Gene loci information

Transcript annotation

  • This transcript has been annotated as Plasma membrane calcium-transporting ATPase 3.

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.t2 TSS g16778.t2 10988236 10988236
chr_4 g16778 g16778.t2 isoform g16778.t2 10988935 11008078
chr_4 g16778 g16778.t2 exon g16778.t2.exon1 10988935 10989292
chr_4 g16778 g16778.t2 cds g16778.t2.CDS1 10988935 10989292
chr_4 g16778 g16778.t2 exon g16778.t2.exon2 10989665 10989948
chr_4 g16778 g16778.t2 cds g16778.t2.CDS2 10989665 10989948
chr_4 g16778 g16778.t2 exon g16778.t2.exon3 10990010 10990220
chr_4 g16778 g16778.t2 cds g16778.t2.CDS3 10990010 10990220
chr_4 g16778 g16778.t2 exon g16778.t2.exon4 10995265 10995698
chr_4 g16778 g16778.t2 cds g16778.t2.CDS4 10995265 10995698
chr_4 g16778 g16778.t2 exon g16778.t2.exon5 10995775 10996017
chr_4 g16778 g16778.t2 cds g16778.t2.CDS5 10995775 10996017
chr_4 g16778 g16778.t2 exon g16778.t2.exon6 10996078 10996319
chr_4 g16778 g16778.t2 cds g16778.t2.CDS6 10996078 10996319
chr_4 g16778 g16778.t2 exon g16778.t2.exon7 10996380 10996836
chr_4 g16778 g16778.t2 cds g16778.t2.CDS7 10996380 10996836
chr_4 g16778 g16778.t2 exon g16778.t2.exon8 10996899 10996986
chr_4 g16778 g16778.t2 cds g16778.t2.CDS8 10996899 10996986
chr_4 g16778 g16778.t2 exon g16778.t2.exon9 10997045 10997769
chr_4 g16778 g16778.t2 cds g16778.t2.CDS9 10997045 10997769
chr_4 g16778 g16778.t2 exon g16778.t2.exon10 10997831 10997982
chr_4 g16778 g16778.t2 cds g16778.t2.CDS10 10997831 10997982
chr_4 g16778 g16778.t2 exon g16778.t2.exon11 10998326 10998470
chr_4 g16778 g16778.t2 cds g16778.t2.CDS11 10998326 10998470
chr_4 g16778 g16778.t2 exon g16778.t2.exon12 11007794 11008078
chr_4 g16778 g16778.t2 cds g16778.t2.CDS12 11007794 11008078
chr_4 g16778 g16778.t2 TTS g16778.t2 NA NA

