General information for g8497.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Rap guanine nucleotide exchange factor 4.
Parent gene
- The parent gene g8497 is located on chr_2: 30980604..31025322 (+ 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 | g8497 | g8497.t3 | isoform | g8497.t3 | 30980604 | 31025322 |
| chr_2 | g8497 | g8497.t3 | exon | g8497.t3.exon1 | 30980604 | 30980638 |
| chr_2 | g8497 | g8497.t3 | cds | g8497.t3.CDS1 | 30980604 | 30980638 |
| chr_2 | g8497 | g8497.t3 | exon | g8497.t3.exon2 | 30996912 | 30997054 |
| chr_2 | g8497 | g8497.t3 | cds | g8497.t3.CDS2 | 30996912 | 30997054 |
| chr_2 | g8497 | g8497.t3 | exon | g8497.t3.exon3 | 30997148 | 30997245 |
| chr_2 | g8497 | g8497.t3 | cds | g8497.t3.CDS3 | 30997148 | 30997245 |
| chr_2 | g8497 | g8497.t3 | exon | g8497.t3.exon4 | 31004725 | 31004776 |
| chr_2 | g8497 | g8497.t3 | cds | g8497.t3.CDS4 | 31004725 | 31004776 |
| chr_2 | g8497 | g8497.t3 | exon | g8497.t3.exon5 | 31004845 | 31004939 |
| chr_2 | g8497 | g8497.t3 | cds | g8497.t3.CDS5 | 31004845 | 31004939 |
| chr_2 | g8497 | g8497.t3 | exon | g8497.t3.exon6 | 31008768 | 31008905 |
| chr_2 | g8497 | g8497.t3 | cds | g8497.t3.CDS6 | 31008768 | 31008905 |
| chr_2 | g8497 | g8497.t3 | exon | g8497.t3.exon7 | 31010016 | 31010067 |
| chr_2 | g8497 | g8497.t3 | cds | g8497.t3.CDS7 | 31010016 | 31010067 |
| chr_2 | g8497 | g8497.t3 | exon | g8497.t3.exon8 | 31010134 | 31010228 |
| chr_2 | g8497 | g8497.t3 | cds | g8497.t3.CDS8 | 31010134 | 31010228 |
| chr_2 | g8497 | g8497.t3 | exon | g8497.t3.exon9 | 31011645 | 31011873 |
| chr_2 | g8497 | g8497.t3 | cds | g8497.t3.CDS9 | 31011645 | 31011873 |
| chr_2 | g8497 | g8497.t3 | exon | g8497.t3.exon10 | 31011991 | 31012174 |
| chr_2 | g8497 | g8497.t3 | cds | g8497.t3.CDS10 | 31011991 | 31012174 |
| chr_2 | g8497 | g8497.t3 | exon | g8497.t3.exon11 | 31013314 | 31013459 |
| chr_2 | g8497 | g8497.t3 | cds | g8497.t3.CDS11 | 31013314 | 31013459 |
| chr_2 | g8497 | g8497.t3 | exon | g8497.t3.exon12 | 31014531 | 31014675 |
| chr_2 | g8497 | g8497.t3 | cds | g8497.t3.CDS12 | 31014531 | 31014675 |
| chr_2 | g8497 | g8497.t3 | exon | g8497.t3.exon13 | 31016411 | 31016744 |
