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.t7 isoform g3059.t7 22372707 22374036
chr_3 g3059 g3059.t7 exon g3059.t7.exon1 22372707 22373836
chr_3 g3059 g3059.t7 cds g3059.t7.CDS1 22372709 22373785
chr_3 g3059 g3059.t7 exon g3059.t7.exon2 22373935 22374036
chr_3 g3059 g3059.t7 TSS g3059.t7 NA NA
chr_3 g3059 g3059.t7 TTS g3059.t7 NA NA

Sequences

>g3059.t7 Gene=g3059 Length=1232
GTATTAGCTCTTTTTGAAGAACATGAGGGTATTGAAGCATTCGTAGAACCATTTGTAATT
TTACTTATTTTAATTGCTAATGCTGTTGTTGGTGTTTGGCAAGAACGAAATGCAGAGTCA
GCAATTGAAGCCCTCAAAGAATATGAACCCGAAATGGGTAAAGTCGTTCGTCAGGATAAG
TCCGGAGTACAAAAACTCCGTGCCAAAGAGATTGTACCAGGTGATATCGTTGAAGTGTCA
GTCGGTGACAAAATTCCAGCTGATATTCGTTTAATTAAGATCTACTCAACGACAATTCGT
ATTGATCAATCTATCTTGACTGGTGAATCAGTTTCAGTCATTAAACACACTGATGCTGTC
CCAGATCCACGCGCTGTCAACCAAGATAAGAAAAATATTTTGTTCTCAGGAACTAATGTT
GCCGCTGGTAAGGCACGTGGTATCGTTATTGGAACTGGCCTTAACACTGCTATCGGTAAA
ATTCGTACTGAAATGTCAGAAACTGAAGAAATTAAGACACCATTGCAACAAAAATTGGAT
GAATTCGGTGAACAATTGTCAAAGGTCATTTCAATCATTTGCGTTGCTGTCTGGGCTATC
AACATTGGTCACTTTAACGATCCAGCTCATGGTGGTTCATGGATTAAGGGAGCTATCTAT
TATTTCAAGATTGCTGTCGCTTTGGCTGTCGCTGCTATTCCAGAAGGTTTACCAGCTGTT
ATTACCACTTGTTTGGCTTTGGGTACTCGTCGTATGGCCAAGAAGAACGCTATTGTCCGC
TCATTGCCATCAGTTGAAACTCTCGGTTGCACATCTGTCATTTGCTCAGATAAGACTGGT
ACATTGACAACAAATCAAATGTCAGTTGCTCGCGCATTCGTTTTTGAAAAGGTTGAAGGA
AATGATAGCAGTTTCACAGAATTCGAAATTACTGGATCAACATACGAACCAGTTGGTGAT
CTTTTCTACAAAGGTTCAAAGGCAAAGGCATCAGATTATGAAGTACTCCAAGAACTCGCT
ACCATTTGCGTCATGTGTAACGACTCTGCTATTGATTTCAACGAAGTTAAGCAAGTTTTC
GAGAAAGTCGGTGAAGCCACTGAAACTGCACTTATTGTTCTTGCCGAAAAATTGAACCCA
TTCTCAGTTCCAAAGACCGGTTTGGATCGTCGTTCAGCTGCTATTGTCGTTCGTCAGGAA
ATTGAGACTAAATGGAAGAAAGAATTTACACT

>g3059.t7 Gene=g3059 Length=359
MGKVVRQDKSGVQKLRAKEIVPGDIVEVSVGDKIPADIRLIKIYSTTIRIDQSILTGESV
SVIKHTDAVPDPRAVNQDKKNILFSGTNVAAGKARGIVIGTGLNTAIGKIRTEMSETEEI
KTPLQQKLDEFGEQLSKVISIICVAVWAINIGHFNDPAHGGSWIKGAIYYFKIAVALAVA
AIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICSDKTGTLTTNQMSVAR
AFVFEKVEGNDSSFTEFEITGSTYEPVGDLFYKGSKAKASDYEVLQELATICVMCNDSAI
DFNEVKQVFEKVGEATETALIVLAEKLNPFSVPKTGLDRRSAAIVVRQEIETKWKKEFT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g3059.t7 Gene3D G3DSA:2.70.150.10 - 1 95 3.6E-35
12 g3059.t7 Gene3D G3DSA:1.20.1110.10 - 96 245 4.4E-48
10 g3059.t7 Gene3D G3DSA:3.40.1110.10 - 255 359 1.8E-6
3 g3059.t7 PANTHER PTHR42861:SF18 SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 2 1 359 1.1E-168
4 g3059.t7 PANTHER PTHR42861 CALCIUM-TRANSPORTING ATPASE 1 359 1.1E-168
5 g3059.t7 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 51 65 1.6E-10
6 g3059.t7 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 224 238 1.6E-10
1 g3059.t7 Pfam PF00122 E1-E2 ATPase 8 204 1.0E-52
2 g3059.t7 Pfam PF13246 Cation transport ATPase (P-type) 294 340 3.2E-5
13 g3059.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 134 -
16 g3059.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 135 155 -
15 g3059.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 156 166 -
17 g3059.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 167 196 -
14 g3059.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 197 359 -
20 g3059.t7 ProSitePatterns PS00154 E1-E2 ATPases phosphorylation site. 226 232 -
9 g3059.t7 SUPERFAMILY SSF81653 Calcium ATPase, transduction domain A 8 111 1.12E-27
8 g3059.t7 SUPERFAMILY SSF81665 Calcium ATPase, transmembrane domain M 115 218 4.45E-36
7 g3059.t7 SUPERFAMILY SSF81660 Metal cation-transporting ATPase, ATP-binding domain N 231 358 7.85E-24
21 g3059.t7 TIGRFAM TIGR01494 ATPase_P-type: HAD ATPase, P-type, family IC 100 247 4.8E-27
19 g3059.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 135 154 -
18 g3059.t7 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