Sequences

>g16778.t2 Gene=g16778 Length=3624
ATGGCAACAATAAACGGTCGACCAGCGAAGTATCGCATAACGCTAAAAGAGCTTCGTGAA
TTGATGGAACATCGAGGACATGAAGGAATTCAAAGAGTATCAGATTATGGTGGCGTGCAA
GGAATTATGGAACGTTTATATACATCAGAAGACAAAGGTCTTAGTGGCAATAGACAGGAC
GTTGAGCATCGCCGTGAGACATTTGGTTCAAACGTTATTCCACCTAAACCACCGAAGACA
TTTTTCCAACTCGTATGCGAAGCCATTCAAGACATTACACTGATTATTTTGATTATATCC
GCAGTCATCTCGCTTTTACTGTCATTTTATCAACCAAAAGATGATTCAGGCGATGCTGCT
ATCGTGGAAGAAGATGAGCATCACGGCTGGATAGAAGGTTTCGCAATTTTAGTATCAGTT
ATCGTTGTTGTTATTGTTACAGCATTTAATGACTACTCCAAAGAGCGACAATTTCGCGGT
TTACAATCGCGTATTGAAGGTGAACATAAATTTTCCGTCATACGTAATGGCGAAGCGATA
CAAATTTTGGTCGGTGATATTGTTGTTGGTGATATTTGTCAAATCAAATATGGTGATCTG
CTGCCAGCGGATGGTATTTTAATTCAAAGCAATGACTTGAAGATTGATGAATCATCACTA
ACGGGTGAATCAGATCATGTAAAGAAAGGTGAAACAGTTGATCCAATGGTGTTATCAGGT
ACACATGTGATGGAAGGTAGCGGTAAAATAGTTGTCACTGCAGTTGGTGTCAATTCGCAA
GCTGGTATCATTTTCACATTACTTGGTGCCGCTGTTGATGAACAAGAACAGGCGATTAAG
AAAATGAAAAAGGGCGAACAAGGTCAGGTGACATCAAATAGTCACATTACTCATGATAAT
AATGGCACAGGCAATGATTTAGAGGCCTTCCATGGTCACTATGCTGCAAAGAATCCTGAA
GCAACAACTGAACGTGCCGCTACACCAAATCGTGATGAAGTACCATCAGGTGGTGGTCAT
AAGAAAGAAAAGAGTGTATTGCAAGCAAAACTTACAAAGCTTGCCATTCAAATCGGTTAT
GCTGGCTCCACAATTGCTGTGTTAACAGTTGCTATTTTAGTTATACAATTCTGCGTAACC
AAATTCGTCATAGAAAATAGCCCATGGAAGAGTATTTACTTCAATGATTTAGTCAAACAT
TTTATTATCGGTGTCACTGTGCTTGTAGTTGCAGTGCCCGAAGGCTTACCATTAGCTGTT
ACATTATCACTCGCTTATTCTGTAAAGAAAATGATGAAGGATAACAATTTGGTGCGTCAT
TTGGACGCTTGCGAAACGATGGGTAATGCCACTGCCATTTGTAGCGATAAGACTGGTACA
TTAACCACAAACCGCATGACGGTCGTACAATCATACATTTGCGAGAAACTCATGAAGGTT
ACACCGAAATTTTCTGACATACCAAATGAGGTTGGTCCGAAAATTATTGAGGGCATCAGC
GTCAATTCGGCCTATACGTCACAACTTATGCCTGGCCCAAATCCTGGTGACCTTCCAATG
CAAGTTGGTAACAAGACCGAGTGCGCACTTCTCGGCTTTGTTGAAGGTCTTGGCAAAAGT
TATCAGCAAATTCGTGAAAGAATTCCTGAAAAGGCTTTTGTGCGTGTCTATACTTTCAAT
TCAGACCGTAAATCAATGAGTACAGTAATTGCTTTGCCCAATGGTGGCTATCGATTGTAC
ACCAAGGGCGCTTCTGAAATTATTCTTAAAAAATGCGCCTTCATTTATGGTCATGAAGGA
CGTCTTGAGAAATTTACACGTGACATGCAAGAACGTCTGCTGCATCAAGTGATTGAACCA
ATGGCTTGTGATGGTCTACGTACCATTTCAATTGCTTATCGTGACTTTGTTCGTGGTGCC
GGTAAAGCGGGCATAAATGAAGTGCATCTTGGGCCAAACGATGAGCCCAATTGGGAAGAT
GAGGCAAATACGGTTAACAACCTCACGTGCTTGTGTGTCGTTGGCATTGAGGATCCGGTT
CGTCCTGAAGTGCCCGATGCTATTCGAAAGTGCCAGAAGGCCGGTATAACTGTACGAATG
GTCACTGGTGATAATATAAATACAGCTCGATCAATTGCTACAAAATGTGGCATTTTAAGA
CCGCAAGATGATTTCTTAATTCTTGAAGGCAAAGAATTTAATCGTAGAATTCGAGATAGT
AATGGAGATATTCAACAACATTTATTGGATAAAGTTTGGCCTAAACTTCGTGTATTGGCA
CGTTCATCACCAACTGATAAATACAATTTAGTCAAAGGTATAATTGATAGCAAGATAAAT
GAAAGTCGTGAAGTAGTGGCGGTAACAGGTGATGGTACCAATGATGGTCCTGCATTGAAG
AAAGCAGATGTTGGTTTTGCTATGGGTATTGCAGGCACAGATGTTGCTAAAGAAGCATCT
GACATTATTTTGACTGACGATAATTTCTCGTCAATCGTGAAAGCAGTCATGTGGGGTCGT
AATGTTTATGACTCAATTGCCAAGTTCTTACAATTTCAATTGACCGTTAATGTTGTCGCT
GTCATTGTTGCATTCATCGGTGCATGTGCTGTACAAGATTCACCACTTAAAGCAGTACAA
ATGTTATGGGTGAATCTTATTATGGACACACTCGCGTCGTTAGCCTTAGCCACGGAAATG
CCAACACCAGATTTACTCCTGCGTAAACCCTATGGTCGTACGAAGCCGCTTATATCGCGC
ACGATGATGAAAAATATTCTTGGTCAAGCATTGTATCAGTTGATCGTTATTTTTGGCCTC
CTTTTCGCTGGTGAACGTCTTTTTGACATTGAATCAGGTCGTGGTGCAGAACTTCATGCT
GAACCATCACAGCACTTTACCATTATCTTTAATACTTTTGTGCTAATGACGCTTTTCAAT
GAGCTCAATGCACGTAAAATTCACGGACAGAGAAACATTTTCCAAGGAATTTTCACAAAT
CCAATTTTCTATTCCATTTGGATTATTACTTGGGTGTCACAAGTCATCATCATTCAATAT
GGCAAAATGGCATTCTCAACAAAAGCTTTAACTCTCGAACAATGGCTCTGGTGCTTATTT
TTCGGCATGGGCACACTAATATGGGGTCAAATTGTTACAACAATTCCAACACGTAAATTA
CCGAAAATATTATCTTGGGGTCGCGGTCATCCAGAAGAATACACGGAAGCTATCAATCTT
GGTGGAGATGATTCACGTTATGATCCAATGGATGATAATAAAAAACCACGTGCCGGTCAA
ATTCTTTGGATTCGCGGTCTAACACGACTTCAGACTCAGTTACGAGTAATTCGTGCGTTC
AAGTCAACATTGGAAGATTTGGAAGATCGTCGTTCAATTCATAGTTTGAGAAGTTTGCGA
AACATGCATGTCGCACAGACACCTGTAACAGCATCGTTACTTTATGCCAACAGACAATTC
CTCAGAGGTCTCAATCGTGATCAATCACCACCAGCAAGCATAACCATTCAAGTACCAACA
TCACCAATCAACATCAATGAAATGAATGCGCGCTATATTGATGACGATGGTCCCGATGAC
CGATCGAGTGAAACTCGCATTTGA

