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.t3 isoform g3059.t3 22371502 22373836
chr_3 g3059 g3059.t3 exon g3059.t3.exon1 22371502 22371646
chr_3 g3059 g3059.t3 cds g3059.t3.CDS1 22371503 22371646
chr_3 g3059 g3059.t3 exon g3059.t3.exon2 22371704 22372381
chr_3 g3059 g3059.t3 cds g3059.t3.CDS2 22371704 22372381
chr_3 g3059 g3059.t3 exon g3059.t3.exon3 22372448 22373836
chr_3 g3059 g3059.t3 cds g3059.t3.CDS3 22372448 22373785
chr_3 g3059 g3059.t3 TSS g3059.t3 NA NA
chr_3 g3059 g3059.t3 TTS g3059.t3 NA NA

Sequences

>g3059.t3 Gene=g3059 Length=2212
GAACGAAATGCAGAGTCAGCAATTGAAGCCCTCAAAGAATATGAACCCGAAATGGGTAAA
GTCGTTCGTCAGGATAAGTCCGGAGTACAAAAACTCCGTGCCAAAGAGATTGTACCAGGT
GATATCGTTGAAGTGTCAGTCGGTGACAAAATTCCAGCTGATATTCGTTTAATTAAGATC
TACTCAACGACAATTCGTATTGATCAATCTATCTTGACTGGTGAATCAGTTTCAGTCATT
AAACACACTGATGCTGTCCCAGATCCACGCGCTGTCAACCAAGATAAGAAAAATATTTTG
TTCTCAGGAACTAATGTTGCCGCTGGTAAGGCACGTGGTATCGTTATTGGAACTGGCCTT
AACACTGCTATCGGTAAAATTCGTACTGAAATGTCAGAAACTGAAGAAATTAAGACACCA
TTGCAACAAAAATTGGATGAATTCGGTGAACAATTGTCAAAGGTCATTTCAATCATTTGC
GTTGCTGTCTGGGCTATCAACATTGGTCACTTTAACGATCCAGCTCATGGTGGTTCATGG
ATTAAGGGAGCTATCTATTATTTCAAGATTGCTGTCGCTTTGGCTGTCGCTGCTATTCCA
GAAGGTTTACCAGCTGTTATTACCACTTGTTTGGCTTTGGGTACTCGTCGTATGGCCAAG
AAGAACGCTATTGTCCGCTCATTGCCATCAGTTGAAACTCTCGGTTGCACATCTGTCATT
TGCTCAGATAAGACTGGTACATTGACAACAAATCAAATGTCAGTTGCTCGCGCATTCGTT
TTTGAAAAGGTTGAAGGAAATGATAGCAGTTTCACAGAATTCGAAATTACTGGATCAACA
TACGAACCAGTTGGTGATCTTTTCTACAAAGGTTCAAAGGCAAAGGCATCAGATTATGAA
GTACTCCAAGAACTCGCTACCATTTGCGTCATGTGTAACGACTCTGCTATTGATTTCAAC
GAAGTTAAGCAAGTTTTCGAGAAAGTCGGTGAAGCCACTGAAACTGCACTTATTGTTCTT
GCCGAAAAATTGAACCCATTCTCAGTTCCAAAGACCGGTTTGGATCGTCGTTCAGCTGCT
ATTGTCGTTCGTCAGGAAATTGAGACTAAATGGAAGAAAGAATTTACACTTGAATTCTCA
CGTGATCGTAAATCAATGTCATCATACTGCACACCACTTAAATCATCAAAACTCGGAACT
GGACCAAAAATGTTCTGCAAAGGTGCTCCAGAAGGTGTTTTGGATCGTTGCACACATGCT
CGCGTTGGCACAAGCAAAGTCCCACTTACATCAACACTCAAACAACGCATTTTGGATCTC
ACTCGTCAATACGGTACCGGTCGTGACACACTTCGTTGCCTTGCTTTGGCCACTGGCGAT
TCTCCAATGAAACCAGAAGACATGGATCTTAATGATTCAACCAAATTCTATACTTATGAA
ATTAATCTTACATTCGTTGGTGTGGTAGGAATGTTGGATCCACCACGTAAAGAAGTCTTT
GATTCAATTGTTCGCTGTCGTGCTGCTGGTATTCGTGTTATTGTCATTACTGGTGACAAC
AAGGCCACTGCTGAAGCTATTTGCCGTCGTATTGGAGTTTTCGGTGAAGATGAAGACACA
ACTGGAAAATCATACTCAGGTCGTGAATTTGATGACTTGCCAGTTCATGAACAAAAACAA
GCTTGCGCTCGTGCTCGTCTCTTCTCACGTGTAGAGCCAGCTCACAAGTCAAAGATTGTC
GAATATTTGCAAAGCATGAATGAAATCTCAGCTATGACAGGTGATGGTGTCAATGACGCT
CCTGCTTTGAAAAAGGCTGAAATTGGTATTGCTATGGGTTCTGGTACTGCTGTCGCTAAA
TCTGCTTCAGAAATGGTTCTCGCTGACGATAACTTCTCATCAATTGTCGCTGCCGTTGAA
GAAGGTCGTGCCATTTACAACAACATGAAACAATTCATTCGTTATCTCATTTCATCAAAC
ATTGGTGAGGTTGTCTCAATTTTCTTGACTGCTGCTCTTGGCTTACCAGAAGCTCTCATT
CCCGTTCAATTGTTGTGGGTCAACTTGGTTACTGATGGTCTCCCAGCTACAGCTCTTGGT
TTTAATCCACCTGATTTAGATATTATGACTAAGCCACCACGTAAAGCCGATGAAGGTCTT
ATTTCAGGATGGTTGTTCTTCCGTTACATGGCTATTGGTGGTTATGTTGGTG

