General information for g3059.t13
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.t13 | isoform | g3059.t13 | 22373308 | 22377454 |
| chr_3 | g3059 | g3059.t13 | exon | g3059.t13.exon1 | 22373308 | 22373836 |
| chr_3 | g3059 | g3059.t13 | cds | g3059.t13.CDS1 | 22373309 | 22373785 |
| chr_3 | g3059 | g3059.t13 | exon | g3059.t13.exon2 | 22373931 | 22374036 |
| chr_3 | g3059 | g3059.t13 | exon | g3059.t13.exon3 | 22375071 | 22375171 |
| chr_3 | g3059 | g3059.t13 | exon | g3059.t13.exon4 | 22377283 | 22377454 |
| chr_3 | g3059 | g3059.t13 | TSS | g3059.t13 | 22378056 | 22378056 |
| chr_3 | g3059 | g3059.t13 | TTS | g3059.t13 | NA | NA |
Sequences
>g3059.t13 Gene=g3059 Length=908
AATAATTGAATCTTAGATTATACGACACAATAAATTAATAATCAAGTCTCAATAATGGAG
GACGCCCATTGCAAGACATCCGACGAGGTGTTAAAGTACTTCGGCACAAATGAAGAATTA
GGATTAACGCCAGATCAAGTCAAACAATATCAGGCTAAATACGGACCTAATGAACTTCCA
GCCGAGGAAGGCAAAACAATATGGCAATTAGTACTTGAACAGTTTGACGATCTTTTAGTT
AAAATTTTGTTATTGGCTGCTATTATTTCATTTGTATTAGCTCTTTTTGAAGAACATGAG
GGTATTGAAGCATTCGTAGAACCATTTGTAATTTTACTTATTTTAATTGCTAATGCTGTT
GTTGGTGTTTGGCAAGTGAGAACGAAATGCAGAGTCAGCAATTGAAGCCCTCAAAGAATA
TGAACCCGAAATGGGTAAAGTCGTTCGTCAGGATAAGTCCGGAGTACAAAAACTCCGTGC
CAAAGAGATTGTACCAGGTGATATCGTTGAAGTGTCAGTCGGTGACAAAATTCCAGCTGA
TATTCGTTTAATTAAGATCTACTCAACGACAATTCGTATTGATCAATCTATCTTGACTGG
TGAATCAGTTTCAGTCATTAAACACACTGATGCTGTCCCAGATCCACGCGCTGTCAACCA
AGATAAGAAAAATATTTTGTTCTCAGGAACTAATGTTGCCGCTGGTAAGGCACGTGGTAT
CGTTATTGGAACTGGCCTTAACACTGCTATCGGTAAAATTCGTACTGAAATGTCAGAAAC
TGAAGAAATTAAGACACCATTGCAACAAAAATTGGATGAATTCGGTGAACAATTGTCAAA
GGTCATTTCAATCATTTGCGTTGCTGTCTGGGCTATCAACATTGGTCACTTTAACGATCC
AGCTCATG
>g3059.t13 Gene=g3059 Length=159
MGKVVRQDKSGVQKLRAKEIVPGDIVEVSVGDKIPADIRLIKIYSTTIRIDQSILTGESV
SVIKHTDAVPDPRAVNQDKKNILFSGTNVAAGKARGIVIGTGLNTAIGKIRTEMSETEEI
KTPLQQKLDEFGEQLSKVISIICVAVWAINIGHFNDPAH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g3059.t13 | Gene3D | G3DSA:2.70.150.10 | - | 1 | 116 | 0e+00 |
| 7 | g3059.t13 | Gene3D | G3DSA:1.20.1110.10 | - | 117 | 159 | 0e+00 |
| 2 | g3059.t13 | PANTHER | PTHR42861:SF18 | SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 2 | 1 | 159 | 0e+00 |
| 3 | g3059.t13 | PANTHER | PTHR42861 | CALCIUM-TRANSPORTING ATPASE | 1 | 159 | 0e+00 |
| 1 | g3059.t13 | Pfam | PF00122 | E1-E2 ATPase | 8 | 157 | 0e+00 |
| 5 | g3059.t13 | SUPERFAMILY | SSF81653 | Calcium ATPase, transduction domain A | 7 | 111 | 0e+00 |
| 4 | g3059.t13 | SUPERFAMILY | SSF81665 | Calcium ATPase, transmembrane domain M | 115 | 155 | 9e-07 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
