
LVKILLLAAIISFVLALFEEHEGIEAFVEPFVILLILIANAVVGVWQERNAESAIEALKE
YEPEMGKVVRQDKSGVQKLRAKEIVPGDIVEVSVGDKIPADIRLIKIYSTTIRIDQSILT
GESVSVIKHTDAVPDPRAVNQDKKNILFSGTNVAAGKARGIVIGTGLNTAIGKIRTEMSE
TEEIKTPLQQKLDEFGEQLSKVISIICVAVWAINIGHFNDPAH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g3059.t16 | Gene3D | G3DSA:2.70.150.10 | - | 1 | 64 | 4.7E-12 |
| 8 | g3059.t16 | Gene3D | G3DSA:2.70.150.10 | - | 97 | 219 | 4.2E-42 |
| 9 | g3059.t16 | Gene3D | G3DSA:1.20.1110.10 | - | 220 | 283 | 2.9E-11 |
| 3 | g3059.t16 | PANTHER | PTHR42861:SF18 | SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 2 | 2 | 283 | 1.6E-137 |
| 4 | g3059.t16 | PANTHER | PTHR42861 | CALCIUM-TRANSPORTING ATPASE | 2 | 283 | 1.6E-137 |
| 2 | g3059.t16 | Pfam | PF00690 | Cation transporter/ATPase, N-terminus | 6 | 72 | 1.2E-19 |
| 1 | g3059.t16 | Pfam | PF00122 | E1-E2 ATPase | 122 | 281 | 3.0E-39 |
| 11 | g3059.t16 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 59 | - |
| 14 | g3059.t16 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 60 | 78 | - |
| 10 | g3059.t16 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 79 | 86 | - |
| 13 | g3059.t16 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 87 | 106 | - |
| 12 | g3059.t16 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 107 | 283 | - |
| 17 | g3059.t16 | SMART | SM00831 | Cation_ATPase_N_a_2 | 3 | 77 | 1.2E-19 |
| 5 | g3059.t16 | SUPERFAMILY | SSF81665 | Calcium ATPase, transmembrane domain M | 1 | 279 | 1.14E-43 |
| 6 | g3059.t16 | SUPERFAMILY | SSF81653 | Calcium ATPase, transduction domain A | 131 | 235 | 5.49E-28 |
| 18 | g3059.t16 | TIGRFAM | TIGR01494 | ATPase_P-type: HAD ATPase, P-type, family IC | 92 | 203 | 3.1E-19 |
| 16 | g3059.t16 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 60 | 77 | - |
| 15 | g3059.t16 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 87 | 106 | - |
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.
