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.t5 isoform g3059.t5 22371708 22377400
chr_3 g3059 g3059.t5 exon g3059.t5.exon1 22371708 22372381
chr_3 g3059 g3059.t5 cds g3059.t5.CDS1 22371710 22372381
chr_3 g3059 g3059.t5 exon g3059.t5.exon2 22372448 22373836
chr_3 g3059 g3059.t5 cds g3059.t5.CDS2 22372448 22373836
chr_3 g3059 g3059.t5 exon g3059.t5.exon3 22373935 22374036
chr_3 g3059 g3059.t5 cds g3059.t5.CDS3 22373935 22374036
chr_3 g3059 g3059.t5 exon g3059.t5.exon4 22375071 22375171
chr_3 g3059 g3059.t5 cds g3059.t5.CDS4 22375071 22375171
chr_3 g3059 g3059.t5 exon g3059.t5.exon5 22377283 22377400
chr_3 g3059 g3059.t5 cds g3059.t5.CDS5 22377283 22377400
chr_3 g3059 g3059.t5 TSS g3059.t5 22378056 22378056
chr_3 g3059 g3059.t5 TTS g3059.t5 NA NA

Sequences

>g3059.t5 Gene=g3059 Length=2384
ATGGAGGACGCCCATTGCAAGACATCCGACGAGGTGTTAAAGTACTTCGGCACAAATGAA
GAATTAGGATTAACGCCAGATCAAGTCAAACAATATCAGGCTAAATACGGACCTAATGAA
CTTCCAGCCGAGGAAGGCAAAACAATATGGCAATTAGTACTTGAACAGTTTGACGATCTT
TTAGTTAAAATTTTGTTATTGGCTGCTATTATTTCATTTGTATTAGCTCTTTTTGAAGAA
CATGAGGGTATTGAAGCATTCGTAGAACCATTTGTAATTTTACTTATTTTAATTGCTAAT
GCTGTTGTTGGTGTTTGGCAAGAACGAAATGCAGAGTCAGCAATTGAAGCCCTCAAAGAA
TATGAACCCGAAATGGGTAAAGTCGTTCGTCAGGATAAGTCCGGAGTACAAAAACTCCGT
GCCAAAGAGATTGTACCAGGTGATATCGTTGAAGTGTCAGTCGGTGACAAAATTCCAGCT
GATATTCGTTTAATTAAGATCTACTCAACGACAATTCGTATTGATCAATCTATCTTGACT
GGTGAATCAGTTTCAGTCATTAAACACACTGATGCTGTCCCAGATCCACGCGCTGTCAAC
CAAGATAAGAAAAATATTTTGTTCTCAGGAACTAATGTTGCCGCTGGTAAGGCACGTGGT
ATCGTTATTGGAACTGGCCTTAACACTGCTATCGGTAAAATTCGTACTGAAATGTCAGAA
ACTGAAGAAATTAAGACACCATTGCAACAAAAATTGGATGAATTCGGTGAACAATTGTCA
