Gene loci information

Transcript annotation

  • This transcript has been annotated as Plasma membrane calcium-transporting ATPase 4.

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_4 g16778 g16778.t4 TSS g16778.t4 10988236 10988236
chr_4 g16778 g16778.t4 isoform g16778.t4 10988935 10990220
chr_4 g16778 g16778.t4 exon g16778.t4.exon1 10988935 10989292
chr_4 g16778 g16778.t4 cds g16778.t4.CDS1 10988935 10989292
chr_4 g16778 g16778.t4 exon g16778.t4.exon2 10989665 10989948
chr_4 g16778 g16778.t4 cds g16778.t4.CDS2 10989665 10989948
chr_4 g16778 g16778.t4 exon g16778.t4.exon3 10990010 10990220
chr_4 g16778 g16778.t4 cds g16778.t4.CDS3 10990010 10990219
chr_4 g16778 g16778.t4 TTS g16778.t4 10990207 10990207

Sequences

>g16778.t4 Gene=g16778 Length=853
ATGGCAACAATAAACGGTCGACCAGCGAAGTATCGCATAACGCTAAAAGAGCTTCGTGAA
TTGATGGAACATCGAGGACATGAAGGAATTCAAAGAGTATCAGATTATGGTGGCGTGCAA
GGAATTATGGAACGTTTATATACATCAGAAGACAAAGGTCTTAGTGGCAATAGACAGGAC
GTTGAGCATCGCCGTGAGACATTTGGTTCAAACGTTATTCCACCTAAACCACCGAAGACA
TTTTTCCAACTCGTATGCGAAGCCATTCAAGACATTACACTGATTATTTTGATTATATCC
GCAGTCATCTCGCTTTTACTGTCATTTTATCAACCAAAAGATGATTCAGGCGATGCTGCT
ATCGTGGAAGAAGATGAGCATCACGGCTGGATAGAAGGTTTCGCAATTTTAGTATCAGTT
ATCGTTGTTGTTATTGTTACAGCATTTAATGACTACTCCAAAGAGCGACAATTTCGCGGT
TTACAATCGCGTATTGAAGGTGAACATAAATTTTCCGTCATACGTAATGGCGAAGCGATA
CAAATTTTGGTCGGTGATATTGTTGTTGGTGATATTTGTCAAATCAAATATGGTGATCTG
CTGCCAGCGGATGGTATTTTAATTCAAAGCAATGACTTGAAGATTGATGAATCATCACTA
ACGGGTGAATCAGATCATGTAAAGAAAGGTGAAACAGTTGATCCAATGGTGTTATCAGGT
ACACATGTGATGGAAGGTAGCGGTAAAATAGTTGTCACTGCAGTTGGTGTCAATTCGCAA
GCTGGTATCATTTTCACATTACTTGGTGCCGCTGTTGATGAACAAGAACAGGCGATTAAG
AAAATGAAAAAGG

>g16778.t4 Gene=g16778 Length=284
MATINGRPAKYRITLKELRELMEHRGHEGIQRVSDYGGVQGIMERLYTSEDKGLSGNRQD
VEHRRETFGSNVIPPKPPKTFFQLVCEAIQDITLIILIISAVISLLLSFYQPKDDSGDAA
IVEEDEHHGWIEGFAILVSVIVVVIVTAFNDYSKERQFRGLQSRIEGEHKFSVIRNGEAI
QILVGDIVVGDICQIKYGDLLPADGILIQSNDLKIDESSLTGESDHVKKGETVDPMVLSG
THVMEGSGKIVVTAVGVNSQAGIIFTLLGAAVDEQEQAIKKMKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g16778.t4 Gene3D G3DSA:2.70.150.10 - 47 271 3.4E-44
8 g16778.t4 Gene3D G3DSA:1.20.1110.10 - 87 282 3.4E-44
3 g16778.t4 PANTHER PTHR24093:SF435 PLASMA MEMBRANE CALCIUM-TRANSPORTING ATPASE 4 12 275 5.2E-131
4 g16778.t4 PANTHER PTHR24093 CATION TRANSPORTING ATPASE 12 275 5.2E-131
2 g16778.t4 Pfam PF00690 Cation transporter/ATPase, N-terminus 37 104 4.8E-15
1 g16778.t4 Pfam PF00122 E1-E2 ATPase 169 282 6.4E-26
9 g16778.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 91 -
12 g16778.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 92 110 -
11 g16778.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 111 129 -
13 g16778.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 130 149 -
10 g16778.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 150 284 -
16 g16778.t4 SMART SM00831 Cation_ATPase_N_a_2 35 109 2.8E-7
5 g16778.t4 SUPERFAMILY SSF81665 Calcium ATPase, transmembrane domain M 37 167 6.28E-26
6 g16778.t4 SUPERFAMILY SSF81653 Calcium ATPase, transduction domain A 170 267 1.7E-26
17 g16778.t4 TIGRFAM TIGR01494 ATPase_P-type: HAD ATPase, P-type, family IC 136 257 7.4E-20
14 g16778.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 92 110 -
15 g16778.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 130 149 -

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:0070588 calcium ion transmembrane transport BP
GO:0005524 ATP binding MF
GO:0005388 P-type calcium transporter activity MF
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.

Raw TPM values