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.t4 isoform g3059.t4 22371702 22373308
chr_3 g3059 g3059.t4 exon g3059.t4.exon1 22371702 22372381
chr_3 g3059 g3059.t4 cds g3059.t4.CDS1 22371704 22372381
chr_3 g3059 g3059.t4 exon g3059.t4.exon2 22372448 22373308
chr_3 g3059 g3059.t4 cds g3059.t4.CDS2 22372448 22373185
chr_3 g3059 g3059.t4 TSS g3059.t4 NA NA
chr_3 g3059 g3059.t4 TTS g3059.t4 NA NA

Sequences

>g3059.t4 Gene=g3059 Length=1541
GGTGGTTCATGGATTAAGGGAGCTATCTATTATTTCAAGATTGCTGTCGCTTTGGCTGTC
GCTGCTATTCCAGAAGGTTTACCAGCTGTTATTACCACTTGTTTGGCTTTGGGTACTCGT
CGTATGGCCAAGAAGAACGCTATTGTCCGCTCATTGCCATCAGTTGAAACTCTCGGTTGC
ACATCTGTCATTTGCTCAGATAAGACTGGTACATTGACAACAAATCAAATGTCAGTTGCT
CGCGCATTCGTTTTTGAAAAGGTTGAAGGAAATGATAGCAGTTTCACAGAATTCGAAATT
ACTGGATCAACATACGAACCAGTTGGTGATCTTTTCTACAAAGGTTCAAAGGCAAAGGCA
TCAGATTATGAAGTACTCCAAGAACTCGCTACCATTTGCGTCATGTGTAACGACTCTGCT
ATTGATTTCAACGAAGTTAAGCAAGTTTTCGAGAAAGTCGGTGAAGCCACTGAAACTGCA
CTTATTGTTCTTGCCGAAAAATTGAACCCATTCTCAGTTCCAAAGACCGGTTTGGATCGT
CGTTCAGCTGCTATTGTCGTTCGTCAGGAAATTGAGACTAAATGGAAGAAAGAATTTACA
CTTGAATTCTCACGTGATCGTAAATCAATGTCATCATACTGCACACCACTTAAATCATCA
AAACTCGGAACTGGACCAAAAATGTTCTGCAAAGGTGCTCCAGAAGGTGTTTTGGATCGT
TGCACACATGCTCGCGTTGGCACAAGCAAAGTCCCACTTACATCAACACTCAAACAACGC
ATTTTGGATCTCACTCGTCAATACGGTACCGGTCGTGACACACTTCGTTGCCTTGCTTTG
GCCACTGGCGATTCTCCAATGAAACCAGAAGACATGGATCTTAATGATTCAACCAAATTC
TATACTTATGAAATTAATCTTACATTCGTTGGTGTGGTAGGAATGTTGGATCCACCACGT
AAAGAAGTCTTTGATTCAATTGTTCGCTGTCGTGCTGCTGGTATTCGTGTTATTGTCATT
ACTGGTGACAACAAGGCCACTGCTGAAGCTATTTGCCGTCGTATTGGAGTTTTCGGTGAA
GATGAAGACACAACTGGAAAATCATACTCAGGTCGTGAATTTGATGACTTGCCAGTTCAT
GAACAAAAACAAGCTTGCGCTCGTGCTCGTCTCTTCTCACGTGTAGAGCCAGCTCACAAG
TCAAAGATTGTCGAATATTTGCAAAGCATGAATGAAATCTCAGCTATGACAGGTGATGGT
GTCAATGACGCTCCTGCTTTGAAAAAGGCTGAAATTGGTATTGCTATGGGTTCTGGTACT
GCTGTCGCTAAATCTGCTTCAGAAATGGTTCTCGCTGACGATAACTTCTCATCAATTGTC
GCTGCCGTTGAAGAAGGTCGTGCCATTTACAACAACATGAAACAATTCATTCGTTATCTC
ATTTCATCAAACATTGGTGAGGTTGTCTCAATTTTCTTGACTGCTGCTCTTGGCTTACCA
GAAGCTCTCATTCCCGTTCAATTGTTGTGGGTCAACTTGGT

>g3059.t4 Gene=g3059 Length=472
MAKKNAIVRSLPSVETLGCTSVICSDKTGTLTTNQMSVARAFVFEKVEGNDSSFTEFEIT
GSTYEPVGDLFYKGSKAKASDYEVLQELATICVMCNDSAIDFNEVKQVFEKVGEATETAL
IVLAEKLNPFSVPKTGLDRRSAAIVVRQEIETKWKKEFTLEFSRDRKSMSSYCTPLKSSK
LGTGPKMFCKGAPEGVLDRCTHARVGTSKVPLTSTLKQRILDLTRQYGTGRDTLRCLALA
TGDSPMKPEDMDLNDSTKFYTYEINLTFVGVVGMLDPPRKEVFDSIVRCRAAGIRVIVIT
GDNKATAEAICRRIGVFGEDEDTTGKSYSGREFDDLPVHEQKQACARARLFSRVEPAHKS
KIVEYLQSMNEISAMTGDGVNDAPALKKAEIGIAMGSGTAVAKSASEMVLADDNFSSIVA
AVEEGRAIYNNMKQFIRYLISSNIGEVVSIFLTAALGLPEALIPVQLLWVNL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g3059.t4 Gene3D G3DSA:1.20.1110.10 - 1 472 6.2E-194
12 g3059.t4 Gene3D G3DSA:3.40.50.1000 - 21 420 6.2E-194
13 g3059.t4 Gene3D G3DSA:3.40.1110.10 - 34 277 6.2E-194
3 g3059.t4 PANTHER PTHR42861:SF6 SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 3 1 472 3.6E-231
4 g3059.t4 PANTHER PTHR42861 CALCIUM-TRANSPORTING ATPASE 1 472 3.6E-231
6 g3059.t4 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 24 38 2.9E-36
9 g3059.t4 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 270 281 2.9E-36
5 g3059.t4 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 292 302 2.9E-36
7 g3059.t4 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 376 395 2.9E-36
8 g3059.t4 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 399 411 2.9E-36
2 g3059.t4 Pfam PF13246 Cation transport ATPase (P-type) 94 202 1.9E-19
1 g3059.t4 Pfam PF08282 haloacid dehalogenase-like hydrolase 361 419 7.5E-6
15 g3059.t4 ProSitePatterns PS00154 E1-E2 ATPases phosphorylation site. 26 32 -
17 g3059.t4 SFLD SFLDF00027 p-type atpase 5 428 0.0
18 g3059.t4 SFLD SFLDS00003 Haloacid Dehalogenase 5 428 0.0
11 g3059.t4 SUPERFAMILY SSF56784 HAD-like 22 471 9.7E-48
10 g3059.t4 SUPERFAMILY SSF81660 Metal cation-transporting ATPase, ATP-binding domain N 31 274 3.05E-63
16 g3059.t4 TIGRFAM TIGR01494 ATPase_P-type: HAD ATPase, P-type, family IC 344 461 3.4E-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: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.

Raw TPM values