General information for g3660.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Rho guanine nucleotide exchange factor 12.
Parent gene
- The parent gene g3660 is located on chr_3: 27251963..27253122 (- 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_3 | g3660 | g3660.t1 | TTS | g3660.t1 | 27249338 | 27249338 |
| chr_3 | g3660 | g3660.t1 | isoform | g3660.t1 | 27249531 | 27253122 |
| chr_3 | g3660 | g3660.t1 | exon | g3660.t1.exon1 | 27249531 | 27249611 |
| chr_3 | g3660 | g3660.t1 | cds | g3660.t1.CDS1 | 27249531 | 27249611 |
| chr_3 | g3660 | g3660.t1 | exon | g3660.t1.exon2 | 27249667 | 27249973 |
| chr_3 | g3660 | g3660.t1 | cds | g3660.t1.CDS2 | 27249667 | 27249973 |
| chr_3 | g3660 | g3660.t1 | exon | g3660.t1.exon3 | 27250044 | 27250403 |
| chr_3 | g3660 | g3660.t1 | cds | g3660.t1.CDS3 | 27250044 | 27250403 |
| chr_3 | g3660 | g3660.t1 | exon | g3660.t1.exon4 | 27250466 | 27251027 |
| chr_3 | g3660 | g3660.t1 | cds | g3660.t1.CDS4 | 27250466 | 27251027 |
| chr_3 | g3660 | g3660.t1 | exon | g3660.t1.exon5 | 27251092 | 27251210 |
| chr_3 | g3660 | g3660.t1 | cds | g3660.t1.CDS5 | 27251092 | 27251210 |
| chr_3 | g3660 | g3660.t1 | exon | g3660.t1.exon6 | 27251272 | 27251877 |
| chr_3 | g3660 | g3660.t1 | cds | g3660.t1.CDS6 | 27251272 | 27251877 |
| chr_3 | g3660 | g3660.t1 | exon | g3660.t1.exon7 | 27251963 | 27252177 |
| chr_3 | g3660 | g3660.t1 | cds | g3660.t1.CDS7 | 27251963 | 27252177 |
| chr_3 | g3660 | g3660.t1 | exon | g3660.t1.exon8 | 27252232 | 27252579 |
| chr_3 | g3660 | g3660.t1 | cds | g3660.t1.CDS8 | 27252232 | 27252579 |
| chr_3 | g3660 | g3660.t1 | exon | g3660.t1.exon9 | 27252904 | 27253122 |
| chr_3 | g3660 | g3660.t1 | cds | g3660.t1.CDS9 | 27252904 | 27253122 |
| chr_3 | g3660 | g3660.t1 | TSS | g3660.t1 | 27253221 | 27253221 |
Sequences
>g3660.t1 Gene=g3660 Length=2817
ATGCGAATAAAAAAAGAACGTACGAAGAAAGTTAAAGAACCACATAGATATACTTTCTGG
AAACTCGGATTTAATAATAAACTTGTTGATAAAAGGTTATATAGAAAAACTCATTTCAAA
AAAATAAACAATTCGATTCACCATTCAAACGATTTTACTGAAATTGCTCAAATCCAAATG
TCTGATGATGGACAAGATAAGAATGAAACAAAAACTAATATTTTTAATAGTACAATAAAT
AGTACTTCAACGGAGACGACTTTGGAATATTCAGATCAACATGTCCAACTATTAAAACAA
ATTGATATTTTGTCTTTTGAATCAGATGATGAAATATTAAGTGAAAACAATATTGATGAT
GATTATGAAGCATTTAGTTCACTATCAAATTTAATACTACCTATTAACATTACACAACTT
TCAGTTTTTGTCAATTATACGATGATCCATTCAATATCAGAACCGATTTTGTTCTATTTA
ATCTCTGATTTGTATAAAAAAGGAAGTGTAAAAGACATGAAGAAATGGGCATATGAAATT
TTTTCATGTTTTATTCAAGCATCTGCACCACTTAGATTTTATTCATCAAACTTCAATGAG
TCAATAGTTGGAGATATCGAATCAAAATTAATGCAAATTGATGCCTATAAACCAGTGAAC
ATAATTAGTTCATCATTTGACTTCGAAATATTACGTTTGCTTCGTGAGATTTTTCAAAAA
TCTAGATTTGAAGCACAACAACAGATTACAAAACAACTTCAAGATTTTCAAACTAAACGA
AGGGCGGGTTTGGAAGCATGGTATGGAGCATCTACCGCGGATCTTAAAGTCGCAAAGAAG
AACAAATCAATGCAGCAGAAAATAATAGAAAAAAATTTAATGCCAAAACTGTTAATGATG
