General information for g6855.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Rho guanine nucleotide exchange factor 4.
Parent gene
- The parent gene g6855 is located on chr_2: 19196278..19202766 (- 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_2 | g6855 | g6855.t3 | isoform | g6855.t3 | 19194885 | 19196224 |
| chr_2 | g6855 | g6855.t3 | exon | g6855.t3.exon1 | 19194885 | 19195139 |
| chr_2 | g6855 | g6855.t3 | cds | g6855.t3.CDS1 | 19194887 | 19195139 |
| chr_2 | g6855 | g6855.t3 | exon | g6855.t3.exon2 | 19195200 | 19195469 |
| chr_2 | g6855 | g6855.t3 | cds | g6855.t3.CDS2 | 19195200 | 19195469 |
| chr_2 | g6855 | g6855.t3 | exon | g6855.t3.exon3 | 19195533 | 19196224 |
| chr_2 | g6855 | g6855.t3 | cds | g6855.t3.CDS3 | 19195533 | 19196056 |
| chr_2 | g6855 | g6855.t3 | TSS | g6855.t3 | NA | NA |
| chr_2 | g6855 | g6855.t3 | TTS | g6855.t3 | NA | NA |
Sequences
>g6855.t3 Gene=g6855 Length=1217
GATATTTCACCGCAACTTAAAAGTAACAGTGCCAAAGTAAGACGTGCTAATAGTGCAAAA
GTTTCCACAACAACCAAATCAACAAAAAGCAGCTCAAAGCATTCAGCCAAATCAAAGCGT
TCACTAAGTCAACCGTCAGATTTAGATGTGATTGTGTGTGAAAGCAAAATGATGAGTAAT
TTGGACGATATTAAGCACATTGATGATGATGATGATGCATCGGATACAGATAGTCTTAGT
TCAAATCATGTAGATGAAATGGATGAAGAAGAAATTCAGAAAAATGCTGTAGTTTATGCT
GAAGTTCTCTATCAATTTAGAGCGGGTGGACCACAAGAATTATCGCTAGAGAAAGGAACA
TTAGTGGAGGTGATAAAACGTGAGACAGGCCCATGGTGGTGGGGACGAATAAAGTATGAT
GCTATTGTGAATGAAAGTGAACTTGAGATAAAGCAAGGATGGTTTCCTAAAGATTTTGTA
AAGGTGCTTCCCACATATGGAAATCGAAAATTTCTTCACCAACAATCATCAATCGACTGT
GATATCAATAATACAATTCTACCACCATCAACTGCCGCACCAAGCATCTCTTCTAGTCAA
TCAAATAGCGAAATAATGAGAGATAATGTCATCAAAGAATTGCTCGAGACAGAAATTAAT
TATGTTAAGTTACTTAATTCACTTGTCAATGGATTTATAAAAGAAATGAAAGAACGATCT
GATGTTTTCTCATTAGAAAGCATTTTCCTTTTGTTTTCAAATATCGAGCAAATCTATCGT
TTTCAACAAAACTTTTTAGAGGCCCTTCGTATTGCCATTCCTAATGGAAGAATAGCAGAA
GTCTTTTTAGACTTTCAGTCAGCATTTATGGTTTACTCACAGTACTGCAACTCGTATCCA
AGAGCTCTTATGGAGCTAGAAAACTTTTCGAATAATAAAGAAGCCACTGCAATATTAGAA
AGCTGTCGTATCGCACAAAATTTACCCGAATTACCATTATCAGCGCATTTATTAGCGCCT
ATACAAAGAATTTGTCGATATCCTTTGCACTTAAGTGAACTTGTGAAACATTCAAAGACC
CGCAAAGAAATTCTTCTTAAAATGGATGTGCATCAATTGAGTAAAAATGACCTTGAAACA
ATTGATTGTAAAGAAATGTTTGATCTGTCATTAAATGCAATGAAGCGAGTTACAGAGATG
GTAAACGAAGGCAAAAG
>g6855.t3 Gene=g6855 Length=349
MMSNLDDIKHIDDDDDASDTDSLSSNHVDEMDEEEIQKNAVVYAEVLYQFRAGGPQELSL
EKGTLVEVIKRETGPWWWGRIKYDAIVNESELEIKQGWFPKDFVKVLPTYGNRKFLHQQS
SIDCDINNTILPPSTAAPSISSSQSNSEIMRDNVIKELLETEINYVKLLNSLVNGFIKEM
KERSDVFSLESIFLLFSNIEQIYRFQQNFLEALRIAIPNGRIAEVFLDFQSAFMVYSQYC
NSYPRALMELENFSNNKEATAILESCRIAQNLPELPLSAHLLAPIQRICRYPLHLSELVK
HSKTRKEILLKMDVHQLSKNDLETIDCKEMFDLSLNAMKRVTEMVNEGK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g6855.t3 | CDD | cd00174 | SH3 | 43 | 103 | 8.44764E-12 |
| 9 | g6855.t3 | CDD | cd00160 | RhoGEF | 151 | 346 | 1.52234E-37 |
| 7 | g6855.t3 | Gene3D | G3DSA:2.30.30.40 | SH3 Domains | 31 | 107 | 1.7E-16 |
| 8 | g6855.t3 | Gene3D | G3DSA:1.20.900.10 | - | 129 | 349 | 8.6E-57 |
| 13 | g6855.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 31 | - |
| 3 | g6855.t3 | PANTHER | PTHR45834:SF3 | RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 3, ISOFORM L | 21 | 349 | 1.7E-104 |
| 4 | g6855.t3 | PANTHER | PTHR45834 | RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 9-RELATED | 21 | 349 | 1.7E-104 |
| 1 | g6855.t3 | Pfam | PF00018 | SH3 domain | 46 | 100 | 5.5E-6 |
| 2 | g6855.t3 | Pfam | PF00621 | RhoGEF domain | 154 | 307 | 2.2E-36 |
| 15 | g6855.t3 | ProSiteProfiles | PS50002 | Src homology 3 (SH3) domain profile. | 39 | 109 | 21.461 |
| 14 | g6855.t3 | ProSiteProfiles | PS50010 | Dbl homology (DH) domain profile. | 150 | 348 | 31.115 |
| 11 | g6855.t3 | SMART | SM00326 | SH3_2 | 42 | 108 | 5.0E-11 |
| 12 | g6855.t3 | SMART | SM00325 | RhoGEF_3 | 154 | 347 | 2.3E-36 |
| 6 | g6855.t3 | SUPERFAMILY | SSF50044 | SH3-domain | 40 | 109 | 1.84E-14 |
| 5 | g6855.t3 | SUPERFAMILY | SSF48065 | DBL homology domain (DH-domain) | 137 | 347 | 1.11E-44 |
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 |
| 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. There were no conditions that were differentially expressed