General information for g3059.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Calcium-transporting ATPase sarcoplasmic/endoplasmic reticulum type.
Parent gene
- The parent gene g3059 is located on chr_3: 22373974..22380788 (- strand)
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.t1 | isoform | g3059.t1 | 22371372 | 22377400 |
| chr_3 | g3059 | g3059.t1 | exon | g3059.t1.exon1 | 22371372 | 22371406 |
| chr_3 | g3059 | g3059.t1 | cds | g3059.t1.CDS1 | 22371372 | 22371406 |
| chr_3 | g3059 | g3059.t1 | exon | g3059.t1.exon2 | 22371505 | 22371646 |
| chr_3 | g3059 | g3059.t1 | cds | g3059.t1.CDS2 | 22371505 | 22371646 |
| chr_3 | g3059 | g3059.t1 | exon | g3059.t1.exon3 | 22371704 | 22372381 |
| chr_3 | g3059 | g3059.t1 | cds | g3059.t1.CDS3 | 22371704 | 22372381 |
| chr_3 | g3059 | g3059.t1 | exon | g3059.t1.exon4 | 22372448 | 22373836 |
| chr_3 | g3059 | g3059.t1 | cds | g3059.t1.CDS4 | 22372448 | 22373836 |
| chr_3 | g3059 | g3059.t1 | exon | g3059.t1.exon5 | 22373935 | 22374036 |
| chr_3 | g3059 | g3059.t1 | cds | g3059.t1.CDS5 | 22373935 | 22374036 |
| chr_3 | g3059 | g3059.t1 | exon | g3059.t1.exon6 | 22375071 | 22375171 |
| chr_3 | g3059 | g3059.t1 | cds | g3059.t1.CDS6 | 22375071 | 22375171 |
| chr_3 | g3059 | g3059.t1 | exon | g3059.t1.exon7 | 22377283 | 22377400 |
| chr_3 | g3059 | g3059.t1 | cds | g3059.t1.CDS7 | 22377283 | 22377400 |
| chr_3 | g3059 | g3059.t1 | TSS | g3059.t1 | 22378056 | 22378056 |
| chr_3 | g3059 | g3059.t1 | TTS | g3059.t1 | NA | NA |
Sequences
>g3059.t1 Gene=g3059 Length=2565
ATGGAGGACGCCCATTGCAAGACATCCGACGAGGTGTTAAAGTACTTCGGCACAAATGAA
GAATTAGGATTAACGCCAGATCAAGTCAAACAATATCAGGCTAAATACGGACCTAATGAA
CTTCCAGCCGAGGAAGGCAAAACAATATGGCAATTAGTACTTGAACAGTTTGACGATCTT
TTAGTTAAAATTTTGTTATTGGCTGCTATTATTTCATTTGTATTAGCTCTTTTTGAAGAA
CATGAGGGTATTGAAGCATTCGTAGAACCATTTGTAATTTTACTTATTTTAATTGCTAAT
GCTGTTGTTGGTGTTTGGCAAGAACGAAATGCAGAGTCAGCAATTGAAGCCCTCAAAGAA
TATGAACCCGAAATGGGTAAAGTCGTTCGTCAGGATAAGTCCGGAGTACAAAAACTCCGT
GCCAAAGAGATTGTACCAGGTGATATCGTTGAAGTGTCAGTCGGTGACAAAATTCCAGCT
GATATTCGTTTAATTAAGATCTACTCAACGACAATTCGTATTGATCAATCTATCTTGACT
GGTGAATCAGTTTCAGTCATTAAACACACTGATGCTGTCCCAGATCCACGCGCTGTCAAC
CAAGATAAGAAAAATATTTTGTTCTCAGGAACTAATGTTGCCGCTGGTAAGGCACGTGGT
ATCGTTATTGGAACTGGCCTTAACACTGCTATCGGTAAAATTCGTACTGAAATGTCAGAA
ACTGAAGAAATTAAGACACCATTGCAACAAAAATTGGATGAATTCGGTGAACAATTGTCA
AAGGTCATTTCAATCATTTGCGTTGCTGTCTGGGCTATCAACATTGGTCACTTTAACGAT