>g3059.t3 Gene=g3059 Length=720
MGKVVRQDKSGVQKLRAKEIVPGDIVEVSVGDKIPADIRLIKIYSTTIRIDQSILTGESV
SVIKHTDAVPDPRAVNQDKKNILFSGTNVAAGKARGIVIGTGLNTAIGKIRTEMSETEEI
KTPLQQKLDEFGEQLSKVISIICVAVWAINIGHFNDPAHGGSWIKGAIYYFKIAVALAVA
AIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICSDKTGTLTTNQMSVAR
AFVFEKVEGNDSSFTEFEITGSTYEPVGDLFYKGSKAKASDYEVLQELATICVMCNDSAI
DFNEVKQVFEKVGEATETALIVLAEKLNPFSVPKTGLDRRSAAIVVRQEIETKWKKEFTL
EFSRDRKSMSSYCTPLKSSKLGTGPKMFCKGAPEGVLDRCTHARVGTSKVPLTSTLKQRI
LDLTRQYGTGRDTLRCLALATGDSPMKPEDMDLNDSTKFYTYEINLTFVGVVGMLDPPRK
EVFDSIVRCRAAGIRVIVITGDNKATAEAICRRIGVFGEDEDTTGKSYSGREFDDLPVHE
QKQACARARLFSRVEPAHKSKIVEYLQSMNEISAMTGDGVNDAPALKKAEIGIAMGSGTA
VAKSASEMVLADDNFSSIVAAVEEGRAIYNNMKQFIRYLISSNIGEVVSIFLTAALGLPE
ALIPVQLLWVNLVTDGLPATALGFNPPDLDIMTKPPRKADEGLISGWLFFRYMAIGGYVG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g3059.t3 Gene3D G3DSA:2.70.150.10 - 1 116 1.0E-46
20 g3059.t3 Gene3D G3DSA:1.20.1110.10 - 117 720 0.0
17 g3059.t3 Gene3D G3DSA:3.40.50.1000 - 206 614 0.0
18 g3059.t3 Gene3D G3DSA:3.40.1110.10 - 234 478 0.0
5 g3059.t3 PANTHER PTHR42861:SF18 SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 2 1 720 0.0
6 g3059.t3 PANTHER PTHR42861 CALCIUM-TRANSPORTING ATPASE 1 720 0.0
7 g3059.t3 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 51 65 2.8E-42
10 g3059.t3 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 224 238 2.8E-42
12 g3059.t3 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 470 481 2.8E-42
11 g3059.t3 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 492 502 2.8E-42
9 g3059.t3 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 576 595 2.8E-42
8 g3059.t3 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 599 611 2.8E-42
2 g3059.t3 Pfam PF00122 E1-E2 ATPase 8 204 4.8E-52
4 g3059.t3 Pfam PF13246 Cation transport ATPase (P-type) 294 402 3.8E-19
3 g3059.t3 Pfam PF08282 haloacid dehalogenase-like hydrolase 561 619 1.2E-5
1 g3059.t3 Pfam PF00689 Cation transporting ATPase, C-terminus 659 717 4.2E-18
21 g3059.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 134 -
24 g3059.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 135 155 -
23 g3059.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 156 166 -
25 g3059.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 167 196 -
22 g3059.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 197 720 -
26 g3059.t3 ProSitePatterns PS00154 E1-E2 ATPases phosphorylation site. 226 232 -
30 g3059.t3 SFLD SFLDF00027 p-type atpase 205 628 0.0
31 g3059.t3 SFLD SFLDG00002 C1.7: P-type atpase like 205 628 0.0
15 g3059.t3 SUPERFAMILY SSF81653 Calcium ATPase, transduction domain A 8 111 3.66E-27
14 g3059.t3 SUPERFAMILY SSF81665 Calcium ATPase, transmembrane domain M 115 719 1.7E-74
13 g3059.t3 SUPERFAMILY SSF81660 Metal cation-transporting ATPase, ATP-binding domain N 231 474 2.42E-62
16 g3059.t3 SUPERFAMILY SSF56784 HAD-like 460 624 3.16E-44
29 g3059.t3 TIGRFAM TIGR01116 ATPase-IIA1_Ca: calcium-translocating P-type ATPase, SERCA-type 13 720 6.0E-276
27 g3059.t3 TIGRFAM TIGR01494 ATPase_P-type: HAD ATPase, P-type, family IC 101 247 1.6E-26
28 g3059.t3 TIGRFAM TIGR01494 ATPase_P-type: HAD ATPase, P-type, family IC 544 661 6.9E-34

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

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.

Raw TPM values