AAGGTCATTTCAATCATTTGCGTTGCTGTCTGGGCTATCAACATTGGTCACTTTAACGAT
CCAGCTCATGGTGGTTCATGGATTAAGGGAGCTATCTATTATTTCAAGATTGCTGTCGCT
TTGGCTGTCGCTGCTATTCCAGAAGGTTTACCAGCTGTTATTACCACTTGTTTGGCTTTG
GGTACTCGTCGTATGGCCAAGAAGAACGCTATTGTCCGCTCATTGCCATCAGTTGAAACT
CTCGGTTGCACATCTGTCATTTGCTCAGATAAGACTGGTACATTGACAACAAATCAAATG
TCAGTTGCTCGCGCATTCGTTTTTGAAAAGGTTGAAGGAAATGATAGCAGTTTCACAGAA
TTCGAAATTACTGGATCAACATACGAACCAGTTGGTGATCTTTTCTACAAAGGTTCAAAG
GCAAAGGCATCAGATTATGAAGTACTCCAAGAACTCGCTACCATTTGCGTCATGTGTAAC
GACTCTGCTATTGATTTCAACGAAGTTAAGCAAGTTTTCGAGAAAGTCGGTGAAGCCACT
GAAACTGCACTTATTGTTCTTGCCGAAAAATTGAACCCATTCTCAGTTCCAAAGACCGGT
TTGGATCGTCGTTCAGCTGCTATTGTCGTTCGTCAGGAAATTGAGACTAAATGGAAGAAA
GAATTTACACTTGAATTCTCACGTGATCGTAAATCAATGTCATCATACTGCACACCACTT
AAATCATCAAAACTCGGAACTGGACCAAAAATGTTCTGCAAAGGTGCTCCAGAAGGTGTT
TTGGATCGTTGCACACATGCTCGCGTTGGCACAAGCAAAGTCCCACTTACATCAACACTC
AAACAACGCATTTTGGATCTCACTCGTCAATACGGTACCGGTCGTGACACACTTCGTTGC
CTTGCTTTGGCCACTGGCGATTCTCCAATGAAACCAGAAGACATGGATCTTAATGATTCA
ACCAAATTCTATACTTATGAAATTAATCTTACATTCGTTGGTGTGGTAGGAATGTTGGAT
CCACCACGTAAAGAAGTCTTTGATTCAATTGTTCGCTGTCGTGCTGCTGGTATTCGTGTT
ATTGTCATTACTGGTGACAACAAGGCCACTGCTGAAGCTATTTGCCGTCGTATTGGAGTT
TTCGGTGAAGATGAAGACACAACTGGAAAATCATACTCAGGTCGTGAATTTGATGACTTG
CCAGTTCATGAACAAAAACAAGCTTGCGCTCGTGCTCGTCTCTTCTCACGTGTAGAGCCA
GCTCACAAGTCAAAGATTGTCGAATATTTGCAAAGCATGAATGAAATCTCAGCTATGACA
GGTGATGGTGTCAATGACGCTCCTGCTTTGAAAAAGGCTGAAATTGGTATTGCTATGGGT
TCTGGTACTGCTGTCGCTAAATCTGCTTCAGAAATGGTTCTCGCTGACGATAACTTCTCA
TCAATTGTCGCTGCCGTTGAAGAAGGTCGTGCCATTTACAACAACATGAAACAATTCATT
CGTTATCTCATTTCATCAAACATTGGTGAGGTTGTCTCAATTTTCTTGACTGCTGCTCTT
GGCTTACCAGAAGCTCTCATTCCCGTTCAATTGTTGTGGGTCAA