| chr_2 | g8497 | g8497.t3 | cds | g8497.t3.CDS13 | 31016411 | 31016744 |
| chr_2 | g8497 | g8497.t3 | exon | g8497.t3.exon14 | 31017589 | 31017796 |
| chr_2 | g8497 | g8497.t3 | cds | g8497.t3.CDS14 | 31017589 | 31017796 |
| chr_2 | g8497 | g8497.t3 | exon | g8497.t3.exon15 | 31017884 | 31018314 |
| chr_2 | g8497 | g8497.t3 | cds | g8497.t3.CDS15 | 31017884 | 31018314 |
| chr_2 | g8497 | g8497.t3 | exon | g8497.t3.exon16 | 31023701 | 31023834 |
| chr_2 | g8497 | g8497.t3 | cds | g8497.t3.CDS16 | 31023701 | 31023834 |
| chr_2 | g8497 | g8497.t3 | exon | g8497.t3.exon17 | 31024352 | 31024522 |
| chr_2 | g8497 | g8497.t3 | cds | g8497.t3.CDS17 | 31024352 | 31024522 |
| chr_2 | g8497 | g8497.t3 | exon | g8497.t3.exon18 | 31024757 | 31024935 |
| chr_2 | g8497 | g8497.t3 | cds | g8497.t3.CDS18 | 31024757 | 31024935 |
| chr_2 | g8497 | g8497.t3 | exon | g8497.t3.exon19 | 31025201 | 31025322 |
| chr_2 | g8497 | g8497.t3 | cds | g8497.t3.CDS19 | 31025201 | 31025322 |
| chr_2 | g8497 | g8497.t3 | TSS | g8497.t3 | NA | NA |
| chr_2 | g8497 | g8497.t3 | TTS | g8497.t3 | NA | NA |
Sequences
>g8497.t3 Gene=g8497 Length=2991
ATGGCAATGGAATGGATAAATGCTATTGATAAAAGACCTTGTGATCGTAATATGAGAGAT
GTAGAACTAATAGCGTGTCGTCTACGTCGAGTGGAGCCTCTTTGTAGATTAACAAACTCA
GCACTACAACAGCTAGCAATGTGCGGTTTTTATGAGGATTTAGAAAAAGGAGTGACTTTA
TTTCGTGCTGGCGAACAAGGACGTTATTGGTATGCAGTATTAGGAGGACAATTGGAAGTT
CGATATCATCATGCAGCTGCCGATAGCGACACAAAAAAAAATAAAGAGCTCATGAATGAC
GTGATATTAAACTGCAAATTTAAAAATGGCTTTGCGTCGCCAATCAGTCAAAATGCACCC
GTGTCACCCACAAAAAAGCAGCTGTCACCTGATCATCCAAATCCGGCTCTTCCAATAACA
GAAACCCAAAGTGTATTGAGTGTTGGTGCAACATTTGGCGAGTCCGTATTAGGTGATTTG
CCTCGTGATAGCACAGTAGTAACAAAAACAACATGTGAACTACTGCGAGTTGAGCAACAA
GACTTTCGTTTAATATGGGAGAAAAATAAAGAGCTCATGAATGACGTGATATTAAACTGC
AAATTTAAAAATGGCTTTGCGTCGCCAATCAGTCAGAATGCACCCGTGTCACCCACAAAA
AAGCAGCTGTCACCTGATCATCCAAATCCGGCTCTTCCAATAACAGAATCACCAAGTCCT
GCAATGACAAAAATGGGATGGGCATTAAGAGCACTTTTATTAAGCGACAGTAATGGATGT
CTAAAAGATCGAAAAGTATCGGGACGATTGATAAGAAAGTGCGCACCGGGCAGTGAATTG
GTCGATTGGTTAATGAATTTATCACCAGTCGTGCACACGCGAATTCAAGCGACTGGCATG
TGGCAAGCACTTCTTGAGGAAGGTGTTATATCTCATGTGGCAAAAGAGCAACCGTTCAAA
GACAAAGTTTTTCTCTATCGCTTTCGCTCTGATGAAGATGGAAGTGGCACGATGCCGTCA
ACAGATGATATAAATTCGGCCAATGAACATATAAAAGAAGGATTGACAGCATTACTTCAT