>g16778.t2 Gene=g16778 Length=1207
MATINGRPAKYRITLKELRELMEHRGHEGIQRVSDYGGVQGIMERLYTSEDKGLSGNRQD
VEHRRETFGSNVIPPKPPKTFFQLVCEAIQDITLIILIISAVISLLLSFYQPKDDSGDAA
IVEEDEHHGWIEGFAILVSVIVVVIVTAFNDYSKERQFRGLQSRIEGEHKFSVIRNGEAI
QILVGDIVVGDICQIKYGDLLPADGILIQSNDLKIDESSLTGESDHVKKGETVDPMVLSG
THVMEGSGKIVVTAVGVNSQAGIIFTLLGAAVDEQEQAIKKMKKGEQGQVTSNSHITHDN
NGTGNDLEAFHGHYAAKNPEATTERAATPNRDEVPSGGGHKKEKSVLQAKLTKLAIQIGY
AGSTIAVLTVAILVIQFCVTKFVIENSPWKSIYFNDLVKHFIIGVTVLVVAVPEGLPLAV
TLSLAYSVKKMMKDNNLVRHLDACETMGNATAICSDKTGTLTTNRMTVVQSYICEKLMKV
TPKFSDIPNEVGPKIIEGISVNSAYTSQLMPGPNPGDLPMQVGNKTECALLGFVEGLGKS
YQQIRERIPEKAFVRVYTFNSDRKSMSTVIALPNGGYRLYTKGASEIILKKCAFIYGHEG
RLEKFTRDMQERLLHQVIEPMACDGLRTISIAYRDFVRGAGKAGINEVHLGPNDEPNWED
EANTVNNLTCLCVVGIEDPVRPEVPDAIRKCQKAGITVRMVTGDNINTARSIATKCGILR
PQDDFLILEGKEFNRRIRDSNGDIQQHLLDKVWPKLRVLARSSPTDKYNLVKGIIDSKIN
ESREVVAVTGDGTNDGPALKKADVGFAMGIAGTDVAKEASDIILTDDNFSSIVKAVMWGR
NVYDSIAKFLQFQLTVNVVAVIVAFIGACAVQDSPLKAVQMLWVNLIMDTLASLALATEM
PTPDLLLRKPYGRTKPLISRTMMKNILGQALYQLIVIFGLLFAGERLFDIESGRGAELHA
EPSQHFTIIFNTFVLMTLFNELNARKIHGQRNIFQGIFTNPIFYSIWIITWVSQVIIIQY
GKMAFSTKALTLEQWLWCLFFGMGTLIWGQIVTTIPTRKLPKILSWGRGHPEEYTEAINL
GGDDSRYDPMDDNKKPRAGQILWIRGLTRLQTQLRVIRAFKSTLEDLEDRRSIHSLRSLR
NMHVAQTPVTASLLYANRQFLRGLNRDQSPPASITIQVPTSPININEMNARYIDDDGPDD
RSSETRI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
47 g16778.t2 CDD cd02081 P-type_ATPase_Ca_PMCA-like 61 922 0.0
25 g16778.t2 Coils Coil Coil 1110 1130 -
22 g16778.t2 Gene3D G3DSA:2.70.150.10 - 143 269 2.1E-28
24 g16778.t2 Gene3D G3DSA:1.20.1110.10 - 336 485 8.5E-39
21 g16778.t2 Gene3D G3DSA:3.40.1110.10 - 503 659 4.5E-15
20 g16778.t2 Gene3D G3DSA:3.40.50.1000 - 674 805 1.1E-5
23 g16778.t2 Gene3D G3DSA:1.20.1110.10 - 806 1060 5.0E-76
60 g16778.t2 MobiDBLite mobidb-lite consensus disorder prediction 319 342 -
8 g16778.t2 PANTHER PTHR24093 CATION TRANSPORTING ATPASE 10 1069 0.0
9 g16778.t2 PANTHER PTHR24093:SF284 PLASMA MEMBRANE CALCIUM-TRANSPORTING ATPASE 3 10 1069 0.0
11 g16778.t2 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 216 230 1.4E-38
10 g16778.t2 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 454 468 1.4E-38
12 g16778.t2 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 672 683 1.4E-38
15 g16778.t2 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 694 704 1.4E-38
14 g16778.t2 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 789 808 1.4E-38
13 g16778.t2 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 813 825 1.4E-38
7 g16778.t2 Pfam PF00690 Cation transporter/ATPase, N-terminus 37 104 3.8E-14
4 g16778.t2 Pfam PF00122 E1-E2 ATPase 169 282 7.0E-25
3 g16778.t2 Pfam PF00122 E1-E2 ATPase 341 433 8.4E-9
6 g16778.t2 Pfam PF13246 Cation transport ATPase (P-type) 521 595 1.6E-20
5 g16778.t2 Pfam PF00702 haloacid dehalogenase-like hydrolase 658 803 3.7E-11
1 g16778.t2 Pfam PF00689 Cation transporting ATPase, C-terminus 874 1052 3.0E-43
2 g16778.t2 Pfam PF12424 Plasma membrane calcium transporter ATPase C terminal 1099 1138 2.3E-13
30 g16778.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 91 -
41 g16778.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 92 110 -
36 g16778.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 111 129 -
43 g16778.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 130 149 -
29 g16778.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 150 353 -
