General information for g67.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Sodium/calcium exchanger 3.
Parent gene
- The parent gene g67 is located on chr_3: 489062..490765 (- 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 | g67 | g67.t1 | isoform | g67.t1 | 489062 | 490765 |
| chr_3 | g67 | g67.t1 | exon | g67.t1.exon1 | 489062 | 490765 |
| chr_3 | g67 | g67.t1 | cds | g67.t1.CDS1 | 489062 | 490765 |
| chr_3 | g67 | g67.t1 | TSS | g67.t1 | 491424 | 491424 |
| chr_3 | g67 | g67.t1 | TTS | g67.t1 | NA | NA |
Sequences
>g67.t1 Gene=g67 Length=1704
ATGAAATCGCTGACAAAATTCTTTGTTTTTATCATCGCAACAATACTCAGCTGTAGCAGC
ATAATATCTGTAGTTGCTGCTGATAATACCACAGTCGAGCCTGAGCATGATGACACAGTT
TGTACGGAAGATGGATTAGTTCTGCCAGTATGGATGCCACAAATCGGAATTTCCCTAGGT
GATCGCTTTGCACGTGGTGCTGTATACTTTTTCGCACTATTTTATCTCTTCATTGGTGTC
TCAATTGTCTCTGATCGTTTTATGGCAGCCATTGAAGTTATCACATCAAAAGAAAAAGAA
GTCAAAGTTAAAAAGCCAAATGGTGAAGTTCAAATTGTTGTTGTTCGTGTATGGAATGAA
ACTGTTGCCAATTTAACACTTATGGCACTTGGTTCAAGCGCTCCCGAAATTTTGCTCTCC
GTCATTGAAATGTTTGCAAAAAATTTCAAAGCTGGTGATCTTGGTCCCGGCACAATCGTT
GGCTCAGCTGCTTATAATCTTTTTGTAATTATTGCCATTTGCGTGCTGGTAATTCCAAAT
GGAGAAGTTCGAAAAATTAAACATTTGCGTGTATTTTTCGTCACAGCAACTTGGTCAGTT
TTTGCTTATATTTGGCTCTATCTCATTCTCGATGTCTTCTCACCAAATGTTGTTGATATT
TGGGAAGGTTTTGTGACTTTCCTTATGTTCCCAGCAACTGTCATTACCGCATATATTGCT
GATCGTCGTTTATTGATTTATAAATATATTGGCAAACGTTATCGTATGAATAAACGTGGT
GTAATGGTGCAAACGGAAGCATCAGAGCAAACATTAGAAATGAATAATCATTTGGATGAT
AATTTTAAAGGACTTGAAGATGGTGCAATGAATGAAGAAGTTCGTGAATTTGAAGACTCA
CGTAAAGAATATATCACAACATTAAAAGAATTACGCAAGAAATATCCACAACATGATTTA
GAGCAACTTGAAATTATGGCACATGAGCAAATTATGAATAAAGGCCCAAAATCGAGAGCT
TTCTATCGAATTCAAGCAACACGTAAAATGATGGGTAGCGGAAATATTATGAGAAAAATA
TCTGAACGTGCACAAAGTGATTTAAGTGAAGTTAAAGCTGAATTGCAACGTGTTGATGTG
ATTGACCAAACTGATGATGGACATGCTTGTAAAGTTTATTTTGAACCTGGTCATTATACA
GTTATGGAGAGTGTTGGTGATTTTGAATTACGTGTTGTACGTCGTGGTGATTTGTCACAA
GTTGTAACAGTTGATTTTGAAACTGAAGATGGCTCAGCTGAAGCTGGCAGTGACTATATT
GGCAAAAAAGGAACTTTAACTTTTGCACCAGGTGTTGATGAACAGCGCTTCCGTATTGAG
GTCATTGATGACGATGTTTTTGAACAAGATGAACATTTTTATGTTCGTTTAAGTAATGTC
AGTGATAATGCAACATTAACAACACCAAAAGTCGCAACTGTCATGATTCTCGATGACGAT
CATGGTGGTATTTTCGCATTTACTACCAAAGATCATGAGCTCGTTGAATCGGTCGGTACT
TATGAGCTTACTGTTCAACGTTATTCGGGTGCGCGCGGTAAAGTCGTTATACCATATTGG
ACTGAAGACGGAACGGCCAAATCTGGAAAGGATTACGAAGGAATGCGCGGTGAATTGGTA
TTTGAAAACAACGAAATTGAGTGA
>g67.t1 Gene=g67 Length=567
MKSLTKFFVFIIATILSCSSIISVVAADNTTVEPEHDDTVCTEDGLVLPVWMPQIGISLG
DRFARGAVYFFALFYLFIGVSIVSDRFMAAIEVITSKEKEVKVKKPNGEVQIVVVRVWNE
TVANLTLMALGSSAPEILLSVIEMFAKNFKAGDLGPGTIVGSAAYNLFVIIAICVLVIPN
GEVRKIKHLRVFFVTATWSVFAYIWLYLILDVFSPNVVDIWEGFVTFLMFPATVITAYIA
DRRLLIYKYIGKRYRMNKRGVMVQTEASEQTLEMNNHLDDNFKGLEDGAMNEEVREFEDS
RKEYITTLKELRKKYPQHDLEQLEIMAHEQIMNKGPKSRAFYRIQATRKMMGSGNIMRKI
SERAQSDLSEVKAELQRVDVIDQTDDGHACKVYFEPGHYTVMESVGDFELRVVRRGDLSQ
VVTVDFETEDGSAEAGSDYIGKKGTLTFAPGVDEQRFRIEVIDDDVFEQDEHFYVRLSNV
SDNATLTTPKVATVMILDDDHGGIFAFTTKDHELVESVGTYELTVQRYSGARGKVVIPYW
TEDGTAKSGKDYEGMRGELVFENNEIE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g67.t1 | Coils | Coil | Coil | 294 | 314 | - |
| 11 | g67.t1 | Gene3D | G3DSA:1.20.1420.30 | - | 119 | 247 | 1.9E-12 |
| 12 | g67.t1 | Gene3D | G3DSA:2.60.40.2030 | - | 388 | 501 | 7.1E-46 |
| 13 | g67.t1 | Gene3D | G3DSA:2.60.40.2030 | - | 503 | 567 | 2.6E-21 |
| 5 | g67.t1 | PANTHER | PTHR11878 | SODIUM/CALCIUM EXCHANGER | 10 | 565 | 8.3E-194 |
