General information for g42.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Sodium/calcium exchanger 1.
Parent gene
- The parent gene g42 is located on chr_3: 404141..405267 (- 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 | g42 | g42.t1 | TTS | g42.t1 | 404097 | 404097 |
| chr_3 | g42 | g42.t1 | isoform | g42.t1 | 404141 | 405267 |
| chr_3 | g42 | g42.t1 | exon | g42.t1.exon1 | 404141 | 404354 |
| chr_3 | g42 | g42.t1 | cds | g42.t1.CDS1 | 404141 | 404354 |
| chr_3 | g42 | g42.t1 | exon | g42.t1.exon2 | 404408 | 404582 |
| chr_3 | g42 | g42.t1 | cds | g42.t1.CDS2 | 404408 | 404582 |
| chr_3 | g42 | g42.t1 | exon | g42.t1.exon3 | 404650 | 404808 |
| chr_3 | g42 | g42.t1 | cds | g42.t1.CDS3 | 404650 | 404808 |
| chr_3 | g42 | g42.t1 | exon | g42.t1.exon4 | 404875 | 404997 |
| chr_3 | g42 | g42.t1 | cds | g42.t1.CDS4 | 404875 | 404997 |
| chr_3 | g42 | g42.t1 | exon | g42.t1.exon5 | 405056 | 405145 |
| chr_3 | g42 | g42.t1 | cds | g42.t1.CDS5 | 405056 | 405145 |
| chr_3 | g42 | g42.t1 | exon | g42.t1.exon6 | 405261 | 405267 |
| chr_3 | g42 | g42.t1 | cds | g42.t1.CDS6 | 405261 | 405267 |
| chr_3 | g42 | g42.t1 | TSS | g42.t1 | NA | NA |
Sequences
>g42.t1 Gene=g42 Length=768
ATGTATTATAAGTTAGTACAAAGAGCAAATGCATCGATTTTGATTGGTACATCATCTTGG
AAAGAACAATTTGTTGAAGCATTAACAGTAAATCCTGGTGAAGATGATGATGAAGAAGGA
AATGCAGATGATGAACCACCATCACCTAGCTGTATGGACTATATTATGCACTTCCTTACA
CTCTTTTGGAAAATTATTTTTGCATTCATACCACCAACGGACTTTTATGGTGGTTATCTA
TGCTTCGTAGTTTCAATTTTATGTATTGGCATTGTGACGGCAATCATCGGTGACGTTGCA
TCACATTTTGGTTGCACATTAGGAATTAAAGATTCAGTAACTGCTATCGTTTTTGTAGCA
CTTGGAACGAGTATTCCAGATACGTTTGCAAGTAAAGTAGCAGCTATTCAGGATAAATAT
GCAGATGCTAGTGTAGGCAACGTCACGGGAAGTAATGTTGTCAATGTATTTTTGGGAATT
GGTTTGGCATGGACAATGGCAGCTGTCTATCATAATGTATATAATGGTCAACCATTCAGA
GTGCCATCGGGAAACCTCGCTTTCTCAGTAACGCTTTTCTGTTCGGAAGCAGCAATTGCA
ATTATGATTTTGCTGTTACGTAGAAATAAAAGTATCGGTGGTGAACTTGGAGGACCTCCA
GTAGCAAAATATATGACTGCAACAGCCCTCATCGGTTTGTGGCTTATATATCTTATTGTA
AGCAGTTTAGAGGCCTATGGTGTCATTAAAGTTGGCGCAGAAAAGTAA
>g42.t1 Gene=g42 Length=255
MYYKLVQRANASILIGTSSWKEQFVEALTVNPGEDDDEEGNADDEPPSPSCMDYIMHFLT
LFWKIIFAFIPPTDFYGGYLCFVVSILCIGIVTAIIGDVASHFGCTLGIKDSVTAIVFVA
LGTSIPDTFASKVAAIQDKYADASVGNVTGSNVVNVFLGIGLAWTMAAVYHNVYNGQPFR
VPSGNLAFSVTLFCSEAAIAIMILLLRRNKSIGGELGGPPVAKYMTATALIGLWLIYLIV
SSLEAYGVIKVGAEK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g42.t1 | Gene3D | G3DSA:1.20.1420.30 | - | 48 | 243 | 2.7E-13 |
| 2 | g42.t1 | PANTHER | PTHR11878 | SODIUM/CALCIUM EXCHANGER | 4 | 250 | 1.5E-111 |
| 3 | g42.t1 | PANTHER | PTHR11878:SF8 | SODIUM/CALCIUM EXCHANGER 2 | 4 | 250 | 1.5E-111 |
| 5 | g42.t1 | PRINTS | PR01259 | Na+/Ca2+ exchanger signature | 83 | 95 | 1.9E-27 |
| 7 | g42.t1 | PRINTS | PR01259 | Na+/Ca2+ exchanger signature | 96 | 107 | 1.9E-27 |
| 6 | g42.t1 | PRINTS | PR01259 | Na+/Ca2+ exchanger signature | 109 | 121 | 1.9E-27 |
| 4 | g42.t1 | PRINTS | PR01259 | Na+/Ca2+ exchanger signature | 122 | 135 | 1.9E-27 |
| 1 | g42.t1 | Pfam | PF01699 | Sodium/calcium exchanger protein | 79 | 241 | 1.3E-26 |
| 16 | g42.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 53 | - |
| 24 | g42.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 54 | 70 | - |
| 18 | g42.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 71 | 75 | - |
| 22 | g42.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 76 | 100 | - |
| 14 | g42.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 101 | 152 | - |
| 21 | g42.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 153 | 174 | - |
| 19 | g42.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 175 | 185 | - |
| 23 | g42.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 186 | 206 | - |
| 15 | g42.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 207 | 226 | - |
| 20 | g42.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 227 | 249 | - |
| 17 | g42.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 250 | 255 | - |
| 8 | g42.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 75 | 97 | - |
| 12 | g42.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 112 | 131 | - |
| 11 | g42.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 152 | 174 | - |
| 9 | g42.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 184 | 206 | - |
| 10 | g42.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 227 | 249 | - |
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: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.