CGTGGACCAGATGCTACACTTAGATTGATTTTACGTAAACCATCCCATGAGAGAACGCAA
GAGGAATTGGAATTAGTGTTTGAAGAATTACTACACATTCCGGCCTTATCGCACCTTTCA
ACATCAATTAAGCGTGAACTTGCTTCAATCATTGTTTTTGAATCTCATGCTCAAGCGGGC
ACAGTTTTATTTAATCAAGGTGATGAGGGTAGATCGTGGTATATTTTACAAAAAGGCAAA
GTGGATGTTGTAATTCATGGGAAAGGAACGGTAGCAACACTCAAAGAAGGAGACGACTTT
GGAAAACTTGCACTCATAAATGATGCCCCAAGATATACTGTGATGTCGGGGACGCCGTCA
AAAATGCTCGAACATTTATTAGATACTAGATTAGGTGTACAAATGGGACCAAATGATGAT
TCGTTTTTAGATGACTTTTTATTGACGCACATTGTTTTTATGCCAGTCGCACAATTAGTT
GATGAATTAGCAAGCCATTATCATAATGATATGGATATGGATGGAAATCGATCTGGTGCT
GACAGTCCTGAAGATTATGATTATTTGATAACATGTAAAAAGCGTGTTGTACAATTTATT
CAACGTTGGGTTATGGCTGTTCGTCATGCAGTTTTTGAAGATCCCGCAGCAGCACATTTC
ATTGAGGAAATTGCAACAGATGTTGAATCAGATCCAGCCTTGCAAGAAGAAGCCGGAATT
ATTCATCACGTGTTGACACAAATGTCACGCTATCAAGAAGACAGACAACAAAATGCTGGA
CAAAAATGGAAATTGCCATCGAATGGTCAACCTATAACACTGTTTAGTGGCAATGTTACA
GCGACCCGATCTATTATACGCATGGATGATGACATTATTTTTCGTGTCTATTGTGCTGAC
CATACTTTTTGTACTTTACGTTTTCCCATCTATACAACCGCTGAGGTGATAAAAATTTGT
GCAGCTGACAAGCTACAGATTACAGCAAATCGTGGACCAGAAGATTTAGTATTAGTTGAA
GTAAAATCAAATGGTGAACGAGTGATTTTTAAGGACAATGATTTAAGTATTCCAACAGCA
CTTTCACTCAATGGGAGAATTTTTGTGTCACCAAAGGATCATTTAGATGCTCTTACGCCA
CTACCTGAACAGGAGGGTGCAACGGAAGGCTTAGAAATGGATGTCGAGGCATTACCTACA
AAAGACTTGGCTTATCATATGACATTATTTGATTGGGACCTCTTTTGGAGTGTACACGAA
TACGAGCTTTTATATCATACATTTGGCAAGCATCATTTCAATAAGAATACGAGTAATCTT
GACGTTTTTATAAGACGCTTCAATGAGATCCAATATTGGGTCGTGACGGAAATGGTCTCA
ACATCAAATTTAAATAAACGTGTAGCGCTGTTGAAGAAGTTTATAAAGCTTGCTGCTTAC
TGCAAAGAGTACCAAAACTTGAACGCATTTTTTGCCATCATTATGGGAATGTCAAATTCG
GCTGTATCACGTTTAACACAAACTTGGGACAAATTGCCATCAAAATTTCGAAAGCTCTTT
ACTGAATTTGAAGCACTAATTGATCCAAGTCGAAATCATCGTGCATACAGAATGTCAGTT
GGAAAATTACAGCCGCCTGTGATTCCATTTATGCCATTATTGTTGAAGGATATGACATTT
GCACACGAAGGTAATAAAACAAGTGTCGATGGTCTTGTGAATTTTGAAAAAATGCATATG
ATGGCGTCGACTATGAGAGCTGTGAGATTTTGTCGGTCTAGACATTTGGTTTTGGATCCA
CCATCACCAAAAAACAATGATTCACAAATTCGCTCATATATCAGCTGCTTCCGTGTAATC
GACTGCCAAAAAACATTAAATGCAATGTCAAAGAAAATTGAGCCCCGATAA
>g8497.t3 Gene=g8497 Length=996
MAMEWINAIDKRPCDRNMRDVELIACRLRRVEPLCRLTNSALQQLAMCGFYEDLEKGVTL
FRAGEQGRYWYAVLGGQLEVRYHHAAADSDTKKNKELMNDVILNCKFKNGFASPISQNAP
VSPTKKQLSPDHPNPALPITETQSVLSVGATFGESVLGDLPRDSTVVTKTTCELLRVEQQ