| 6 | g67.t1 | PANTHER | PTHR11878:SF26 | NCX4A | 10 | 565 | 8.3E-194 |
| 3 | g67.t1 | Pfam | PF01699 | Sodium/calcium exchanger protein | 69 | 237 | 2.6E-29 |
| 4 | g67.t1 | Pfam | PF16494 | C-terminal extension of sodium/calcium exchanger domain | 242 | 364 | 1.0E-41 |
| 1 | g67.t1 | Pfam | PF03160 | Calx-beta domain | 381 | 478 | 2.6E-30 |
| 2 | g67.t1 | Pfam | PF03160 | Calx-beta domain | 492 | 565 | 1.6E-18 |
| 21 | g67.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 26 | - |
| 22 | g67.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 6 | - |
| 23 | g67.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 7 | 18 | - |
| 29 | g67.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 19 | 26 | - |
| 19 | g67.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 27 | 67 | - |
| 28 | g67.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 68 | 89 | - |
| 17 | g67.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 90 | 124 | - |
| 27 | g67.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 125 | 146 | - |
| 20 | g67.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 147 | 157 | - |
| 24 | g67.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 158 | 179 | - |
| 16 | g67.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 180 | 190 | - |
| 25 | g67.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 191 | 208 | - |
| 18 | g67.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 209 | 219 | - |
| 26 | g67.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 220 | 240 | - |
| 15 | g67.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 241 | 567 | - |
| 40 | g67.t1 | ProSiteProfiles | PS51257 | Prokaryotic membrane lipoprotein lipid attachment site profile. | 1 | 18 | 6.0 |
| 37 | g67.t1 | SMART | SM00237 | NIbeta_1 | 379 | 478 | 8.4E-44 |
| 38 | g67.t1 | SMART | SM00237 | NIbeta_1 | 492 | 567 | 9.9E-16 |
| 7 | g67.t1 | SUPERFAMILY | SSF141072 | CalX-like | 392 | 501 | 2.88E-35 |
| 8 | g67.t1 | SUPERFAMILY | SSF141072 | CalX-like | 503 | 566 | 9.81E-13 |
| 10 | g67.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 27 | - |
| 30 | g67.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 26 | - |
| 9 | g67.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 27 | - |
| 39 | g67.t1 | TIGRFAM | TIGR00845 | caca: sodium/calcium exchanger 1 | 28 | 567 | 4.9E-247 |
| 36 | g67.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 26 | - |
| 34 | g67.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 62 | 84 | - |
| 33 | g67.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 124 | 146 | - |
| 32 | g67.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 156 | 178 | - |
| 31 | g67.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 191 | 209 | - |
| 35 | g67.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 224 | 246 | - |
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:0016020 | membrane | CC |
| GO:0055085 | transmembrane transport | BP |
| GO:0005432 | calcium:sodium antiporter activity | MF |
| GO:0016021 | integral component of membrane | CC |
| GO:0007154 | cell communication | BP |
| GO:0006816 | calcium ion transport | BP |
KEGG
Orthology
- This transcript has been annotated with K05849 (solute carrier family 8 (sodium/calcium exchanger))
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.