CCAGCTCATGGTGGTTCATGGATTAAGGGAGCTATCTATTATTTCAAGATTGCTGTCGCT
TTGGCTGTCGCTGCTATTCCAGAAGGTTTACCAGCTGTTATTACCACTTGTTTGGCTTTG
GGTACTCGTCGTATGGCCAAGAAGAACGCTATTGTCCGCTCATTGCCATCAGTTGAAACT
CTCGGTTGCACATCTGTCATTTGCTCAGATAAGACTGGTACATTGACAACAAATCAAATG
TCAGTTGCTCGCGCATTCGTTTTTGAAAAGGTTGAAGGAAATGATAGCAGTTTCACAGAA
TTCGAAATTACTGGATCAACATACGAACCAGTTGGTGATCTTTTCTACAAAGGTTCAAAG
GCAAAGGCATCAGATTATGAAGTACTCCAAGAACTCGCTACCATTTGCGTCATGTGTAAC
GACTCTGCTATTGATTTCAACGAAGTTAAGCAAGTTTTCGAGAAAGTCGGTGAAGCCACT
GAAACTGCACTTATTGTTCTTGCCGAAAAATTGAACCCATTCTCAGTTCCAAAGACCGGT
TTGGATCGTCGTTCAGCTGCTATTGTCGTTCGTCAGGAAATTGAGACTAAATGGAAGAAA
GAATTTACACTTGAATTCTCACGTGATCGTAAATCAATGTCATCATACTGCACACCACTT
AAATCATCAAAACTCGGAACTGGACCAAAAATGTTCTGCAAAGGTGCTCCAGAAGGTGTT
TTGGATCGTTGCACACATGCTCGCGTTGGCACAAGCAAAGTCCCACTTACATCAACACTC
AAACAACGCATTTTGGATCTCACTCGTCAATACGGTACCGGTCGTGACACACTTCGTTGC
CTTGCTTTGGCCACTGGCGATTCTCCAATGAAACCAGAAGACATGGATCTTAATGATTCA
ACCAAATTCTATACTTATGAAATTAATCTTACATTCGTTGGTGTGGTAGGAATGTTGGAT
CCACCACGTAAAGAAGTCTTTGATTCAATTGTTCGCTGTCGTGCTGCTGGTATTCGTGTT
ATTGTCATTACTGGTGACAACAAGGCCACTGCTGAAGCTATTTGCCGTCGTATTGGAGTT
TTCGGTGAAGATGAAGACACAACTGGAAAATCATACTCAGGTCGTGAATTTGATGACTTG
CCAGTTCATGAACAAAAACAAGCTTGCGCTCGTGCTCGTCTCTTCTCACGTGTAGAGCCA
GCTCACAAGTCAAAGATTGTCGAATATTTGCAAAGCATGAATGAAATCTCAGCTATGACA
GGTGATGGTGTCAATGACGCTCCTGCTTTGAAAAAGGCTGAAATTGGTATTGCTATGGGT
TCTGGTACTGCTGTCGCTAAATCTGCTTCAGAAATGGTTCTCGCTGACGATAACTTCTCA
TCAATTGTCGCTGCCGTTGAAGAAGGTCGTGCCATTTACAACAACATGAAACAATTCATT
CGTTATCTCATTTCATCAAACATTGGTGAGGTTGTCTCAATTTTCTTGACTGCTGCTCTT
GGCTTACCAGAAGCTCTCATTCCCGTTCAATTGTTGTGGGTCAACTTGGTTACTGATGGT
CTCCCAGCTACAGCTCTTGGTTTTAATCCACCTGATTTAGATATTATGACTAAGCCACCA
CGTAAAGCCGATGAAGGTCTTATTTCAGGATGGTTGTTCTTCCGTTACATGGCTATTGGT
GGTTATGTTGTTGCCCAAAATTCACCGCGTGGAGGTGATGGTTAA
>g3059.t1 Gene=g3059 Length=854
MEDAHCKTSDEVLKYFGTNEELGLTPDQVKQYQAKYGPNELPAEEGKTIWQLVLEQFDDL
LVKILLLAAIISFVLALFEEHEGIEAFVEPFVILLILIANAVVGVWQERNAESAIEALKE
YEPEMGKVVRQDKSGVQKLRAKEIVPGDIVEVSVGDKIPADIRLIKIYSTTIRIDQSILT
GESVSVIKHTDAVPDPRAVNQDKKNILFSGTNVAAGKARGIVIGTGLNTAIGKIRTEMSE
TEEIKTPLQQKLDEFGEQLSKVISIICVAVWAINIGHFNDPAHGGSWIKGAIYYFKIAVA
LAVAAIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICSDKTGTLTTNQM
SVARAFVFEKVEGNDSSFTEFEITGSTYEPVGDLFYKGSKAKASDYEVLQELATICVMCN
DSAIDFNEVKQVFEKVGEATETALIVLAEKLNPFSVPKTGLDRRSAAIVVRQEIETKWKK
EFTLEFSRDRKSMSSYCTPLKSSKLGTGPKMFCKGAPEGVLDRCTHARVGTSKVPLTSTL
KQRILDLTRQYGTGRDTLRCLALATGDSPMKPEDMDLNDSTKFYTYEINLTFVGVVGMLD