DFRLIWEKNKELMNDVILNCKFKNGFASPISQNAPVSPTKKQLSPDHPNPALPITESPSP
AMTKMGWALRALLLSDSNGCLKDRKVSGRLIRKCAPGSELVDWLMNLSPVVHTRIQATGM
WQALLEEGVISHVAKEQPFKDKVFLYRFRSDEDGSGTMPSTDDINSANEHIKEGLTALLH
RGPDATLRLILRKPSHERTQEELELVFEELLHIPALSHLSTSIKRELASIIVFESHAQAG
TVLFNQGDEGRSWYILQKGKVDVVIHGKGTVATLKEGDDFGKLALINDAPRYTVMSGTPS
KMLEHLLDTRLGVQMGPNDDSFLDDFLLTHIVFMPVAQLVDELASHYHNDMDMDGNRSGA
DSPEDYDYLITCKKRVVQFIQRWVMAVRHAVFEDPAAAHFIEEIATDVESDPALQEEAGI
IHHVLTQMSRYQEDRQQNAGQKWKLPSNGQPITLFSGNVTATRSIIRMDDDIIFRVYCAD
HTFCTLRFPIYTTAEVIKICAADKLQITANRGPEDLVLVEVKSNGERVIFKDNDLSIPTA
LSLNGRIFVSPKDHLDALTPLPEQEGATEGLEMDVEALPTKDLAYHMTLFDWDLFWSVHE
YELLYHTFGKHHFNKNTSNLDVFIRRFNEIQYWVVTEMVSTSNLNKRVALLKKFIKLAAY
CKEYQNLNAFFAIIMGMSNSAVSRLTQTWDKLPSKFRKLFTEFEALIDPSRNHRAYRMSV
GKLQPPVIPFMPLLLKDMTFAHEGNKTSVDGLVNFEKMHMMASTMRAVRFCRSRHLVLDP
PSPKNNDSQIRSYISCFRVIDCQKTLNAMSKKIEPR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 20 | g8497.t3 | CDD | cd00038 | CAP_ED | 36 | 197 | 8.36796E-11 |
| 22 | g8497.t3 | CDD | cd04437 | DEP_Epac | 245 | 373 | 4.78712E-52 |
| 21 | g8497.t3 | CDD | cd00038 | CAP_ED | 395 | 484 | 2.49418E-15 |
| 23 | g8497.t3 | CDD | cd06224 | REM | 478 | 598 | 6.12411E-16 |
| 19 | g8497.t3 | CDD | cd00155 | RasGEF | 755 | 992 | 1.73927E-72 |
| 17 | g8497.t3 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 236 | 339 | 5.7E-25 |
| 18 | g8497.t3 | Gene3D | G3DSA:2.60.120.10 | Jelly Rolls | 341 | 480 | 5.6E-47 |
| 15 | g8497.t3 | Gene3D | G3DSA:1.20.870.10 | Son of sevenless (SoS) protein Chain: S domain 1 | 481 | 627 | 6.6E-36 |
| 14 | g8497.t3 | Gene3D | G3DSA:3.10.20.90 | - | 635 | 742 | 5.0E-36 |
| 16 | g8497.t3 | Gene3D | G3DSA:1.10.840.10 | Son of sevenless (Sos) protein Chain | 747 | 996 | 2.2E-90 |
| 6 | g8497.t3 | PANTHER | PTHR23113:SF175 | RAP GUANINE NUCLEOTIDE EXCHANGE FACTOR 4 | 143 | 471 | 9.6E-282 |
| 8 | g8497.t3 | PANTHER | PTHR23113 | GUANINE NUCLEOTIDE EXCHANGE FACTOR | 143 | 471 | 9.6E-282 |
| 5 | g8497.t3 | PANTHER | PTHR23113:SF175 | RAP GUANINE NUCLEOTIDE EXCHANGE FACTOR 4 | 471 | 996 | 9.6E-282 |
| 7 | g8497.t3 | PANTHER | PTHR23113 | GUANINE NUCLEOTIDE EXCHANGE FACTOR | 471 | 996 | 9.6E-282 |
| 2 | g8497.t3 | Pfam | PF00610 | Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) | 261 | 328 | 1.5E-15 |
