General information for g3059.t6
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.t6 | isoform | g3059.t6 | 22372448 | 22373308 |
| chr_3 | g3059 | g3059.t6 | exon | g3059.t6.exon1 | 22372448 | 22373308 |
| chr_3 | g3059 | g3059.t6 | cds | g3059.t6.CDS1 | 22372448 | 22373185 |
| chr_3 | g3059 | g3059.t6 | TSS | g3059.t6 | NA | NA |
| chr_3 | g3059 | g3059.t6 | TTS | g3059.t6 | NA | NA |
Sequences
>g3059.t6 Gene=g3059 Length=861
GGTGGTTCATGGATTAAGGGAGCTATCTATTATTTCAAGATTGCTGTCGCTTTGGCTGTC
GCTGCTATTCCAGAAGGTTTACCAGCTGTTATTACCACTTGTTTGGCTTTGGGTACTCGT
CGTATGGCCAAGAAGAACGCTATTGTCCGCTCATTGCCATCAGTTGAAACTCTCGGTTGC
ACATCTGTCATTTGCTCAGATAAGACTGGTACATTGACAACAAATCAAATGTCAGTTGCT
CGCGCATTCGTTTTTGAAAAGGTTGAAGGAAATGATAGCAGTTTCACAGAATTCGAAATT
ACTGGATCAACATACGAACCAGTTGGTGATCTTTTCTACAAAGGTTCAAAGGCAAAGGCA
TCAGATTATGAAGTACTCCAAGAACTCGCTACCATTTGCGTCATGTGTAACGACTCTGCT
ATTGATTTCAACGAAGTTAAGCAAGTTTTCGAGAAAGTCGGTGAAGCCACTGAAACTGCA
CTTATTGTTCTTGCCGAAAAATTGAACCCATTCTCAGTTCCAAAGACCGGTTTGGATCGT
CGTTCAGCTGCTATTGTCGTTCGTCAGGAAATTGAGACTAAATGGAAGAAAGAATTTACA
CTTGAATTCTCACGTGATCGTAAATCAATGTCATCATACTGCACACCACTTAAATCATCA
AAACTCGGAACTGGACCAAAAATGTTCTGCAAAGGTGCTCCAGAAGGTGTTTTGGATCGT
TGCACACATGCTCGCGTTGGCACAAGCAAAGTCCCACTTACATCAACACTCAAACAACGC
ATTTTGGATCTCACTCGTCAATACGGTACCGGTCGTGACACACTTCGTTGCCTTGCTTTG
GCCACTGGCGATTCTCCAATG
>g3059.t6 Gene=g3059 Length=246
MAKKNAIVRSLPSVETLGCTSVICSDKTGTLTTNQMSVARAFVFEKVEGNDSSFTEFEIT
GSTYEPVGDLFYKGSKAKASDYEVLQELATICVMCNDSAIDFNEVKQVFEKVGEATETAL
IVLAEKLNPFSVPKTGLDRRSAAIVVRQEIETKWKKEFTLEFSRDRKSMSSYCTPLKSSK
LGTGPKMFCKGAPEGVLDRCTHARVGTSKVPLTSTLKQRILDLTRQYGTGRDTLRCLALA
TGDSPM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g3059.t6 | Gene3D | G3DSA:3.40.1110.10 | - | 34 | 246 | 2.3E-53 |
| 2 | g3059.t6 | PANTHER | PTHR42861:SF18 | SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 2 | 1 | 246 | 3.1E-94 |
| 3 | g3059.t6 | PANTHER | PTHR42861 | CALCIUM-TRANSPORTING ATPASE | 1 | 246 | 3.1E-94 |
| 1 | g3059.t6 | Pfam | PF13246 | Cation transport ATPase (P-type) | 94 | 202 | 5.0E-20 |
| 5 | g3059.t6 | ProSitePatterns | PS00154 | E1-E2 ATPases phosphorylation site. | 26 | 32 | - |
| 4 | g3059.t6 | SUPERFAMILY | SSF81660 | Metal cation-transporting ATPase, ATP-binding domain N | 31 | 245 | 1.07E-55 |
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:0000166 | nucleotide binding | MF |
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