PPRKEVFDSIVRCRAAGIRVIVITGDNKATAEAICRRIGVFGEDEDTTGKSYSGREFDDL
PVHEQKQACARARLFSRVEPAHKSKIVEYLQSMNEISAMTGDGVNDAPALKKAEIGIAMG
SGTAVAKSASEMVLADDNFSSIVAAVEEGRAIYNNMKQFIRYLISSNIGEVVSIFLTAAL
GLPEALIPVQLLWVNLVTDGLPATALGFNPPDLDIMTKPPRKADEGLISGWLFFRYMAIG
GYVVAQNSPRGGDG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 36 | g3059.t1 | CDD | cd02083 | P-type_ATPase_SERCA | 5 | 843 | 0.0 |
| 21 | g3059.t1 | Gene3D | G3DSA:2.70.150.10 | - | 1 | 64 | 2.2E-11 |
| 20 | g3059.t1 | Gene3D | G3DSA:2.70.150.10 | - | 97 | 241 | 2.2E-54 |
| 22 | g3059.t1 | Gene3D | G3DSA:1.20.1110.10 | - | 242 | 843 | 0.0 |
| 18 | g3059.t1 | Gene3D | G3DSA:3.40.50.1000 | - | 330 | 738 | 0.0 |
| 19 | g3059.t1 | Gene3D | G3DSA:3.40.1110.10 | - | 358 | 602 | 0.0 |
| 6 | g3059.t1 | PANTHER | PTHR42861:SF18 | SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 2 | 2 | 845 | 0.0 |
| 7 | g3059.t1 | PANTHER | PTHR42861 | CALCIUM-TRANSPORTING ATPASE | 2 | 845 | 0.0 |
| 10 | g3059.t1 | PRINTS | PR00119 | P-type cation-transporting ATPase superfamily signature | 175 | 189 | 7.0E-42 |
| 11 | g3059.t1 | PRINTS | PR00119 | P-type cation-transporting ATPase superfamily signature | 348 | 362 | 7.0E-42 |
| 13 | g3059.t1 | PRINTS | PR00119 | P-type cation-transporting ATPase superfamily signature | 594 | 605 | 7.0E-42 |
| 12 | g3059.t1 | PRINTS | PR00119 | P-type cation-transporting ATPase superfamily signature | 616 | 626 | 7.0E-42 |
| 8 | g3059.t1 | PRINTS | PR00119 | P-type cation-transporting ATPase superfamily signature | 700 | 719 | 7.0E-42 |
| 9 | g3059.t1 | PRINTS | PR00119 | P-type cation-transporting ATPase superfamily signature | 723 | 735 | 7.0E-42 |
| 5 | g3059.t1 | Pfam | PF00690 | Cation transporter/ATPase, N-terminus | 6 | 72 | 6.4E-19 |
| 2 | g3059.t1 | Pfam | PF00122 | E1-E2 ATPase | 122 | 328 | 1.4E-52 |
| 4 | g3059.t1 | Pfam | PF13246 | Cation transport ATPase (P-type) | 418 | 526 | 4.9E-19 |
| 3 | g3059.t1 | Pfam | PF08282 | haloacid dehalogenase-like hydrolase | 685 | 743 | 1.5E-5 |
| 1 | g3059.t1 | Pfam | PF00689 | Cation transporting ATPase, C-terminus | 783 | 843 | 2.9E-18 |
| 23 | g3059.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 59 | - |
| 31 | g3059.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 60 | 78 | - |
| 29 | g3059.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 79 | 83 | - |
| 34 | g3059.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 84 | 106 | - |
