Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Rho guanine nucleotide exchange factor 12.

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 g15265 g15265.t2 TSS g15265.t2 4708841 4708841
chr_4 g15265 g15265.t2 isoform g15265.t2 4708998 4713732
chr_4 g15265 g15265.t2 exon g15265.t2.exon1 4708998 4709532
chr_4 g15265 g15265.t2 cds g15265.t2.CDS1 4709218 4709532
chr_4 g15265 g15265.t2 exon g15265.t2.exon2 4709674 4709853
chr_4 g15265 g15265.t2 cds g15265.t2.CDS2 4709674 4709853
chr_4 g15265 g15265.t2 exon g15265.t2.exon3 4713623 4713732
chr_4 g15265 g15265.t2 cds g15265.t2.CDS3 4713623 4713730
chr_4 g15265 g15265.t2 TTS g15265.t2 NA NA

Sequences

>g15265.t2 Gene=g15265 Length=825
ATCACAACAAAGCAATGGCACATCTTCACCATCATCACCACAACCACCTTCATCACTAAA
TTCTTCCAAAAAGTCTTCAGAAAATGGCAGTAATCATCAACGACAGCGAAGTGGAAAACT
TTTATTAGAAAATCTCAATATTACATCGTCAAATGGCAGCGAAAGACCAAAGCCACAAAT
TCTTGAACTTGTAATAAACAAGGACAAATATGGCTACGGTATGAAAGTGTCAGGTGAAAA
TCCAGTATTTGTAGATAGTGTCAAAGAAGGTGGTGCAGCTTTTCGTGCTGGTTTACATGC
TGCCGATATGATTTTGCGTGTTAATGGACATAATGTGAGATACTCAACGCATGCTGAAGT
TGTGCAGCTGATGAAAGCAACTCAAAATGTTGAATTGACTGTGCAGAGAAATGCGAGAAA
TTTTGCATTACCACTTGGTGGTTCCAACAGTCCTGTTATTATTGGTGCAACCACACCTAA
CACACCGACACCTACTAGTCAGAGAAATAGTATTACAGCACCACTGCCTGTTGATCACAA
CAAGCGAATGGAAGTAGAATTTACAAAAATGCATACACTCTTTATGATGCTCGAGCAGGA
GAAGAAAAATCTCGAAAAATTGCGTGAGAATGAGTCACAAAATGGAAATGAAATTGTGCG
TGCTGAAGCAAATATTCGAACACTTCAAGAGCAATTAAAACAATGGACTGGCGATAAATC
ATCAAAAAAGCATCACAGAAATGTATCAAATCCCGACATATCACCACCTGGTACACCACC
ACCACCATATCAGCAACAACATCAAATTCAAGCAGCACAAACAAA

>g15265.t2 Gene=g15265 Length=201
MKVSGENPVFVDSVKEGGAAFRAGLHAADMILRVNGHNVRYSTHAEVVQLMKATQNVELT
VQRNARNFALPLGGSNSPVIIGATTPNTPTPTSQRNSITAPLPVDHNKRMEVEFTKMHTL
FMMLEQEKKNLEKLRENESQNGNEIVRAEANIRTLQEQLKQWTGDKSSKKHHRNVSNPDI
SPPGTPPPPYQQQHQIQAAQT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g15265.t2 CDD cd00992 PDZ_signaling 6 62 1.7702E-16
6 g15265.t2 Coils Coil Coil 117 165 -
5 g15265.t2 Gene3D G3DSA:2.30.42.10 - 1 69 1.6E-19
9 g15265.t2 MobiDBLite mobidb-lite consensus disorder prediction 161 201 -
2 g15265.t2 PANTHER PTHR45872:SF2 RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 2, ISOFORM D 1 197 2.2E-33
3 g15265.t2 PANTHER PTHR45872 RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 2, ISOFORM D 1 197 2.2E-33
1 g15265.t2 Pfam PF00595 PDZ domain 5 62 1.1E-11
10 g15265.t2 ProSiteProfiles PS50106 PDZ domain profile. 1 54 12.707
8 g15265.t2 SMART SM00228 pdz_new 1 65 3.6E-13
4 g15265.t2 SUPERFAMILY SSF50156 PDZ domain-like 6 66 3.02E-17

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 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. There were no conditions that were differentially expressed