ATTGAAGAAATGGAAACTGAAGAGCATAAAAATAATTTTAATCGAAGAATTTTATTATCT
GCATTATCAACGGTTATTCATCAAACATTTCGGCCAAGTATCAGTTATTTTGCTTCAATC
GATCAATTTGTGTCTTGTGGCAATTTATCGAGTAAACCAGAAATTTGCATTAATGGTCAT
CGACTTGTGCCAAAAATTTGTTATTCAAGTACATATTGTGATTACTGTTTGAAAATACTT
TGGGGACTTGCACCACAAGGTTATCGATGCAAATGCGGTATAAAAATTCATACAACATGC
ATTGATTTGCTTACGGGAACATGCATGTTAAATGATAATATTGAATTTGAAGATGAAACT
AGTCATAATGAATCAAAGGATTCTTCTAAACTCATGGAATTTGTTCAAGCGACATTAGGA
AATCAGCGCATTGAAAACTATAAACGAACAAAAGGAAGTCGTCCAAAGTCTGATCCTGGT
CTTTATAGACAAGTTTCTGATTCTTCTTCAGATGATGGAATGAATGAAAATATTTGGAAT
AATGATATTTCTATGGAAATTCCCAAATTATCAGAAATTGCAAAGAAACGACGAGAAATA
ATATTAGAACTTTTTGAAACTGAAAGGCGTCATGTGAAAGTTCTTAAGATACTTCATAAC
GTATTTTATGAACCATTGAAAAGGAGTAAGGCAATTTCTGATGAACTTGCTGATATGATC
TTTCCACCTTCATTTTTGGTTATAAAAGATTGGCATATCTCATTTGAAACTATGCTGAAG
AAAGAATGGCATGAACAAAATGGAATTCTTTTGGAAATTGGAAGATGCGTTTCAATATTT
GAAGGTGCTTATGGAAATATTCTCAAAGAAAATGCAGCAAATTTCTGTGCTGGTCAGCAA
AGTGCTTTAGATGCCTTGAAAGCCGCACGTAGAAAAAATGAACCACTTCAAAGAGCATTG
ATTAAAGCTGAATCGCATAAAGGATGCCGAAGATTGCAGCTTAAAGATTTGATATTGTCA
TTGCTACAACGACTTACCAAGTATCCATTATTATTTGAAAGAATTTCAAAATATACTGAG
GGAAATGATCAAGAAAAAATCAAAAAAGCTGTTGAATCATCGAAGACAATTCTAAATTTT
GTCAACTTAGCTGTCAAAAATGCAGAGGAAATTCGTTTAATACATCAAAAACTTGATAAA
ACGCAGTTTGAGAGAGATGCACCAGTTGAGTTTAAAAACTTTAACCTCTTGAATTACAGA
CTTCTCAATAGTAGCAACATGATAATTAGAAAAGGCACTCAATCAATACGAGTTTTGCTT
TTTGATAAGCTTTTGGTTTTTCTTCACAAGACTGAGGATCGATATATATTGAAGTTTTCT
GAAAATTTAAAGTATCCTGTCATGAAGATTCACAATATTATAGTCCGCTCAAATGCAACA
GATAATAAATCATTCTATTTGATTTTTCAAGACGATGCAAATTCACAGATGATTGAGTTG
ATAGTAAAAAGTGAAGTAGAAGCCGAAACTTGGATACGTAATATTAATGATGCAGTTGCC
AAGGCAAATAATACAATAACTTTAAAAAGAAGATCATCAGCAGAATCTGCTCAAGCTATG
TTAAGAAGCGAGTCAAAGAGCTTGAAAAAGCAATCTGATCTGGCTTCAATCGCAAAAACT
TTACAGATTCAGGCAAAGTTTACTGAAGAATGGATTCAAGCAGCACAGCAGAAAATGAAA
ATGACACAATCAAATTGGGATCAAAATAGTTTATGTGAAGTTGACAATATCAACATTACA
GTAAACACTCTTAATCGGCTCATTTCACAATTATCGATAAAAATTGCGGAACGTGATCAT
GAACGAGAATTGTATACGAAAGAAAACTTGAGACTTCGGGAGTTACACAAATTATAA
>g3660.t1 Gene=g3660 Length=938
MRIKKERTKKVKEPHRYTFWKLGFNNKLVDKRLYRKTHFKKINNSIHHSNDFTEIAQIQM
SDDGQDKNETKTNIFNSTINSTSTETTLEYSDQHVQLLKQIDILSFESDDEILSENNIDD
DYEAFSSLSNLILPINITQLSVFVNYTMIHSISEPILFYLISDLYKKGSVKDMKKWAYEI
FSCFIQASAPLRFYSSNFNESIVGDIESKLMQIDAYKPVNIISSSFDFEILRLLREIFQK
SRFEAQQQITKQLQDFQTKRRAGLEAWYGASTADLKVAKKNKSMQQKIIEKNLMPKLLMM
IEEMETEEHKNNFNRRILLSALSTVIHQTFRPSISYFASIDQFVSCGNLSSKPEICINGH
RLVPKICYSSTYCDYCLKILWGLAPQGYRCKCGIKIHTTCIDLLTGTCMLNDNIEFEDET
SHNESKDSSKLMEFVQATLGNQRIENYKRTKGSRPKSDPGLYRQVSDSSSDDGMNENIWN
NDISMEIPKLSEIAKKRREIILELFETERRHVKVLKILHNVFYEPLKRSKAISDELADMI
FPPSFLVIKDWHISFETMLKKEWHEQNGILLEIGRCVSIFEGAYGNILKENAANFCAGQQ
SALDALKAARRKNEPLQRALIKAESHKGCRRLQLKDLILSLLQRLTKYPLLFERISKYTE
GNDQEKIKKAVESSKTILNFVNLAVKNAEEIRLIHQKLDKTQFERDAPVEFKNFNLLNYR