>g3059.t5 Gene=g3059 Length=794
MEDAHCKTSDEVLKYFGTNEELGLTPDQVKQYQAKYGPNELPAEEGKTIWQLVLEQFDDL
LVKILLLAAIISFVLALFEEHEGIEAFVEPFVILLILIANAVVGVWQERNAESAIEALKE
YEPEMGKVVRQDKSGVQKLRAKEIVPGDIVEVSVGDKIPADIRLIKIYSTTIRIDQSILT
GESVSVIKHTDAVPDPRAVNQDKKNILFSGTNVAAGKARGIVIGTGLNTAIGKIRTEMSE
TEEIKTPLQQKLDEFGEQLSKVISIICVAVWAINIGHFNDPAHGGSWIKGAIYYFKIAVA
LAVAAIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICSDKTGTLTTNQM
SVARAFVFEKVEGNDSSFTEFEITGSTYEPVGDLFYKGSKAKASDYEVLQELATICVMCN
DSAIDFNEVKQVFEKVGEATETALIVLAEKLNPFSVPKTGLDRRSAAIVVRQEIETKWKK
EFTLEFSRDRKSMSSYCTPLKSSKLGTGPKMFCKGAPEGVLDRCTHARVGTSKVPLTSTL
KQRILDLTRQYGTGRDTLRCLALATGDSPMKPEDMDLNDSTKFYTYEINLTFVGVVGMLD
PPRKEVFDSIVRCRAAGIRVIVITGDNKATAEAICRRIGVFGEDEDTTGKSYSGREFDDL
PVHEQKQACARARLFSRVEPAHKSKIVEYLQSMNEISAMTGDGVNDAPALKKAEIGIAMG
SGTAVAKSASEMVLADDNFSSIVAAVEEGRAIYNNMKQFIRYLISSNIGEVVSIFLTAAL
GLPEALIPVQLLWV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
32 g3059.t5 CDD cd02083 P-type_ATPase_SERCA 5 794 0.0
19 g3059.t5 Gene3D G3DSA:2.70.150.10 - 16 241 0.0
20 g3059.t5 Gene3D G3DSA:1.20.1110.10 - 54 794 0.0
17 g3059.t5 Gene3D G3DSA:3.40.50.1000 - 345 744 0.0
18 g3059.t5 Gene3D G3DSA:3.40.1110.10 - 358 601 0.0
5 g3059.t5 PANTHER PTHR42861:SF18 SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 2 2 794 0.0
6 g3059.t5 PANTHER PTHR42861 CALCIUM-TRANSPORTING ATPASE 2 794 0.0
9 g3059.t5 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 175 189 4.7E-42
10 g3059.t5 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 348 362 4.7E-42
12 g3059.t5 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 594 605 4.7E-42
11 g3059.t5 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 616 626 4.7E-42
7 g3059.t5 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 700 719 4.7E-42
8 g3059.t5 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 723 735 4.7E-42
4 g3059.t5 Pfam PF00690 Cation transporter/ATPase, N-terminus 6 72 5.8E-19
1 g3059.t5 Pfam PF00122 E1-E2 ATPase 122 328 1.2E-52
3 g3059.t5 Pfam PF13246 Cation transport ATPase (P-type) 418 526 4.4E-19
2 g3059.t5 Pfam PF08282 haloacid dehalogenase-like hydrolase 685 743 1.4E-5
21 g3059.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 59 -
28 g3059.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 60 78 -
26 g3059.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 79 83 -
30 g3059.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 84 106 -
22 g3059.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 107 258 -
27 g3059.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 259 279 -
25 g3059.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 280 290 -
29 g3059.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 291 320 -
23 g3059.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 321 758 -
31 g3059.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 759 782 -
24 g3059.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 783 794 -
39 g3059.t5 ProSitePatterns PS00154 E1-E2 ATPases phosphorylation site. 350 356 -
44 g3059.t5 SFLD SFLDF00027 p-type atpase 329 752 0.0
45 g3059.t5 SFLD SFLDG00002 C1.7: P-type atpase like 329 752 0.0
38 g3059.t5 SMART SM00831 Cation_ATPase_N_a_2 3 77 1.2E-19
14 g3059.t5 SUPERFAMILY SSF81665 Calcium ATPase, transmembrane domain M 1 794 5.89E-91
15 g3059.t5 SUPERFAMILY SSF81653 Calcium ATPase, transduction domain A 131 235 3.53E-27
13 g3059.t5 SUPERFAMILY SSF81660 Metal cation-transporting ATPase, ATP-binding domain N 355 598 2.88E-62
16 g3059.t5 SUPERFAMILY SSF56784 HAD-like 584 748 3.69E-44
43 g3059.t5 TIGRFAM TIGR01116 ATPase-IIA1_Ca: calcium-translocating P-type ATPase, SERCA-type 53 794 1.9E-276
42 g3059.t5 TIGRFAM TIGR01494 ATPase_P-type: HAD ATPase, P-type, family IC 92 203 2.1E-18
41 g3059.t5 TIGRFAM TIGR01494 ATPase_P-type: HAD ATPase, P-type, family IC 225 371 2.1E-26
40 g3059.t5 TIGRFAM TIGR01494 ATPase_P-type: HAD ATPase, P-type, family IC 668 785 8.0E-34
37 g3059.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 60 77 -
34 g3059.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 87 106 -
36 g3059.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 259 278 -
33 g3059.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 298 320 -
35 g3059.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 759 781 -

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:0005388 P-type calcium transporter activity MF
GO:0000166 nucleotide binding MF
GO:0016021 integral component of membrane CC
GO:0006816 calcium ion transport BP

KEGG

Orthology

Pathway

This gene does not belong to any 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. There were no conditions that were differentially expressed