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.t9 isoform g3059.t9 22372707 22380788
chr_3 g3059 g3059.t9 exon g3059.t9.exon1 22372707 22373836
chr_3 g3059 g3059.t9 cds g3059.t9.CDS1 22372709 22373836
chr_3 g3059 g3059.t9 exon g3059.t9.exon2 22373935 22374036
chr_3 g3059 g3059.t9 cds g3059.t9.CDS2 22373935 22374036
chr_3 g3059 g3059.t9 exon g3059.t9.exon3 22375071 22375171
chr_3 g3059 g3059.t9 cds g3059.t9.CDS3 22375071 22375171
chr_3 g3059 g3059.t9 exon g3059.t9.exon4 22377283 22377454
chr_3 g3059 g3059.t9 cds g3059.t9.CDS4 22377283 22377400
chr_3 g3059 g3059.t9 exon g3059.t9.exon5 22380704 22380788
chr_3 g3059 g3059.t9 TSS g3059.t9 22380898 22380898
chr_3 g3059 g3059.t9 TTS g3059.t9 NA NA

Sequences

>g3059.t9 Gene=g3059 Length=1590
TTTTTTCTCCTCGTGAAGTGTGTAGTTTATTTAATGTCAATCGATAATAAGTGAGAAATA
AAAAATTATTTAAAGTCAGATAATTAATAATTGAATCTTAGATTATACGACACAATAAAT
TAATAATCAAGTCTCAATAATGGAGGACGCCCATTGCAAGACATCCGACGAGGTGTTAAA
GTACTTCGGCACAAATGAAGAATTAGGATTAACGCCAGATCAAGTCAAACAATATCAGGC
TAAATACGGACCTAATGAACTTCCAGCCGAGGAAGGCAAAACAATATGGCAATTAGTACT
TGAACAGTTTGACGATCTTTTAGTTAAAATTTTGTTATTGGCTGCTATTATTTCATTTGT
ATTAGCTCTTTTTGAAGAACATGAGGGTATTGAAGCATTCGTAGAACCATTTGTAATTTT
ACTTATTTTAATTGCTAATGCTGTTGTTGGTGTTTGGCAAGAACGAAATGCAGAGTCAGC
AATTGAAGCCCTCAAAGAATATGAACCCGAAATGGGTAAAGTCGTTCGTCAGGATAAGTC
CGGAGTACAAAAACTCCGTGCCAAAGAGATTGTACCAGGTGATATCGTTGAAGTGTCAGT
CGGTGACAAAATTCCAGCTGATATTCGTTTAATTAAGATCTACTCAACGACAATTCGTAT
TGATCAATCTATCTTGACTGGTGAATCAGTTTCAGTCATTAAACACACTGATGCTGTCCC
AGATCCACGCGCTGTCAACCAAGATAAGAAAAATATTTTGTTCTCAGGAACTAATGTTGC
CGCTGGTAAGGCACGTGGTATCGTTATTGGAACTGGCCTTAACACTGCTATCGGTAAAAT
TCGTACTGAAATGTCAGAAACTGAAGAAATTAAGACACCATTGCAACAAAAATTGGATGA
ATTCGGTGAACAATTGTCAAAGGTCATTTCAATCATTTGCGTTGCTGTCTGGGCTATCAA
CATTGGTCACTTTAACGATCCAGCTCATGGTGGTTCATGGATTAAGGGAGCTATCTATTA
TTTCAAGATTGCTGTCGCTTTGGCTGTCGCTGCTATTCCAGAAGGTTTACCAGCTGTTAT
TACCACTTGTTTGGCTTTGGGTACTCGTCGTATGGCCAAGAAGAACGCTATTGTCCGCTC
ATTGCCATCAGTTGAAACTCTCGGTTGCACATCTGTCATTTGCTCAGATAAGACTGGTAC
ATTGACAACAAATCAAATGTCAGTTGCTCGCGCATTCGTTTTTGAAAAGGTTGAAGGAAA
TGATAGCAGTTTCACAGAATTCGAAATTACTGGATCAACATACGAACCAGTTGGTGATCT
TTTCTACAAAGGTTCAAAGGCAAAGGCATCAGATTATGAAGTACTCCAAGAACTCGCTAC
CATTTGCGTCATGTGTAACGACTCTGCTATTGATTTCAACGAAGTTAAGCAAGTTTTCGA
GAAAGTCGGTGAAGCCACTGAAACTGCACTTATTGTTCTTGCCGAAAAATTGAACCCATT
CTCAGTTCCAAAGACCGGTTTGGATCGTCGTTCAGCTGCTATTGTCGTTCGTCAGGAAAT
TGAGACTAAATGGAAGAAAGAATTTACACT