LLNSSNMIIRKGTQSIRVLLFDKLLVFLHKTEDRYILKFSENLKYPVMKIHNIIVRSNAT
DNKSFYLIFQDDANSQMIELIVKSEVEAETWIRNINDAVAKANNTITLKRRSSAESAQAM
LRSESKSLKKQSDLASIAKTLQIQAKFTEEWIQAAQQKMKMTQSNWDQNSLCEVDNINIT
VNTLNRLISQLSIKIAERDHERELYTKENLRLRELHKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g3660.t1 | CDD | cd00029 | C1 | 360 | 408 | 4.8813E-12 |
| 19 | g3660.t1 | CDD | cd00160 | RhoGEF | 497 | 682 | 6.27251E-28 |
| 14 | g3660.t1 | Gene3D | G3DSA:1.20.58.1850 | - | 122 | 330 | 4.1E-38 |
| 12 | g3660.t1 | Gene3D | G3DSA:3.30.60.20 | - | 348 | 422 | 2.1E-13 |
| 13 | g3660.t1 | Gene3D | G3DSA:1.20.900.10 | - | 478 | 699 | 2.3E-49 |
| 11 | g3660.t1 | Gene3D | G3DSA:2.30.29.30 | - | 700 | 832 | 9.7E-27 |
| 23 | g3660.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 446 | 469 | - |
| 5 | g3660.t1 | PANTHER | PTHR45872:SF2 | RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 2, ISOFORM D | 48 | 874 | 7.9E-150 |
| 6 | g3660.t1 | PANTHER | PTHR45872 | RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 2, ISOFORM D | 48 | 874 | 7.9E-150 |
| 2 | g3660.t1 | Pfam | PF09128 | Regulator of G protein signalling-like domain | 125 | 328 | 7.7E-29 |
| 4 | g3660.t1 | Pfam | PF00130 | Phorbol esters/diacylglycerol binding domain (C1 domain) | 360 | 408 | 1.1E-6 |
| 1 | g3660.t1 | Pfam | PF00621 | RhoGEF domain | 500 | 682 | 1.3E-28 |
| 3 | g3660.t1 | Pfam | PF17838 | PH domain | 710 | 819 | 9.9E-25 |
| 15 | g3660.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 175 | - |
| 17 | g3660.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 176 | 194 | - |
| 16 | g3660.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 195 | 938 | - |
| 25 | g3660.t1 | ProSiteProfiles | PS50081 | Zinc finger phorbol-ester/DAG-type profile. | 359 | 408 | 11.095 |
| 24 | g3660.t1 | ProSiteProfiles | PS50010 | Dbl homology (DH) domain profile. | 496 | 684 | 24.199 |
| 26 | g3660.t1 | ProSiteProfiles | PS50003 | PH domain profile. | 720 | 820 | 7.059 |
| 22 | g3660.t1 | SMART | SM00109 | c1_12 | 358 | 408 | 4.5E-6 |
| 20 | g3660.t1 | SMART | SM00325 | RhoGEF_3 | 500 | 683 | 8.3E-32 |
| 21 | g3660.t1 | SMART | SM00233 | PH_update | 721 | 822 | 0.0015 |
| 10 | g3660.t1 | SUPERFAMILY | SSF48097 | Regulator of G-protein signaling, RGS | 136 | 310 | 7.65E-21 |
| 7 | g3660.t1 | SUPERFAMILY | SSF57889 | Cysteine-rich domain | 353 | 410 | 7.48E-12 |
| 9 | g3660.t1 | SUPERFAMILY | SSF48065 | DBL homology domain (DH-domain) | 488 | 696 | 1.44E-36 |
| 8 | g3660.t1 | SUPERFAMILY | SSF50729 | PH domain-like | 706 | 819 | 4.59E-19 |
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:0035556 | intracellular signal transduction | BP |
| GO:0005085 | guanyl-nucleotide exchange factor activity | MF |
| GO:0005737 | cytoplasm | CC |
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