Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Rho guanine nucleotide exchange factor 4.

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_2 g6855 g6855.t2 isoform g6855.t2 19194351 19195469
chr_2 g6855 g6855.t2 exon g6855.t2.exon1 19194351 19195139
chr_2 g6855 g6855.t2 cds g6855.t2.CDS1 19194353 19195139
chr_2 g6855 g6855.t2 exon g6855.t2.exon2 19195200 19195469
chr_2 g6855 g6855.t2 cds g6855.t2.CDS2 19195200 19195456
chr_2 g6855 g6855.t2 TSS g6855.t2 NA NA
chr_2 g6855 g6855.t2 TTS g6855.t2 NA NA

Sequences

>g6855.t2 Gene=g6855 Length=1059
ATTTATAAAAGAAATGAAAGAACGATCTGATGTTTTCTCATTAGAAAGCATTTTCCTTTT
GTTTTCAAATATCGAGCAAATCTATCGTTTTCAACAAAACTTTTTAGAGGCCCTTCGTAT
TGCCATTCCTAATGGAAGAATAGCAGAAGTCTTTTTAGACTTTCAGTCAGCATTTATGGT
TTACTCACAGTACTGCAACTCGTATCCAAGAGCTCTTATGGAGCTAGAAAACTTTTCGAA
TAATAAAGAAGCCACTGCAATATTAGAAAGCTGTCGTATCGCACAAAATTTACCCGAATT
ACCATTATCAGCGCATTTATTAGCGCCTATACAAAGAATTTGTCGATATCCTTTGCACTT
AAGTGAACTTGTGAAACATTCAAAGACCCGCAAAGAAATTCTTCTTAAAATGGATGTGCA
TCAATTGAGTAAAAATGACCTTGAAACAATTGATTGTAAAGAAATGTTTGATCTGTCATT
AAATGCAATGAAGCGAGTTACAGAGATGGTAAACGAAGGCAAAAGACATAGTGAATATTT
ATCGCGAATTCAAGCAAGATTTGAAAATTTTCAAGGACCATCAATAAATCTGCATAGTAC
TAGACTTTTTCTTCAGACAGACGCAATTAGAGTGTCACCAAATCTATGGAATAATACTTA
TACACTCTTCTTATTTGATCGACAGTTGGTGTATTGCAAAAAAGACCTTTTAAAGCGTAC
TAGCTACATCTACAAAGGACGAATATTTCTTGACAACTGTCGTATTCTCAATTTACCTGA
CGGTCGCATGTTTGGCGTCAATTTGAAAAATGCTTTAAGAATATTTTGTGAAGCTCGTGG
AAAATGGTTTGACTTTTGCTTCCGTTCAAATTCAAGCAAGACGAGATTTCTCAATACGCT
CTCAGCTGAAAGACAATTTTGCGGATCAAGTTTATTTGTGTCTGAAATTGCTTCCGGTTT
GGACGATGATAATTTGTCAGATGATCAGAATGTACTAAATCTTAATTATGATGAGCGACC
AATTGATGTTGAACATGGAGTAACTGCAAATGGAAATTC

>g6855.t2 Gene=g6855 Length=348
MKERSDVFSLESIFLLFSNIEQIYRFQQNFLEALRIAIPNGRIAEVFLDFQSAFMVYSQY
CNSYPRALMELENFSNNKEATAILESCRIAQNLPELPLSAHLLAPIQRICRYPLHLSELV
KHSKTRKEILLKMDVHQLSKNDLETIDCKEMFDLSLNAMKRVTEMVNEGKRHSEYLSRIQ
ARFENFQGPSINLHSTRLFLQTDAIRVSPNLWNNTYTLFLFDRQLVYCKKDLLKRTSYIY
KGRIFLDNCRILNLPDGRMFGVNLKNALRIFCEARGKWFDFCFRSNSSKTRFLNTLSAER
QFCGSSLFVSEIASGLDDDNLSDDQNVLNLNYDERPIDVEHGVTANGN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g6855.t2 CDD cd00160 RhoGEF 1 167 0.0000
11 g6855.t2 CDD cd01224 PH_Collybistin_ASEF 173 306 0.0000
9 g6855.t2 Gene3D G3DSA:1.20.900.10 - 1 188 0.0000
8 g6855.t2 Gene3D G3DSA:2.30.29.30 - 191 312 0.0000
2 g6855.t2 PANTHER PTHR45834:SF3 RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 3, ISOFORM L 1 313 0.0000
3 g6855.t2 PANTHER PTHR45834 RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 9-RELATED 1 313 0.0000
1 g6855.t2 Pfam PF00621 RhoGEF domain 7 128 0.0000
10 g6855.t2 ProSiteProfiles PS50010 Dbl homology (DH) domain profile. 1 169 22.7250
6 g6855.t2 SMART SM00325 RhoGEF_3 1 168 0.0000
7 g6855.t2 SMART SM00233 PH_update 192 303 0.0056
5 g6855.t2 SUPERFAMILY SSF48065 DBL homology domain (DH-domain) 4 186 0.0000
4 g6855.t2 SUPERFAMILY SSF50729 PH domain-like 172 303 0.0000

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:0005085 guanyl-nucleotide exchange factor activity 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.

Raw TPM values