40 g16778.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 354 377 -
32 g16778.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 378 396 -
46 g16778.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 397 426 -
27 g16778.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 427 848 -
38 g16778.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 849 870 -
35 g16778.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 871 881 -
37 g16778.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 882 906 -
31 g16778.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 907 925 -
39 g16778.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 926 944 -
33 g16778.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 945 963 -
44 g16778.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 964 982 -
28 g16778.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 983 1001 -
42 g16778.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 1002 1022 -
34 g16778.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1023 1033 -
45 g16778.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 1034 1055 -
26 g16778.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1056 1207 -
59 g16778.t2 ProSitePatterns PS00154 E1-E2 ATPases phosphorylation site. 456 462 -
65 g16778.t2 SFLD SFLDF00027 p-type atpase 436 841 0.0
66 g16778.t2 SFLD SFLDG00002 C1.7: P-type atpase like 436 841 0.0
58 g16778.t2 SMART SM00831 Cation_ATPase_N_a_2 35 109 2.8E-7
17 g16778.t2 SUPERFAMILY SSF81665 Calcium ATPase, transmembrane domain M 37 1061 7.45E-121
18 g16778.t2 SUPERFAMILY SSF81653 Calcium ATPase, transduction domain A 170 267 1.83E-25
19 g16778.t2 SUPERFAMILY SSF56784 HAD-like 453 893 4.29E-51
16 g16778.t2 SUPERFAMILY SSF81660 Metal cation-transporting ATPase, ATP-binding domain N 460 684 2.83E-45
63 g16778.t2 TIGRFAM TIGR01494 ATPase_P-type: HAD ATPase, P-type, family IC 136 257 8.8E-19
64 g16778.t2 TIGRFAM TIGR01517 ATPase-IIB_Ca: calcium-translocating P-type ATPase, PMCA-type 341 950 4.4E-227
61 g16778.t2 TIGRFAM TIGR01494 ATPase_P-type: HAD ATPase, P-type, family IC 374 476 5.9E-23
62 g16778.t2 TIGRFAM TIGR01494 ATPase_P-type: HAD ATPase, P-type, family IC 755 869 1.0E-29
51 g16778.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 92 110 -
53 g16778.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 130 149 -
57 g16778.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 250 272 -
55 g16778.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 358 380 -
56 g16778.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 401 423 -
54 g16778.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 849 871 -
52 g16778.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 925 944 -
50 g16778.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 964 983 -
48 g16778.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 996 1018 -
49 g16778.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 1033 1052 -

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:0016020 membrane CC
GO:0005524 ATP binding MF
GO:0005388 P-type calcium transporter activity MF
GO:0000166 nucleotide binding MF
GO:0016021 integral component of membrane CC

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

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