>g3059.t9 Gene=g3059 Length=483
MEDAHCKTSDEVLKYFGTNEELGLTPDQVKQYQAKYGPNELPAEEGKTIWQLVLEQFDDL
LVKILLLAAIISFVLALFEEHEGIEAFVEPFVILLILIANAVVGVWQERNAESAIEALKE
YEPEMGKVVRQDKSGVQKLRAKEIVPGDIVEVSVGDKIPADIRLIKIYSTTIRIDQSILT
GESVSVIKHTDAVPDPRAVNQDKKNILFSGTNVAAGKARGIVIGTGLNTAIGKIRTEMSE
TEEIKTPLQQKLDEFGEQLSKVISIICVAVWAINIGHFNDPAHGGSWIKGAIYYFKIAVA
LAVAAIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICSDKTGTLTTNQM
SVARAFVFEKVEGNDSSFTEFEITGSTYEPVGDLFYKGSKAKASDYEVLQELATICVMCN
DSAIDFNEVKQVFEKVGEATETALIVLAEKLNPFSVPKTGLDRRSAAIVVRQEIETKWKK
EFT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g3059.t9 Gene3D G3DSA:2.70.150.10 - 1 64 1.0E-11
13 g3059.t9 Gene3D G3DSA:2.70.150.10 - 97 219 1.2E-41
14 g3059.t9 Gene3D G3DSA:1.20.1110.10 - 220 369 7.9E-48
11 g3059.t9 Gene3D G3DSA:3.40.1110.10 - 379 483 2.9E-6
4 g3059.t9 PANTHER PTHR42861:SF18 SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 2 2 483 3.4E-227
5 g3059.t9 PANTHER PTHR42861 CALCIUM-TRANSPORTING ATPASE 2 483 3.4E-227
6 g3059.t9 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 175 189 2.6E-10
7 g3059.t9 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 348 362 2.6E-10
3 g3059.t9 Pfam PF00690 Cation transporter/ATPase, N-terminus 6 72 2.9E-19
1 g3059.t9 Pfam PF00122 E1-E2 ATPase 122 328 4.3E-53
2 g3059.t9 Pfam PF13246 Cation transport ATPase (P-type) 418 464 4.9E-5
16 g3059.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 59 -
21 g3059.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 60 78 -
19 g3059.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 79 83 -
23 g3059.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 84 106 -
17 g3059.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 107 258 -
20 g3059.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 259 279 -
18 g3059.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 280 290 -
22 g3059.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 291 320 -
15 g3059.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 321 483 -
28 g3059.t9 ProSitePatterns PS00154 E1-E2 ATPases phosphorylation site. 350 356 -
29 g3059.t9 SMART SM00831 Cation_ATPase_N_a_2 3 77 1.2E-19
9 g3059.t9 SUPERFAMILY SSF81665 Calcium ATPase, transmembrane domain M 1 342 5.62E-73
10 g3059.t9 SUPERFAMILY SSF81653 Calcium ATPase, transduction domain A 131 235 1.57E-27
8 g3059.t9 SUPERFAMILY SSF81660 Metal cation-transporting ATPase, ATP-binding domain N 355 482 1.42E-23
30 g3059.t9 TIGRFAM TIGR01494 ATPase_P-type: HAD ATPase, P-type, family IC 92 202 1.1E-18
31 g3059.t9 TIGRFAM TIGR01494 ATPase_P-type: HAD ATPase, P-type, family IC 225 371 9.0E-27
27 g3059.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 60 77 -
25 g3059.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 87 106 -
26 g3059.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 259 278 -
24 g3059.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 298 320 -

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:0000166 nucleotide binding MF
GO:0016021 integral component of membrane CC

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