| 25 | g3059.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 107 | 258 | - |
| 30 | g3059.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 259 | 279 | - |
| 28 | g3059.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 280 | 290 | - |
| 33 | g3059.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 291 | 320 | - |
| 26 | g3059.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 321 | 758 | - |
| 35 | g3059.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 759 | 782 | - |
| 27 | g3059.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 783 | 825 | - |
| 32 | g3059.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 826 | 845 | - |
| 24 | g3059.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 846 | 854 | - |
| 41 | g3059.t1 | ProSitePatterns | PS00154 | E1-E2 ATPases phosphorylation site. | 350 | 356 | - |
| 46 | g3059.t1 | SFLD | SFLDF00027 | p-type atpase | 329 | 752 | 0.0 |
| 47 | g3059.t1 | SFLD | SFLDG00002 | C1.7: P-type atpase like | 329 | 752 | 0.0 |
| 40 | g3059.t1 | SMART | SM00831 | Cation_ATPase_N_a_2 | 3 | 77 | 1.2E-19 |
| 15 | g3059.t1 | SUPERFAMILY | SSF81665 | Calcium ATPase, transmembrane domain M | 1 | 845 | 1.44E-111 |
| 16 | g3059.t1 | SUPERFAMILY | SSF81653 | Calcium ATPase, transduction domain A | 131 | 235 | 3.92E-27 |
| 14 | g3059.t1 | SUPERFAMILY | SSF81660 | Metal cation-transporting ATPase, ATP-binding domain N | 355 | 598 | 3.33E-62 |
| 17 | g3059.t1 | SUPERFAMILY | SSF56784 | HAD-like | 584 | 748 | 4.22E-44 |
| 45 | g3059.t1 | TIGRFAM | TIGR01116 | ATPase-IIA1_Ca: calcium-translocating P-type ATPase, SERCA-type | 53 | 844 | 0.0 |
| 43 | g3059.t1 | TIGRFAM | TIGR01494 | ATPase_P-type: HAD ATPase, P-type, family IC | 92 | 202 | 2.4E-18 |
| 44 | g3059.t1 | TIGRFAM | TIGR01494 | ATPase_P-type: HAD ATPase, P-type, family IC | 225 | 371 | 2.3E-26 |
| 42 | g3059.t1 | TIGRFAM | TIGR01494 | ATPase_P-type: HAD ATPase, P-type, family IC | 668 | 785 | 8.9E-34 |
| 39 | g3059.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 60 | 77 | - |
| 37 | g3059.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 87 | 106 | - |
| 38 | g3059.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 297 | 319 | - |
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 transcript has been annotated with K05853 (P-type Ca2+ transporter type 2A)
Pathway
- This transcript belongs to the following 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.
