Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Na(+)/H(+) exchange regulatory cofactor NHE-RF1.

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_4 g15724 g15724.t3 TTS g15724.t3 6553990 6553990
chr_4 g15724 g15724.t3 isoform g15724.t3 6554288 6563128
chr_4 g15724 g15724.t3 exon g15724.t3.exon1 6554288 6554733
chr_4 g15724 g15724.t3 cds g15724.t3.CDS1 6554725 6554733
chr_4 g15724 g15724.t3 exon g15724.t3.exon2 6562484 6563128
chr_4 g15724 g15724.t3 cds g15724.t3.CDS2 6562484 6563128
chr_4 g15724 g15724.t3 TSS g15724.t3 6563516 6563516

Sequences

>g15724.t3 Gene=g15724 Length=1091
ATGTCATCAACACCAGTACTTTATGAGCCACGTCTTTGTTTAGTAACAAAGCGTAAGGAC
TTTGATGGTTATGGTTTTAATCTTCATGCTGAAAAAGGCAAGCCAGGTCAATATATTGGA
AAAGTCGATGAAAATTCCCCTGCAGAATCTTCTGGTTTGCGACAAGGTGACAGAATTCTT
GAAGTTAATGGCCATAATATCAATTCTGAGACACATAAACAAGTTGTAGAACGAATCAAG
GTCATTCCCAATCAAACAAAATTATTGGTCATTGATCCAAAGGCTGATATACATAATCAT
CAGCAAATGGCATTGATTGAGAAAATAAAGAAAGCAGCAGAAGCAAAAATTGTCGAAAAT
CATAACATTGACAATCACAATAACAACAACAATAATAGCATGACAACAACAAATGGAAGC
GAAAAAATGATAAAAGAAGAAATCAAGCATGAAAATGGCAACAAAAATGGAATAATGAAG
AGCGAAATTGAAATTAAAATTGAAACAAATGGCAATGGCAGCATTAAAAGCACAACATCA
TCCCAAGATTCAAAAGATAAACTTAATTTATCAATGAGTGTTGCTGAAATGCGTGCACAA
TTAAAGAACAAGAAACGGCCTGATGTCAAAAGTGAAGGAATTGATACAACTTGAAAACCC
ATCAGAATTCAAAATATTCCACTATTGATTAAACTGTAAAATATAAATGATTTCGAGAAT
TATTCATTATAAAGGGGTGGAACTTTGATAATTTTCATAAAGTATTAAAAAATTTAGTTT
TTTAGGATACTACATGCAAATTATCAAAAAGCTGTCAAAATCCCATATAAACCTTGGATA
ATTTGATAGATTTTTTGAAAGAGTTCAAAATCTTTGATTTATTCTTCATCCAGTTTTAAA
TTACAAATATAAAATGAGTAATTAATTTAACAGTATTTTTTTGAAAATTATCAAAATTTT
GATTGTTTACAAAAATTAAAAAATAATCGGAAATTTTAAATAAAATTAGAAGTCTTAAAA
TTTAAAACTTTTTTCAAAGAAAATATTTTCAAAAAACTTTTATTTCAATTTATTAAATTC
CTAAAATAAAT

>g15724.t3 Gene=g15724 Length=217
MSSTPVLYEPRLCLVTKRKDFDGYGFNLHAEKGKPGQYIGKVDENSPAESSGLRQGDRIL
EVNGHNINSETHKQVVERIKVIPNQTKLLVIDPKADIHNHQQMALIEKIKKAAEAKIVEN
HNIDNHNNNNNNSMTTTNGSEKMIKEEIKHENGNKNGIMKSEIEIKIETNGNGSIKSTTS
SQDSKDKLNLSMSVAEMRAQLKNKKRPDVKSEGIDTT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g15724.t3 CDD cd00992 PDZ_signaling 10 91 6.82776E-21
5 g15724.t3 Gene3D G3DSA:2.30.42.10 - 8 98 3.8E-33
8 g15724.t3 MobiDBLite mobidb-lite consensus disorder prediction 170 189 -
9 g15724.t3 MobiDBLite mobidb-lite consensus disorder prediction 170 217 -
10 g15724.t3 MobiDBLite mobidb-lite consensus disorder prediction 199 217 -
2 g15724.t3 PANTHER PTHR14191:SF22 GH04176P 4 119 2.5E-57
3 g15724.t3 PANTHER PTHR14191 PDZ DOMAIN CONTAINING PROTEIN 4 119 2.5E-57
1 g15724.t3 Pfam PF00595 PDZ domain 22 90 1.3E-13
11 g15724.t3 ProSiteProfiles PS50106 PDZ domain profile. 14 94 16.787
7 g15724.t3 SMART SM00228 pdz_new 22 94 1.4E-19
4 g15724.t3 SUPERFAMILY SSF50156 PDZ domain-like 7 94 1.21E-23

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

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