| 3 | g8497.t3 | Pfam | PF00027 | Cyclic nucleotide-binding domain | 416 | 483 | 2.9E-11 |
| 1 | g8497.t3 | Pfam | PF00618 | RasGEF N-terminal motif | 474 | 583 | 1.8E-13 |
| 4 | g8497.t3 | Pfam | PF00617 | RasGEF domain | 762 | 938 | 8.2E-51 |
| 24 | g8497.t3 | ProSitePatterns | PS00720 | Ras Guanine-nucleotide exchange factors domain signature. | 908 | 937 | - |
| 35 | g8497.t3 | ProSiteProfiles | PS50042 | cAMP/cGMP binding motif profile. | 33 | 80 | 7.421 |
| 34 | g8497.t3 | ProSiteProfiles | PS50042 | cAMP/cGMP binding motif profile. | 144 | 185 | 8.042 |
| 32 | g8497.t3 | ProSiteProfiles | PS50186 | DEP domain profile. | 255 | 330 | 14.679 |
| 33 | g8497.t3 | ProSiteProfiles | PS50042 | cAMP/cGMP binding motif profile. | 395 | 471 | 20.244 |
| 30 | g8497.t3 | ProSiteProfiles | PS50212 | Ras guanine-nucleotide exchange factors N-terminal domain profile. | 470 | 609 | 21.532 |
| 31 | g8497.t3 | ProSiteProfiles | PS50200 | Ras-associating (RA) domain profile. | 650 | 734 | 15.306 |
| 36 | g8497.t3 | ProSiteProfiles | PS50009 | Ras guanine-nucleotide exchange factors catalytic domain profile. | 759 | 996 | 67.36 |
| 26 | g8497.t3 | SMART | SM00100 | cnmp_10 | 33 | 201 | 0.11 |
| 29 | g8497.t3 | SMART | SM00049 | DEP_3 | 256 | 330 | 1.9E-21 |
| 27 | g8497.t3 | SMART | SM00100 | cnmp_10 | 395 | 511 | 7.7E-9 |
| 25 | g8497.t3 | SMART | SM00229 | rasgefn_5 | 469 | 606 | 8.4E-13 |
| 28 | g8497.t3 | SMART | SM00147 | RasGEF_3 | 755 | 996 | 8.1E-84 |
| 11 | g8497.t3 | SUPERFAMILY | SSF51206 | cAMP-binding domain-like | 14 | 196 | 5.09E-20 |
| 9 | g8497.t3 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain | 241 | 377 | 5.99E-32 |
| 10 | g8497.t3 | SUPERFAMILY | SSF51206 | cAMP-binding domain-like | 369 | 473 | 5.5E-20 |
| 12 | g8497.t3 | SUPERFAMILY | SSF48366 | Ras GEF | 471 | 996 | 2.75E-103 |
| 13 | g8497.t3 | SUPERFAMILY | SSF54236 | Ubiquitin-like | 643 | 749 | 3.31E-30 |
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:0007165 | signal transduction | BP |
| GO:0007264 | small GTPase mediated signal transduction | BP |
| GO:0035556 | intracellular signal transduction | BP |
| 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.
