Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Calcium-transporting ATPase sarcoplasmic/endoplasmic reticulum type.

Parent gene

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.t19 TTS g3059.t19 22373557 22373557
chr_3 g3059 g3059.t19 isoform g3059.t19 22373938 22380788
chr_3 g3059 g3059.t19 exon g3059.t19.exon1 22373938 22374036
chr_3 g3059 g3059.t19 cds g3059.t19.CDS1 22373938 22374036
chr_3 g3059 g3059.t19 exon g3059.t19.exon2 22375071 22375171
chr_3 g3059 g3059.t19 cds g3059.t19.CDS2 22375071 22375171
chr_3 g3059 g3059.t19 exon g3059.t19.exon3 22377283 22377454
chr_3 g3059 g3059.t19 cds g3059.t19.CDS3 22377283 22377400
chr_3 g3059 g3059.t19 exon g3059.t19.exon4 22380704 22380788
chr_3 g3059 g3059.t19 TSS g3059.t19 22380898 22380898

Sequences

>g3059.t19 Gene=g3059 Length=457
TTTTTTCTCCTCGTGAAGTGTGTAGTTTATTTAATGTCAATCGATAATAAGTGAGAAATA
AAAAATTATTTAAAGTCAGATAATTAATAATTGAATCTTAGATTATACGACACAATAAAT
TAATAATCAAGTCTCAATAATGGAGGACGCCCATTGCAAGACATCCGACGAGGTGTTAAA
GTACTTCGGCACAAATGAAGAATTAGGATTAACGCCAGATCAAGTCAAACAATATCAGGC
TAAATACGGACCTAATGAACTTCCAGCCGAGGAAGGCAAAACAATATGGCAATTAGTACT
TGAACAGTTTGACGATCTTTTAGTTAAAATTTTGTTATTGGCTGCTATTATTTCATTTGT
ATTAGCTCTTTTTGAAGAACATGAGGGTATTGAAGCATTCGTAGAACCATTTGTAATTTT
ACTTATTTTAATTGCTAATGCTGTTGTTGGTGTTTGG

>g3059.t19 Gene=g3059 Length=106
MEDAHCKTSDEVLKYFGTNEELGLTPDQVKQYQAKYGPNELPAEEGKTIWQLVLEQFDDL
LVKILLLAAIISFVLALFEEHEGIEAFVEPFVILLILIANAVVGVW

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g3059.t19 Gene3D G3DSA:2.70.150.10 - 1 55 1.2E-7
9 g3059.t19 Gene3D G3DSA:1.20.1110.10 - 56 106 6.1E-18
2 g3059.t19 PANTHER PTHR42861:SF92 CALCIUM-TRANSPORTING ATPASE 2 106 1.3E-36
3 g3059.t19 PANTHER PTHR42861 CALCIUM-TRANSPORTING ATPASE 2 106 1.3E-36
1 g3059.t19 Pfam PF00690 Cation transporter/ATPase, N-terminus 5 72 1.3E-20
11 g3059.t19 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 59 -
14 g3059.t19 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 60 78 -
10 g3059.t19 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 79 86 -
13 g3059.t19 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 87 105 -
12 g3059.t19 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 106 106 -
7 g3059.t19 SMART SM00831 Cation_ATPase_N_a_2 3 77 1.2E-19
6 g3059.t19 SUPERFAMILY SSF81665 Calcium ATPase, transmembrane domain M 1 106 1.44E-27
4 g3059.t19 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 60 78 -
5 g3059.t19 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 83 105 -

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.

Raw TPM values