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.t11 isoform g3059.t11 22372894 22380788
chr_3 g3059 g3059.t11 exon g3059.t11.exon1 22372894 22373836
chr_3 g3059 g3059.t11 cds g3059.t11.CDS1 22372895 22373785
chr_3 g3059 g3059.t11 exon g3059.t11.exon2 22373931 22374036
chr_3 g3059 g3059.t11 exon g3059.t11.exon3 22375071 22375171
chr_3 g3059 g3059.t11 exon g3059.t11.exon4 22377283 22377454
chr_3 g3059 g3059.t11 exon g3059.t11.exon5 22380704 22380788
chr_3 g3059 g3059.t11 TSS g3059.t11 22380898 22380898
chr_3 g3059 g3059.t11 TTS g3059.t11 NA NA

Sequences

>g3059.t11 Gene=g3059 Length=1407
TTTTTTCTCCTCGTGAAGTGTGTAGTTTATTTAATGTCAATCGATAATAAGTGAGAAATA
AAAAATTATTTAAAGTCAGATAATTAATAATTGAATCTTAGATTATACGACACAATAAAT
TAATAATCAAGTCTCAATAATGGAGGACGCCCATTGCAAGACATCCGACGAGGTGTTAAA
GTACTTCGGCACAAATGAAGAATTAGGATTAACGCCAGATCAAGTCAAACAATATCAGGC
TAAATACGGACCTAATGAACTTCCAGCCGAGGAAGGCAAAACAATATGGCAATTAGTACT
TGAACAGTTTGACGATCTTTTAGTTAAAATTTTGTTATTGGCTGCTATTATTTCATTTGT
ATTAGCTCTTTTTGAAGAACATGAGGGTATTGAAGCATTCGTAGAACCATTTGTAATTTT
ACTTATTTTAATTGCTAATGCTGTTGTTGGTGTTTGGCAAGTGAGAACGAAATGCAGAGT
CAGCAATTGAAGCCCTCAAAGAATATGAACCCGAAATGGGTAAAGTCGTTCGTCAGGATA
AGTCCGGAGTACAAAAACTCCGTGCCAAAGAGATTGTACCAGGTGATATCGTTGAAGTGT
CAGTCGGTGACAAAATTCCAGCTGATATTCGTTTAATTAAGATCTACTCAACGACAATTC
GTATTGATCAATCTATCTTGACTGGTGAATCAGTTTCAGTCATTAAACACACTGATGCTG
TCCCAGATCCACGCGCTGTCAACCAAGATAAGAAAAATATTTTGTTCTCAGGAACTAATG
TTGCCGCTGGTAAGGCACGTGGTATCGTTATTGGAACTGGCCTTAACACTGCTATCGGTA
AAATTCGTACTGAAATGTCAGAAACTGAAGAAATTAAGACACCATTGCAACAAAAATTGG
ATGAATTCGGTGAACAATTGTCAAAGGTCATTTCAATCATTTGCGTTGCTGTCTGGGCTA
TCAACATTGGTCACTTTAACGATCCAGCTCATGGTGGTTCATGGATTAAGGGAGCTATCT
ATTATTTCAAGATTGCTGTCGCTTTGGCTGTCGCTGCTATTCCAGAAGGTTTACCAGCTG
TTATTACCACTTGTTTGGCTTTGGGTACTCGTCGTATGGCCAAGAAGAACGCTATTGTCC
GCTCATTGCCATCAGTTGAAACTCTCGGTTGCACATCTGTCATTTGCTCAGATAAGACTG
GTACATTGACAACAAATCAAATGTCAGTTGCTCGCGCATTCGTTTTTGAAAAGGTTGAAG
GAAATGATAGCAGTTTCACAGAATTCGAAATTACTGGATCAACATACGAACCAGTTGGTG
ATCTTTTCTACAAAGGTTCAAAGGCAAAGGCATCAGATTATGAAGTACTCCAAGAACTCG
CTACCATTTGCGTCATGTGTAACGACT

>g3059.t11 Gene=g3059 Length=297
MGKVVRQDKSGVQKLRAKEIVPGDIVEVSVGDKIPADIRLIKIYSTTIRIDQSILTGESV
SVIKHTDAVPDPRAVNQDKKNILFSGTNVAAGKARGIVIGTGLNTAIGKIRTEMSETEEI
KTPLQQKLDEFGEQLSKVISIICVAVWAINIGHFNDPAHGGSWIKGAIYYFKIAVALAVA
AIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICSDKTGTLTTNQMSVAR
AFVFEKVEGNDSSFTEFEITGSTYEPVGDLFYKGSKAKASDYEVLQELATICVMCND

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g3059.t11 Gene3D G3DSA:2.70.150.10 - 1 95 2.5E-35
10 g3059.t11 Gene3D G3DSA:1.20.1110.10 - 96 245 2.9E-48
2 g3059.t11 PANTHER PTHR42861:SF18 SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 2 1 297 1.6E-154
3 g3059.t11 PANTHER PTHR42861 CALCIUM-TRANSPORTING ATPASE 1 297 1.6E-154
4 g3059.t11 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 51 65 1.2E-10
5 g3059.t11 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 224 238 1.2E-10
1 g3059.t11 Pfam PF00122 E1-E2 ATPase 8 204 5.8E-53
11 g3059.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 134 -
14 g3059.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 135 155 -
13 g3059.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 156 166 -
15 g3059.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 167 196 -
12 g3059.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 197 297 -
18 g3059.t11 ProSitePatterns PS00154 E1-E2 ATPases phosphorylation site. 226 232 -
8 g3059.t11 SUPERFAMILY SSF81653 Calcium ATPase, transduction domain A 8 111 7.59E-28
7 g3059.t11 SUPERFAMILY SSF81665 Calcium ATPase, transmembrane domain M 115 218 3.53E-36
6 g3059.t11 SUPERFAMILY SSF81660 Metal cation-transporting ATPase, ATP-binding domain N 231 297 4.77E-10
19 g3059.t11 TIGRFAM TIGR01494 ATPase_P-type: HAD ATPase, P-type, family IC 9 247 9.4E-38
17 g3059.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 135 154 -
16 g3059.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 174 196 -

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

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