General information for g15724.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Na(+)/H(+) exchange regulatory cofactor NHE-RF1.
Parent gene
- The parent gene g15724 is located on chr_4: 6562448..6563516 (- 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_4 | g15724 | g15724.t1 | isoform | g15724.t1 | 6562448 | 6563128 |
| chr_4 | g15724 | g15724.t1 | exon | g15724.t1.exon1 | 6562448 | 6563128 |
| chr_4 | g15724 | g15724.t1 | cds | g15724.t1.CDS1 | 6562448 | 6563128 |
| chr_4 | g15724 | g15724.t1 | TSS | g15724.t1 | 6563516 | 6563516 |
| chr_4 | g15724 | g15724.t1 | TTS | g15724.t1 | NA | NA |
Sequences
>g15724.t1 Gene=g15724 Length=681
ATGTCATCAACACCAGTACTTTATGAGCCACGTCTTTGTTTAGTAACAAAGCGTAAGGAC
TTTGATGGTTATGGTTTTAATCTTCATGCTGAAAAAGGCAAGCCAGGTCAATATATTGGA
AAAGTCGATGAAAATTCCCCTGCAGAATCTTCTGGTTTGCGACAAGGTGACAGAATTCTT
GAAGTTAATGGCCATAATATCAATTCTGAGACACATAAACAAGTTGTAGAACGAATCAAG
GTCATTCCCAATCAAACAAAATTATTGGTCATTGATCCAAAGGCTGATATACATAATCAT
CAGCAAATGGCATTGATTGAGAAAATAAAGAAAGCAGCAGAAGCAAAAATTGTCGAAAAT
CATAACATTGACAATCACAATAACAACAACAATAATAGCATGACAACAACAAATGGAAGC
GAAAAAATGATAAAAGAAGAAATCAAGCATGAAAATGGCAACAAAAATGGAATAATGAAG
AGCGAAATTGAAATTAAAATTGAAACAAATGGCAATGGCAGCATTAAAAGCACAACATCA
TCCCAAGATTCAAAAGATAAACTTAATTTATCAATGAGTGTTGCTGAAATGCGTGCACAA
TTAAAGAACAAGAAACGGCCTGATGTCAAAAGTGAAGGAATTGATGTGAGGAAGAAGTAT
GAAATTGTGCAGCAAATGTAA
>g15724.t1 Gene=g15724 Length=226
MSSTPVLYEPRLCLVTKRKDFDGYGFNLHAEKGKPGQYIGKVDENSPAESSGLRQGDRIL
EVNGHNINSETHKQVVERIKVIPNQTKLLVIDPKADIHNHQQMALIEKIKKAAEAKIVEN
HNIDNHNNNNNNSMTTTNGSEKMIKEEIKHENGNKNGIMKSEIEIKIETNGNGSIKSTTS
SQDSKDKLNLSMSVAEMRAQLKNKKRPDVKSEGIDVRKKYEIVQQM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g15724.t1 | CDD | cd00992 | PDZ_signaling | 10 | 91 | 0.000 |
| 8 | g15724.t1 | Gene3D | G3DSA:2.30.42.10 | - | 8 | 99 | 0.000 |
| 2 | g15724.t1 | PANTHER | PTHR14191:SF22 | GH04176P | 4 | 128 | 0.000 |
| 4 | g15724.t1 | PANTHER | PTHR14191 | PDZ DOMAIN CONTAINING PROTEIN | 4 | 128 | 0.000 |
| 3 | g15724.t1 | PANTHER | PTHR14191:SF22 | GH04176P | 106 | 226 | 0.000 |
| 5 | g15724.t1 | PANTHER | PTHR14191 | PDZ DOMAIN CONTAINING PROTEIN | 106 | 226 | 0.000 |
| 1 | g15724.t1 | Pfam | PF00595 | PDZ domain | 22 | 90 | 0.000 |
| 9 | g15724.t1 | ProSiteProfiles | PS50106 | PDZ domain profile. | 14 | 94 | 16.787 |
| 7 | g15724.t1 | SMART | SM00228 | pdz_new | 22 | 94 | 0.000 |
| 6 | g15724.t1 | SUPERFAMILY | SSF50156 | PDZ domain-like | 7 | 94 | 0.000 |
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:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K13358 (sodium/hydrogen exchange regulatory cofactor NHE-RF2)
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. There were no conditions that were differentially expressed