Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t14 isoform g3059.t14 22373308 22380788
chr_3 g3059 g3059.t14 exon g3059.t14.exon1 22373308 22373836
chr_3 g3059 g3059.t14 cds g3059.t14.CDS1 22373309 22373836
chr_3 g3059 g3059.t14 exon g3059.t14.exon2 22373935 22374029
chr_3 g3059 g3059.t14 cds g3059.t14.CDS2 22373935 22374029
chr_3 g3059 g3059.t14 exon g3059.t14.exon3 22375067 22375171
chr_3 g3059 g3059.t14 cds g3059.t14.CDS3 22375067 22375171
chr_3 g3059 g3059.t14 exon g3059.t14.exon4 22377283 22377454
chr_3 g3059 g3059.t14 cds g3059.t14.CDS4 22377283 22377400
chr_3 g3059 g3059.t14 exon g3059.t14.exon5 22380704 22380788
chr_3 g3059 g3059.t14 TSS g3059.t14 22380898 22380898
chr_3 g3059 g3059.t14 TTS g3059.t14 NA NA

Sequences

>g3059.t14 Gene=g3059 Length=986
TTTTTTCTCCTCGTGAAGTGTGTAGTTTATTTAATGTCAATCGATAATAAGTGAGAAATA
AAAAATTATTTAAAGTCAGATAATTAATAATTGAATCTTAGATTATACGACACAATAAAT
TAATAATCAAGTCTCAATAATGGAGGACGCCCATTGCAAGACATCCGACGAGGTGTTAAA
GTACTTCGGCACAAATGAAGAATTAGGATTAACGCCAGATCAAGTCAAACAATATCAGGC
TAAATACGGACCTAATGAACTTCCAGCCGAGGAAGGCAAAACAATATGGCAATTAGTACT
TGAACAGTTTGACGATCTTTTAGTTAAAATTTTGTTATTGGCTGCTATTATTTCATTTGT
AACTCTTTTTGAAGAACATGAGGGTATTGAAGCATTCGTAGAACCATTTGTAATTTTACT
TATTTTAATTGCTAATGCTGTTGTTGGTGTTTGGCAAGAACGAAATGCAGAGTCAGCAAT
TGAAGCCCTCAAAGAATATGAACCCGAAATGGGTAAAGTCGTTCGTCAGGATAAGTCCGG
AGTACAAAAACTCCGTGCCAAAGAGATTGTACCAGGTGATATCGTTGAAGTGTCAGTCGG
TGACAAAATTCCAGCTGATATTCGTTTAATTAAGATCTACTCAACGACAATTCGTATTGA
TCAATCTATCTTGACTGGTGAATCAGTTTCAGTCATTAAACACACTGATGCTGTCCCAGA
TCCACGCGCTGTCAACCAAGATAAGAAAAATATTTTGTTCTCAGGAACTAATGTTGCCGC
TGGTAAGGCACGTGGTATCGTTATTGGAACTGGCCTTAACACTGCTATCGGTAAAATTCG
TACTGAAATGTCAGAAACTGAAGAAATTAAGACACCATTGCAACAAAAATTGGATGAATT
CGGTGAACAATTGTCAAAGGTCATTTCAATCATTTGCGTTGCTGTCTGGGCTATCAACAT
TGGTCACTTTAACGATCCAGCTCATG

>g3059.t14 Gene=g3059 Length=282
MEDAHCKTSDEVLKYFGTNEELGLTPDQVKQYQAKYGPNELPAEEGKTIWQLVLEQFDDL
LVKILLLAAIISFVTLFEEHEGIEAFVEPFVILLILIANAVVGVWQERNAESAIEALKEY
EPEMGKVVRQDKSGVQKLRAKEIVPGDIVEVSVGDKIPADIRLIKIYSTTIRIDQSILTG
ESVSVIKHTDAVPDPRAVNQDKKNILFSGTNVAAGKARGIVIGTGLNTAIGKIRTEMSET
EEIKTPLQQKLDEFGEQLSKVISIICVAVWAINIGHFNDPAH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g3059.t14 Gene3D G3DSA:2.70.150.10 - 1 64 4.6E-12
7 g3059.t14 Gene3D G3DSA:2.70.150.10 - 96 218 4.2E-42
9 g3059.t14 Gene3D G3DSA:1.20.1110.10 - 219 282 2.9E-11
3 g3059.t14 PANTHER PTHR42861:SF18 SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 2 2 282 1.2E-136
4 g3059.t14 PANTHER PTHR42861 CALCIUM-TRANSPORTING ATPASE 2 282 1.2E-136
2 g3059.t14 Pfam PF00690 Cation transporter/ATPase, N-terminus 6 72 1.2E-19
1 g3059.t14 Pfam PF00122 E1-E2 ATPase 121 280 3.0E-39
11 g3059.t14 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 59 -
13 g3059.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 60 78 -
10 g3059.t14 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 79 84 -
14 g3059.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 85 105 -
12 g3059.t14 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 106 282 -
17 g3059.t14 SMART SM00831 Cation_ATPase_N_a_2 3 77 2.5E-18
5 g3059.t14 SUPERFAMILY SSF81665 Calcium ATPase, transmembrane domain M 1 278 9.29E-43
6 g3059.t14 SUPERFAMILY SSF81653 Calcium ATPase, transduction domain A 130 234 5.49E-28
18 g3059.t14 TIGRFAM TIGR01494 ATPase_P-type: HAD ATPase, P-type, family IC 91 202 3.1E-19
16 g3059.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 60 77 -
15 g3059.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 82 104 -

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. There were no conditions that were differentially expressed