General information for g3057.t1
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 g3057 is located on chr_3: 22366427..22368666 (- 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 | g3057 | g3057.t1 | TTS | g3057.t1 | 22362681 | 22362681 |
| chr_3 | g3057 | g3057.t1 | isoform | g3057.t1 | 22362854 | 22368666 |
| chr_3 | g3057 | g3057.t1 | exon | g3057.t1.exon1 | 22362854 | 22362885 |
| chr_3 | g3057 | g3057.t1 | cds | g3057.t1.CDS1 | 22362854 | 22362885 |
| chr_3 | g3057 | g3057.t1 | exon | g3057.t1.exon2 | 22366745 | 22366862 |
| chr_3 | g3057 | g3057.t1 | cds | g3057.t1.CDS2 | 22366745 | 22366862 |
| chr_3 | g3057 | g3057.t1 | exon | g3057.t1.exon3 | 22366923 | 22367040 |
| chr_3 | g3057 | g3057.t1 | cds | g3057.t1.CDS3 | 22366923 | 22367040 |
| chr_3 | g3057 | g3057.t1 | exon | g3057.t1.exon4 | 22367097 | 22367227 |
| chr_3 | g3057 | g3057.t1 | cds | g3057.t1.CDS4 | 22367097 | 22367227 |
| chr_3 | g3057 | g3057.t1 | exon | g3057.t1.exon5 | 22367763 | 22367823 |
| chr_3 | g3057 | g3057.t1 | cds | g3057.t1.CDS5 | 22367763 | 22367823 |
| chr_3 | g3057 | g3057.t1 | exon | g3057.t1.exon6 | 22367893 | 22367911 |
| chr_3 | g3057 | g3057.t1 | cds | g3057.t1.CDS6 | 22367893 | 22367911 |
| chr_3 | g3057 | g3057.t1 | exon | g3057.t1.exon7 | 22368291 | 22368666 |
| chr_3 | g3057 | g3057.t1 | cds | g3057.t1.CDS7 | 22368291 | 22368666 |
| chr_3 | g3057 | g3057.t1 | TSS | g3057.t1 | NA | NA |
Sequences
>g3057.t1 Gene=g3057 Length=855
ATGGAAAACTGGATCAAATACAAAGAGTTGCCCTCAAAGAAACAACTCGAAGTCGATTTT
TGGAATTTTGTAAACAAAAATCCTAAGTTTAAGGATCAAATGATTAAGGTCGGCAAAACA
TCCTTGGAAAAAGTAAAGGGATTCGCAACATCAGATCAAAATTTAAGATATGGACCACAT
GACAAATACGAAATACTCTATGCAGAAAATATTTTCTGTGAAGCTCCAACTGAAAAGATA
GCTTTAAAAATTGAATCAATGTGCCAGGAAATTACTGAGGAAAGAAGATTTTTGATTGAA
CGCTCAGATGGCAGTGCTGGTGGATTAAGTAGAACGCCGAATCTTCGATTTATCGTTTAT
GTGACTATCTTGAGAAGTGCTGCAACTGTTGGAGGTGCTGCTTGGTGGTTCATGTATTCG
CCTACAGGCCCTAATCTTTCTTTTTGGCAGCTTTCACATCATCTTCAATGCCTCTCTGGT
GGAGAAGACTTCAAGGGAGTTGACTGCAAAGTTTTCGCTGATCCACATCCAATGACAATG
GCTTTGTCAGTACTTGTAACTATTGAAATGTTGAACGCTATGAACAGCTTGTCAGAAAAT
CAATCACTTGTTGCTATGCCTCCATGGACAAATATGTGGCTCGTTGGATCAATGTGCTTG
TCATTTGCTCTTCACTTTGTCATCTTATATGTTGAGGTCCTTTCGGGCGTCTTCCAAGTC
ACACCATTAGACGTTGAAGAATGGATTACCGTAATGAAATTCTCAGTTCCAGTCGTGCTA
TTGGATGAGTTGCTCAAATTCGTTGCTAGACGAATTTCAGATGTTAACGAGGTTGTTATT
GATAAATGGCAATAA
>g3057.t1 Gene=g3057 Length=284
MENWIKYKELPSKKQLEVDFWNFVNKNPKFKDQMIKVGKTSLEKVKGFATSDQNLRYGPH
DKYEILYAENIFCEAPTEKIALKIESMCQEITEERRFLIERSDGSAGGLSRTPNLRFIVY
VTILRSAATVGGAAWWFMYSPTGPNLSFWQLSHHLQCLSGGEDFKGVDCKVFADPHPMTM
ALSVLVTIEMLNAMNSLSENQSLVAMPPWTNMWLVGSMCLSFALHFVILYVEVLSGVFQV
TPLDVEEWITVMKFSVPVVLLDELLKFVARRISDVNEVVIDKWQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g3057.t1 | Gene3D | G3DSA:1.20.1110.10 | - | 102 | 275 | 4.4E-51 |
| 2 | g3057.t1 | PANTHER | PTHR42861:SF18 | SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 2 | 124 | 272 | 8.7E-63 |
| 3 | g3057.t1 | PANTHER | PTHR42861 | CALCIUM-TRANSPORTING ATPASE | 124 | 272 | 8.7E-63 |
| 1 | g3057.t1 | Pfam | PF00689 | Cation transporting ATPase, C-terminus | 117 | 268 | 3.7E-20 |
| 8 | g3057.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 116 | - |
| 12 | g3057.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 117 | 138 | - |
| 10 | g3057.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 139 | 211 | - |
| 11 | g3057.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 212 | 231 | - |
| 9 | g3057.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 232 | 284 | - |
| 6 | g3057.t1 | SUPERFAMILY | SSF81665 | Calcium ATPase, transmembrane domain M | 112 | 272 | 3.4E-30 |
| 4 | g3057.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 117 | 139 | - |
| 5 | g3057.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 209 | 231 | - |
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.
